# Output of GENECONV for sequence file AMELY.final.nex # GENECONV version 1.81 # Command line: GENECONV AMELY.final.nex amelygroup.cfg amelygroupoutg1 # /lp /g1 # Contents of parameter configuration file: # amelygroup.cfg: -Startseed=123 -MaxSimGlobalPval=0.05 # -group EQUIDS Horse_AMELY Przewalskii_AMELY Onager_AMELY # Donkey_AMELY Horse_AMELX Przewalski_AMELX Donkey_AMELX Rhino_AMELX # -group PRIMATES Human_AMELY Chimp_AMELY Macaque_AMELY Human_AMELX # Chimp_AMELX Macaque_AMELX # -group RODENTS Mouse_AMELX Rat_AMELX # -group CARNI Dog_AMELY Cat_AMELY Dog_AMELX Cat_AMELX # -group CETART Cow_AMELY Pig_AMELY Cow_AMELX Pig_AMELX # -group OUT Opossum_AMELX Platypus_AMELX # # AMELY.final.nex: 26 sequences: # Domain=Data; # # Options and features: Using 26 DNA sequences, 2327 aligned bases, # 148 polymorphisms, NEXUS format, NEXUS datatype=nucleotide, # gscale=1 for mismatches, 6 groups defined, maxSimPairPval=0.05, # maxSimGlobPval=0.05, no maxKAPairPval limits, no maxKAGlobPval limits, # simPvals based on 10,000 permutations, # global P-values based on BLAST-like global scores, # fragment limits: minlength=1, minnpolys=2, minscore=2, # pairwise max lists=2000, at most one overlapping fragment, # starting seed=123, contiguous sites with indels are one polymorphism, # 8 indel blocks with up to 1247 sites each, # match (replacement) char in source file is . (2EH). # Groups: # EQUIDS (8): Horse_AMELY Przewalskii_AMELY Onager_AMELY Donkey_AMELY # Horse_AMELX Przewalski_AMELX Donkey_AMELX Rhino_AMELX # PRIMATES (6): Human_AMELY Chimp_AMELY Macaque_AMELY Human_AMELX # Chimp_AMELX Macaque_AMELX # RODENTS (2): Mouse_AMELX Rat_AMELX # CARNI (4): Dog_AMELY Cat_AMELY Dog_AMELX Cat_AMELX # CETART (4): Cow_AMELY Pig_AMELY Cow_AMELX Pig_AMELX # OUT (2): Opossum_AMELX Platypus_AMELX # Looking at within-group fragments only (6 groups) # # Mismatch penalty: 1 * npolys / num_ppen # where `num_ppen' is the number of ``potential penalties'': # sequence differences for inner fragments, # local monomorphisms for outer fragments. # Nucleotide codes in data: T(4755) C(7088) A(5888) G(4140) # Other(38,631) CG/TCAG ratio: 51.34% # Non-nucleotide characters in data: -(2DH)(n=38,335) ?(3FH)(n=296) # 2043 sites with missing data or unrecognized characters. # (These characters are treated as indels for the # purpose of creating indel blocks.) # No sites with all gap or unrecognized characters. # 138 polymorphic and 146 monomorphic sites with no indels. # 2 single polymorphic sites with indels. # 8 indel blocks with more than one site # (each block is treated as a single polymorphism). # 148 polymorphisms to be permuted. # # Comparisons without any fragments (NUCLEOTIDES): # Przewalski_AMELX v Donkey_AMELX (inner frags): No site differences. # # The following are for outer fragments (NUCLEOTIDES): # Przewalski_AMELX (outer sequence frags): No sites are unique. # Donkey_AMELX (outer sequence frags): No sites are unique. # (The entire sequence is NOT counted as a fragment.) # # The starting random number seed is 123. # Simulated P-values are based on 10,000 permutations. # Maximum BLAST-like scores (6 groups): # Inner Max Sim S.D.s above S.D. of # frags Score P-value sim. mean sims # SCORE 9.321 0.0145 1.70 0.0019 # OuterSeq # frags 14.560 0.0000 11.32 1.1256 # # Global lists: 2 I and 2 O significant fragments # Pairwise lists: 15 I and 2 O significant fragments # where I means inner pair, O is outer seq, A is outer pair, and # G means outer group (fragments). # Global P-values are based on BLAST-like global scores. # # Fragment offsets and lengths are in nucleotides. # Note: A polymorphism can be at a run of sites with indels, # which here have up to 1247 sites. # Bases other than `TCAGU' are treated as indels # for the purpose of generating polymorphisms. # # # Global inner fragments (148 polymorphisms, 2327 aligned bases): # (Inner fragments are runs of matching sites with penalties.) # (Sim and BC KA P-values are corrected for multiple comparisons.) # (Fragments are listed only if Sim P-value <= 0.05.) # See earlier in the file for the full restrictions on fragments. # # BC KA means Bonferroni-corrected KA (BLAST-like) Pvalues. # KA Pvalues are NOT corrected for multiple pairwise comparisons. # In the following table, BC Pvalues are KA Pvalues multiplied by 57. # Num Poly is the number of polymorphic sites in the fragment. # Num Dif is the number of mismatches within the fragment. # Tot Difs is the total number of mismatches between two sequences. # MisM Pen is the penalty per mismatch for these two sequences. # # Seq Sim BC KA Aligned Offsets Num Num Tot MisM # Names Pvalue Pvalue Begin End Len Poly Dif Difs Pen. GI Horse_AMELX;Przewalski_AMELX 0.0145 0.00510 455 2327 1873 147 0 1 148 GI Horse_AMELX;Donkey_AMELX 0.0145 0.00510 455 2327 1873 147 0 1 148 # # 2 inner fragments listed. # 2077 overlapping fragments discarded. # # ADDITIONAL PAIRWISE FRAGMENTS with BC Pairwise SimPval < 0.05 # OR LISTED GLOBAL FRAGMENTS with significantly better BC SimPval # Here BC SimPval is the Pairwise Sim Pvalue multiplied by 57. # # Seq BC Sim BC KA Aligned Offsets Num Num Tot MisM # Names Pvalue Pvalue Begin End Len Poly Dif Difs Pen. AI Pig_AMELY;Pig_AMELX 0.0456 0.03894 455 1080 626 146 0 2 74 # # One inner fragment listed. # # # Global outer-sequence fragments (148 polymorphisms, 2327 aligned bases): # (Outer-sequence fragments are runs of sites that are unique in that group.) # (Sim and BC KA P-values are corrected for multiple comparisons.) # (Fragments are listed only if Sim P-value <= 0.05.) # See earlier in the file for the full restrictions on fragments. # # BC KA means Bonferroni-corrected KA (BLAST-like) Pvalues. # KA Pvalues are NOT corrected for multiple pairwise comparisons. # In the following table, BC Pvalues are KA Pvalues multiplied by 24. # Num Poly is the number of polymorphic sites in the fragment. # Num Mat is the number of nonunique sites within the fragment. # Tot Mats is the total number of nonunique sites for that sequence. # MisM Pen is the penalty per nonunique site for this sequence. # # Seq Sim BC KA Aligned Offsets Num Num Tot MisM # Name Pvalue Pvalue Begin End Len Poly Mat Mats Pen. GO Cat_AMELY 0.0000 0.00001 560 576 17 10 0 127 2 GO Opossum_AMELX 0.0206 0.19480 766 1079 314 28 3 69 3 # # 2 outer-sequence fragments listed. # 36 overlapping fragments discarded. # # # Pairwise inner fragments (148 polymorphisms, 2327 aligned bases): # (Inner fragments are runs of matching sites with penalties.) # (P-values are not corrected for multiple comparisons.) # (Fragments are listed only if Sim P-value <= 0.05.) # See earlier in the file for the full restrictions on fragments. # # KA Pvalues are NOT corrected for multiple pairwise comparisons. # Multiply by 57 for Bonferroni-corrected KA Pvalues. # Num Poly is the number of polymorphic sites in the fragment. # Num Dif is the number of mismatches within the fragment. # Tot Difs is the total number of mismatches between two sequences. # MisM Pen is the penalty per mismatch for these two sequences. # # Seq Sim KA Aligned Offsets Num Num Tot MisM # Names Pvalue Pvalue Begin End Len Poly Dif Difs Pen. Group EQUIDS: PI Horse_AMELY;Przewalskii_AMELY 0.0424 0.00489 455 731 277 103 0 4 37 PI Horse_AMELY;Onager_AMELY 0.0329 0.01552 468 731 264 96 0 5 30 PI Horse_AMELY;Donkey_AMELY 0.0063 0.04411 530 724 195 89 0 8 19 PI Przewalskii_AMELY;Onager_AMELY 0.0207 0.00483 468 766 299 111 0 4 37 PI Przewalskii_AMELY;Donkey_AMELY 0.0129 0.04661 530 724 195 89 0 7 22 PI Onager_AMELY;Donkey_AMELY 0.0063 0.04411 530 724 195 89 0 8 19 PI Horse_AMELX;Przewalski_AMELX 0.0145 0.00009 455 2327 1873 147 0 1 148 PI Horse_AMELX;Donkey_AMELX 0.0145 0.00009 455 2327 1873 147 0 1 148 Group PRIMATES: PI Human_AMELX;Chimp_AMELX 0.0016 0.00543 530 1080 551 136 0 3 50 Group RODENTS: PI Mouse_AMELX;Rat_AMELX 0.0187 0.04732 542 1080 539 133 2 7 22 Group CARNI: PI Dog_AMELY;Cat_AMELY 0.0010 0.03659 687 1080 394 66 4 32 5 PI Cat_AMELY;Dog_AMELX 0.0057 0.09112 662 1080 419 81 5 25 6 PI Cat_AMELY;Cat_AMELX 0.0032 0.07251 593 1080 488 109 9 26 6 Group CETART: PI Cow_AMELY;Cow_AMELX 0.0090 0.00478 455 766 312 118 0 4 37 PI Pig_AMELY;Pig_AMELX 0.0008 0.00068 455 1080 626 146 0 2 74 # # 15 inner fragments listed. # 2077 overlapping fragments discarded. # # # Pairwise outer-sequence fragments (148 polymorphisms, 2327 aligned bases): # (Outer-sequence fragments are runs of sites that are unique in that group.) # (P-values are not corrected for multiple comparisons.) # (Fragments are listed only if Sim P-value <= 0.05.) # See earlier in the file for the full restrictions on fragments. # # KA Pvalues are NOT corrected for multiple pairwise comparisons. # Multiply by 24 for Bonferroni-corrected KA Pvalues. # Num Poly is the number of polymorphic sites in the fragment. # Num Mat is the number of nonunique sites within the fragment. # Tot Mats is the total number of nonunique sites for that sequence. # MisM Pen is the penalty per nonunique site for this sequence. # # Seq Sim KA Aligned Offsets Num Num Tot MisM # Name Pvalue Pvalue Begin End Len Poly Mat Mats Pen. Group CARNI: PO Cat_AMELY 0.0000 0.00000 560 576 17 10 0 127 2 Group OUT: PO Opossum_AMELX 0.0032 0.00812 766 1079 314 28 3 69 3 # # 2 outer-sequence fragments listed. # 36 overlapping fragments discarded. # # Output of GENECONV for sequence file ANOS1Y.fas # GENECONV version 1.81 # Command line: GENECONV ANOS1Y.fas anos1group.cfg anos1ygroupoutg1 /lp # /g1 # Contents of parameter configuration file: # anos1group.cfg: -Startseed=123 -MaxSimGlobalPval=0.05 # -group EQUIDS Hor_ANOS1Y Don_ANOS1Y Ona_ANOS1Y Hor_ANOS1 # Prz_ANOS1 Don_ANOS1 # -group OUT Hum_ANOS2P Hum_ANOS1 Chi_ANOS1 Mac_ANOS1 Dog_ANOS1 # Ctl_ANOS1 Ckn_ANOS1 Cat_ANOS1 Pig_ANOS1 Opo_ANOS1 Pla_ANOS1 # Chi_ANOS1Y # # ANOS1Y.fas: 18 sequences. # # Options and features: Using 18 DNA sequences, 6314 aligned bases, # 578 polymorphisms, FASTA format, gscale=1 for mismatches, # 2 groups defined, maxSimPairPval=0.05, maxSimGlobPval=0.05, # no maxKAPairPval limits, no maxKAGlobPval limits, # simPvals based on 10,000 permutations, # global P-values based on BLAST-like global scores, # fragment limits: minlength=1, minnpolys=2, minscore=2, # pairwise max lists=2000, at most one overlapping fragment, # starting seed=123, contiguous sites with indels are one polymorphism, # one indel block with up to 5737 sites each, # no match (replacement) char in source file. # Groups: # EQUIDS (6): Hor_ANOS1Y Don_ANOS1Y Ona_ANOS1Y Hor_ANOS1 Prz_ANOS1 # Don_ANOS1 # OUT (12): Hum_ANOS2P Hum_ANOS1 Chi_ANOS1 Mac_ANOS1 Dog_ANOS1 # Ctl_ANOS1 Ckn_ANOS1 Cat_ANOS1 Pig_ANOS1 Opo_ANOS1 Pla_ANOS1 # Chi_ANOS1Y # Looking at within-group fragments only (2 groups) # # Mismatch penalty: 1 * npolys / num_ppen # where `num_ppen' is the number of ``potential penalties'': # sequence differences for inner fragments, # local monomorphisms for outer fragments. # Nucleotide codes in data: T(18,125) C(15,718) A(19,045) G(14,839) # Other(45,925) CG/TCAG ratio: 45.12% # Non-nucleotide characters in data: ?(3FH)(n=45,925) # 5737 sites with missing data or unrecognized characters. # (These characters are treated as indels for the # purpose of creating indel blocks.) # No sites with all gap or unrecognized characters. # 577 polymorphic and 0 monomorphic sites with no indels. # No single polymorphic sites with indels. # One indel block with more than one site # (each block is treated as a single polymorphism). # 578 polymorphisms to be permuted. # # The starting random number seed is 123. # Simulated P-values are based on 10,000 permutations. # Maximum BLAST-like scores (2 groups): # Inner Max Sim S.D.s above S.D. of # frags Score P-value sim. mean sims # SCORE 23.215 0.0000 15.52 1.2252 # OuterSeq # frags 2.827 0.3211 0.32 1.2624 # # Global lists: 2 I and no O significant fragments # Pairwise lists: 5 I and no O significant fragments # where I means inner pair, O is outer seq, A is outer pair, and # G means outer group (fragments). # Global P-values are based on BLAST-like global scores. # # Fragment offsets and lengths are in nucleotides. # Note: A polymorphism can be at a run of sites with indels, # which here have up to 5737 sites. # Bases other than `TCAGU' are treated as indels # for the purpose of generating polymorphisms. # # # Global inner fragments (578 polymorphisms, 6314 aligned bases): # (Inner fragments are runs of matching sites with penalties.) # (Sim and BC KA P-values are corrected for multiple comparisons.) # (Fragments are listed only if Sim P-value <= 0.05.) # See earlier in the file for the full restrictions on fragments. # # BC KA means Bonferroni-corrected KA (BLAST-like) Pvalues. # KA Pvalues are NOT corrected for multiple pairwise comparisons. # In the following table, BC Pvalues are KA Pvalues multiplied by 81. # Num Poly is the number of polymorphic sites in the fragment. # Num Dif is the number of mismatches within the fragment. # Tot Difs is the total number of mismatches between two sequences. # MisM Pen is the penalty per mismatch for these two sequences. # # Seq Sim BC KA Aligned Offsets Num Num Tot MisM # Names Pvalue Pvalue Begin End Len Poly Dif Difs Pen. GI Ctl_ANOS1;Pig_ANOS1 0.0000 0.00000 44 96 53 53 7 367 2 GI Hum_ANOS2P;Hum_ANOS1 0.0006 0.00134 9 75 67 67 17 391 2 # # 2 inner fragments listed. # 1280 overlapping fragments discarded. # # # Global outer-sequence fragments (578 polymorphisms, 6314 aligned bases): # (Outer-sequence fragments are runs of sites that are unique in that group.) # (Sim and BC KA P-values are corrected for multiple comparisons.) # (Fragments are listed only if Sim P-value <= 0.05.) # See earlier in the file for the full restrictions on fragments. # # # No outer-sequence fragments listed. # # # Pairwise inner fragments (578 polymorphisms, 6314 aligned bases): # (Inner fragments are runs of matching sites with penalties.) # (P-values are not corrected for multiple comparisons.) # (Fragments are listed only if Sim P-value <= 0.05.) # See earlier in the file for the full restrictions on fragments. # # KA Pvalues are NOT corrected for multiple pairwise comparisons. # Multiply by 81 for Bonferroni-corrected KA Pvalues. # Num Poly is the number of polymorphic sites in the fragment. # Num Dif is the number of mismatches within the fragment. # Tot Difs is the total number of mismatches between two sequences. # MisM Pen is the penalty per mismatch for these two sequences. # # Seq Sim KA Aligned Offsets Num Num Tot MisM # Names Pvalue Pvalue Begin End Len Poly Dif Difs Pen. Group OUT: PI Hum_ANOS2P;Hum_ANOS1 0.0000 0.00002 9 75 67 67 17 391 2 PI Ctl_ANOS1;Pig_ANOS1 0.0000 0.00000 44 96 53 53 7 367 2 PI Ckn_ANOS1;Opo_ANOS1 0.0338 0.03872 241 247 7 7 0 429 2 PI Ckn_ANOS1;Pla_ANOS1 0.0362 0.04066 80 87 8 8 0 402 2 PI Ckn_ANOS1;Chi_ANOS1Y 0.0341 0.03872 140 149 10 10 1 429 2 # # 5 inner fragments listed. # 1280 overlapping fragments discarded. # # # Pairwise outer-sequence fragments (578 polymorphisms, 6314 aligned bases): # (Outer-sequence fragments are runs of sites that are unique in that group.) # (P-values are not corrected for multiple comparisons.) # (Fragments are listed only if Sim P-value <= 0.05.) # See earlier in the file for the full restrictions on fragments. # # No outer-sequence fragments listed. # # Output of GENECONV for sequence file ARSFY.fas # GENECONV version 1.81 # Command line: GENECONV ARSFY.fas arsfygroup.cfg arsfygroupoutg1 /lp /g1 # Contents of parameter configuration file: # arsfygroup.cfg: -Startseed=123 -MaxSimGlobalPval=0.05 # -group EQUIDS Hor_ARSFY Hor_ARSF Don_ARSF # -group OUT Rhi_ARSF Hum_ARSF Chi_ARSF Mac_ARSF Dog_ARSF # Cat_ARSF Opo_ARSF # # ARSFY.fas: 10 sequences. # # Options and features: Using 10 DNA sequences, 4715 aligned bases, # 1352 polymorphisms, FASTA format, gscale=1 for mismatches, # 2 groups defined, maxSimPairPval=0.05, maxSimGlobPval=0.05, # no maxKAPairPval limits, no maxKAGlobPval limits, # simPvals based on 10,000 permutations, # global P-values based on BLAST-like global scores, # fragment limits: minlength=1, minnpolys=2, minscore=2, # pairwise max lists=2000, at most one overlapping fragment, # starting seed=123, contiguous sites with indels are one polymorphism, # 6 indel blocks with up to 1931 sites each, # no match (replacement) char in source file. # Groups: # EQUIDS (3): Hor_ARSFY Hor_ARSF Don_ARSF # OUT (7): Rhi_ARSF Hum_ARSF Chi_ARSF Mac_ARSF Dog_ARSF Cat_ARSF # Opo_ARSF # Looking at within-group fragments only (2 groups) # # Mismatch penalty: 1 * npolys / num_ppen # where `num_ppen' is the number of ``potential penalties'': # sequence differences for inner fragments, # local monomorphisms for outer fragments. # Nucleotide codes in data: T(5917) C(5690) A(5645) G(5698) # Other(24,200) CG/TCAG ratio: 49.62% # Non-nucleotide characters in data: -(2DH)(n=24,131) ?(3FH)(n=69) # 3052 sites with missing data or unrecognized characters. # (These characters are treated as indels for the # purpose of creating indel blocks.) # No sites with all gap or unrecognized characters. # 1344 polymorphic and 319 monomorphic sites with no indels. # 2 single polymorphic sites with indels. # 6 indel blocks with more than one site # (each block is treated as a single polymorphism). # 1352 polymorphisms to be permuted. # # The starting random number seed is 123. # Simulated P-values are based on 10,000 permutations. # Maximum BLAST-like scores (2 groups): # Inner Max Sim S.D.s above S.D. of # frags Score P-value sim. mean sims # SCORE 180.905 0.0000 1264.70 0.1380 # OuterSeq # frags 27.449 0.0000 21.64 1.1916 # # Global lists: 2 I and 1 O significant fragments # Pairwise lists: 14 I and 1 O significant fragments # where I means inner pair, O is outer seq, A is outer pair, and # G means outer group (fragments). # Global P-values are based on BLAST-like global scores. # # Fragment offsets and lengths are in nucleotides. # Note: A polymorphism can be at a run of sites with indels, # which here have up to 1931 sites. # Bases other than `TCAGU' are treated as indels # for the purpose of generating polymorphisms. # # # Global inner fragments (1352 polymorphisms, 4715 aligned bases): # (Inner fragments are runs of matching sites with penalties.) # (Sim and BC KA P-values are corrected for multiple comparisons.) # (Fragments are listed only if Sim P-value <= 0.05.) # See earlier in the file for the full restrictions on fragments. # # BC KA means Bonferroni-corrected KA (BLAST-like) Pvalues. # KA Pvalues are NOT corrected for multiple pairwise comparisons. # In the following table, BC Pvalues are KA Pvalues multiplied by 24. # Num Poly is the number of polymorphic sites in the fragment. # Num Dif is the number of mismatches within the fragment. # Tot Difs is the total number of mismatches between two sequences. # MisM Pen is the penalty per mismatch for these two sequences. # # Seq Sim BC KA Aligned Offsets Num Num Tot MisM # Names Pvalue Pvalue Begin End Len Poly Dif Difs Pen. GI Hor_ARSFY;Hor_ARSF 0.0000 0.00000 1096 1362 267 140 4 1053 2 GI Hor_ARSFY;Don_ARSF 0.0000 0.00000 1096 1362 267 140 4 1053 2 # # 2 inner fragments listed. # 29,493 overlapping fragments discarded. # # # Global outer-sequence fragments (1352 polymorphisms, 4715 aligned bases): # (Outer-sequence fragments are runs of sites that are unique in that group.) # (Sim and BC KA P-values are corrected for multiple comparisons.) # (Fragments are listed only if Sim P-value <= 0.05.) # See earlier in the file for the full restrictions on fragments. # # BC KA means Bonferroni-corrected KA (BLAST-like) Pvalues. # KA Pvalues are NOT corrected for multiple pairwise comparisons. # In the following table, BC Pvalues are KA Pvalues multiplied by 10. # Num Poly is the number of polymorphic sites in the fragment. # Num Mat is the number of nonunique sites within the fragment. # Tot Mats is the total number of nonunique sites for that sequence. # MisM Pen is the penalty per nonunique site for this sequence. # # Seq Sim BC KA Aligned Offsets Num Num Tot MisM # Name Pvalue Pvalue Begin End Len Poly Mat Mats Pen. GO Hor_ARSFY 0.0000 0.00000 1537 2524 988 840 101 307 5 # # One outer-sequence fragment listed. # 10,293 overlapping fragments discarded. # # # Pairwise inner fragments (1352 polymorphisms, 4715 aligned bases): # (Inner fragments are runs of matching sites with penalties.) # (P-values are not corrected for multiple comparisons.) # (Fragments are listed only if Sim P-value <= 0.05.) # See earlier in the file for the full restrictions on fragments. # # KA Pvalues are NOT corrected for multiple pairwise comparisons. # Multiply by 24 for Bonferroni-corrected KA Pvalues. # Num Poly is the number of polymorphic sites in the fragment. # Num Dif is the number of mismatches within the fragment. # Tot Difs is the total number of mismatches between two sequences. # MisM Pen is the penalty per mismatch for these two sequences. # # Seq Sim KA Aligned Offsets Num Num Tot MisM # Names Pvalue Pvalue Begin End Len Poly Dif Difs Pen. Group EQUIDS: PI Hor_ARSFY;Hor_ARSF 0.0000 0.00000 1096 1362 267 140 4 1053 2 PI Hor_ARSFY;Don_ARSF 0.0000 0.00000 1096 1362 267 140 4 1053 2 PI Hor_ARSF;Don_ARSF 0.0046 0.03136 1249 2414 1166 940 11 31 44 Group OUT: PI Rhi_ARSF;Hum_ARSF 0.0086 0.01781 2003 2088 86 74 4 355 4 PI Rhi_ARSF;Chi_ARSF 0.0089 0.01781 2003 2088 86 74 4 355 4 PI Rhi_ARSF;Mac_ARSF 0.0187 0.03181 1997 2088 92 80 6 355 4 PI Rhi_ARSF;Dog_ARSF 0.0129 0.02140 1734 1905 172 140 14 311 5 PI Rhi_ARSF;Cat_ARSF 0.0131 0.02172 1752 1837 86 70 3 320 5 PI Rhi_ARSF;Cat_ARSF 0.0323 0.04634 1537 1647 111 95 8 320 5 PI Rhi_ARSF;Opo_ARSF 0.0239 0.02508 2213 2319 107 91 17 555 3 PI Mac_ARSF;Opo_ARSF 0.0242 0.02883 2186 2261 76 62 10 563 3 PI Mac_ARSF;Opo_ARSF 0.0242 0.02883 2099 2145 47 38 4 563 3 PI Dog_ARSF;Opo_ARSF 0.0089 0.00951 2258 2316 59 51 6 540 3 PI Dog_ARSF;Opo_ARSF 0.0176 0.01973 1472 1524 53 45 5 540 3 # # 14 inner fragments listed. # 29,493 overlapping fragments discarded. # # # Pairwise outer-sequence fragments (1352 polymorphisms, 4715 aligned bases): # (Outer-sequence fragments are runs of sites that are unique in that group.) # (P-values are not corrected for multiple comparisons.) # (Fragments are listed only if Sim P-value <= 0.05.) # See earlier in the file for the full restrictions on fragments. # # KA Pvalues are NOT corrected for multiple pairwise comparisons. # Multiply by 10 for Bonferroni-corrected KA Pvalues. # Num Poly is the number of polymorphic sites in the fragment. # Num Mat is the number of nonunique sites within the fragment. # Tot Mats is the total number of nonunique sites for that sequence. # MisM Pen is the penalty per nonunique site for this sequence. # # Seq Sim KA Aligned Offsets Num Num Tot MisM # Name Pvalue Pvalue Begin End Len Poly Mat Mats Pen. Group EQUIDS: PO Hor_ARSFY 0.0000 0.00000 1537 2524 988 840 101 307 5 # # One outer-sequence fragment listed. # 10,293 overlapping fragments discarded. # ################################################################################### # Output of GENECONV for sequence file ARSHY.fas # GENECONV version 1.81 # Command line: GENECONV ARSHY.fas arshygroup.cfg arshygroupoutg1 /lp /g1 # Contents of parameter configuration file: # arshygroup.cfg: -Startseed=123 -MaxSimGlobalPval=0.05 # -group EQUIDS Hor_ARSHY Hor_ARSH Don_ARSH # -group OUT Ctl_ARSH Rhi_ARSH Dog_ARSH Cat_ARSH Hum_ARSH # Chi_ARSH Mac_ARSH Opo_ARSH # # ARSHY.fas: 11 sequences. # # Options and features: Using 11 DNA sequences, 2357 aligned bases, # 482 polymorphisms, FASTA format, gscale=1 for mismatches, # 2 groups defined, maxSimPairPval=0.05, maxSimGlobPval=0.05, # no maxKAPairPval limits, no maxKAGlobPval limits, # simPvals based on 10,000 permutations, # global P-values based on BLAST-like global scores, # fragment limits: minlength=1, minnpolys=2, minscore=2, # pairwise max lists=2000, at most one overlapping fragment, # starting seed=123, contiguous sites with indels are one polymorphism, # 12 indel blocks with up to 475 sites each, # no match (replacement) char in source file. # Groups: # EQUIDS (3): Hor_ARSHY Hor_ARSH Don_ARSH # OUT (8): Ctl_ARSH Rhi_ARSH Dog_ARSH Cat_ARSH Hum_ARSH Chi_ARSH # Mac_ARSH Opo_ARSH # Looking at within-group fragments only (2 groups) # # Mismatch penalty: 1 * npolys / num_ppen # where `num_ppen' is the number of ``potential penalties'': # sequence differences for inner fragments, # local monomorphisms for outer fragments. # Nucleotide codes in data: T(4706) C(5304) A(4349) G(5198) # Other(6370) CG/TCAG ratio: 53.70% # Non-nucleotide characters in data: -(2DH)(n=6370) # 1352 sites with missing data or unrecognized characters. # (These characters are treated as indels for the # purpose of creating indel blocks.) # No sites with all gap or unrecognized characters. # 470 polymorphic and 535 monomorphic sites with no indels. # No single polymorphic sites with indels. # 12 indel blocks with more than one site # (each block is treated as a single polymorphism). # 482 polymorphisms to be permuted. # # The starting random number seed is 123. # Simulated P-values are based on 10,000 permutations. # Maximum BLAST-like scores (2 groups): # Inner Max Sim S.D.s above S.D. of # frags Score P-value sim. mean sims # SCORE 8.910 0.0006 8.89 0.5478 # OuterSeq # frags 3.130 0.1577 1.09 1.2043 # # Global lists: 2 I and no O significant fragments # Pairwise lists: 9 I and 1 O significant fragments # where I means inner pair, O is outer seq, A is outer pair, and # G means outer group (fragments). # Global P-values are based on BLAST-like global scores. # # Fragment offsets and lengths are in nucleotides. # Note: A polymorphism can be at a run of sites with indels, # which here have up to 475 sites. # Bases other than `TCAGU' are treated as indels # for the purpose of generating polymorphisms. # # # Global inner fragments (482 polymorphisms, 2357 aligned bases): # (Inner fragments are runs of matching sites with penalties.) # (Sim and BC KA P-values are corrected for multiple comparisons.) # (Fragments are listed only if Sim P-value <= 0.05.) # See earlier in the file for the full restrictions on fragments. # # BC KA means Bonferroni-corrected KA (BLAST-like) Pvalues. # KA Pvalues are NOT corrected for multiple pairwise comparisons. # In the following table, BC Pvalues are KA Pvalues multiplied by 31. # Num Poly is the number of polymorphic sites in the fragment. # Num Dif is the number of mismatches within the fragment. # Tot Difs is the total number of mismatches between two sequences. # MisM Pen is the penalty per mismatch for these two sequences. # # Seq Sim BC KA Aligned Offsets Num Num Tot MisM # Names Pvalue Pvalue Begin End Len Poly Dif Difs Pen. GI Chi_ARSH;Mac_ARSH 0.0006 0.00418 1 1224 1224 352 20 68 8 GI Hum_ARSH;Chi_ARSH 0.0029 0.01496 1 1379 1379 416 8 46 11 # # 2 inner fragments listed. # 4327 overlapping fragments discarded. # # # Global outer-sequence fragments (482 polymorphisms, 2357 aligned bases): # (Outer-sequence fragments are runs of sites that are unique in that group.) # (Sim and BC KA P-values are corrected for multiple comparisons.) # (Fragments are listed only if Sim P-value <= 0.05.) # See earlier in the file for the full restrictions on fragments. # # # No outer-sequence fragments listed. # # # Pairwise inner fragments (482 polymorphisms, 2357 aligned bases): # (Inner fragments are runs of matching sites with penalties.) # (P-values are not corrected for multiple comparisons.) # (Fragments are listed only if Sim P-value <= 0.05.) # See earlier in the file for the full restrictions on fragments. # # KA Pvalues are NOT corrected for multiple pairwise comparisons. # Multiply by 31 for Bonferroni-corrected KA Pvalues. # Num Poly is the number of polymorphic sites in the fragment. # Num Dif is the number of mismatches within the fragment. # Tot Difs is the total number of mismatches between two sequences. # MisM Pen is the penalty per mismatch for these two sequences. # # Seq Sim KA Aligned Offsets Num Num Tot MisM # Names Pvalue Pvalue Begin End Len Poly Dif Difs Pen. Group OUT: PI Rhi_ARSH;Hum_ARSH 0.0357 0.05261 935 972 38 24 1 190 3 PI Rhi_ARSH;Chi_ARSH 0.0072 0.01203 935 972 38 24 1 209 3 PI Rhi_ARSH;Mac_ARSH 0.0265 0.04538 935 972 38 24 1 192 3 PI Rhi_ARSH;Opo_ARSH 0.0373 0.04150 1311 1839 529 46 12 297 2 PI Cat_ARSH;Hum_ARSH 0.0296 0.04149 800 879 80 34 4 204 3 PI Cat_ARSH;Chi_ARSH 0.0467 0.05478 800 852 53 22 2 230 3 PI Hum_ARSH;Chi_ARSH 0.0000 0.00048 1 1379 1379 416 8 46 11 PI Hum_ARSH;Mac_ARSH 0.0354 0.12199 755 1224 470 234 11 44 11 PI Chi_ARSH;Mac_ARSH 0.0000 0.00013 1 1224 1224 352 20 68 8 # # 9 inner fragments listed. # 4327 overlapping fragments discarded. # # # Pairwise outer-sequence fragments (482 polymorphisms, 2357 aligned bases): # (Outer-sequence fragments are runs of sites that are unique in that group.) # (P-values are not corrected for multiple comparisons.) # (Fragments are listed only if Sim P-value <= 0.05.) # See earlier in the file for the full restrictions on fragments. # # KA Pvalues are NOT corrected for multiple pairwise comparisons. # Multiply by 11 for Bonferroni-corrected KA Pvalues. # Num Poly is the number of polymorphic sites in the fragment. # Num Mat is the number of nonunique sites within the fragment. # Tot Mats is the total number of nonunique sites for that sequence. # MisM Pen is the penalty per nonunique site for this sequence. # # Seq Sim KA Aligned Offsets Num Num Tot MisM # Name Pvalue Pvalue Begin End Len Poly Mat Mats Pen. Group OUT: PO Mac_ARSH 0.0336 0.04279 1650 1829 180 6 1 460 2 # # One outer-sequence fragment listed. # 29 overlapping fragments discarded. # ########################################################################################## # Output of GENECONV for sequence file EIF3CY.fas # GENECONV version 1.81 # Command line: GENECONV EIF3CY.fas eifc3ygroup.cfg eif3cygroupoutg1 /lp # /g1 # Contents of parameter configuration file: # eifc3ygroup.cfg: -Startseed=123 -MaxSimGlobalPval=0.05 # -group EQUIDS Hor_EIF3CY Hor_EIF3C Prz_EIF3C Don_EIF3C # -group OUT Hum_EIF3C Dog_EIF3C Ctl_EIF3C Cat_EIF3C # # EIF3CY.fas: 8 sequences. # # Options and features: Using 8 DNA sequences, 4267 aligned bases, # 502 polymorphisms, FASTA format, gscale=1 for mismatches, # 2 groups defined, maxSimPairPval=0.05, maxSimGlobPval=0.05, # no maxKAPairPval limits, no maxKAGlobPval limits, # simPvals based on 10,000 permutations, # global P-values based on BLAST-like global scores, # fragment limits: minlength=1, minnpolys=2, minscore=2, # pairwise max lists=2000, at most one overlapping fragment, # starting seed=123, contiguous sites with indels are one polymorphism, # 12 indel blocks with up to 285 sites each, # no match (replacement) char in source file. # Groups: # EQUIDS (4): Hor_EIF3CY Hor_EIF3C Prz_EIF3C Don_EIF3C # OUT (4): Hum_EIF3C Dog_EIF3C Ctl_EIF3C Cat_EIF3C # Looking at within-group fragments only (2 groups) # # Mismatch penalty: 1 * npolys / num_ppen # where `num_ppen' is the number of ``potential penalties'': # sequence differences for inner fragments, # local monomorphisms for outer fragments. # Nucleotide codes in data: T(4652) C(6048) A(6369) G(6619) # Other(10,448) CG/TCAG ratio: 53.47% # Non-nucleotide characters in data: -(2DH)(n=10,448) # 1460 sites with missing data or unrecognized characters. # (These characters are treated as indels for the # purpose of creating indel blocks.) # 942 sites with all gap or unrecognized characters. # 486 polymorphic and 2321 monomorphic sites with no indels. # 4 single polymorphic sites with indels. # 12 indel blocks with more than one site # (each block is treated as a single polymorphism). # 502 polymorphisms to be permuted. # # The starting random number seed is 123. # Simulated P-values are based on 10,000 permutations. # Maximum BLAST-like scores (2 groups): # Inner Max Sim S.D.s above S.D. of # frags Score P-value sim. mean sims # SCORE 5.698 0.0106 5.01 0.4792 # OuterSeq # frags 68.943 0.0000 51.97 1.2966 # # Global lists: 6 I and 1 O significant fragments # Pairwise lists: 10 I and 2 O significant fragments # where I means inner pair, O is outer seq, A is outer pair, and # G means outer group (fragments). # Global P-values are based on BLAST-like global scores. # # Fragment offsets and lengths are in nucleotides. # Note: A polymorphism can be at a run of sites with indels, # which here have up to 285 sites. # Bases other than `TCAGU' are treated as indels # for the purpose of generating polymorphisms. # # # Global inner fragments (502 polymorphisms, 4267 aligned bases): # (Inner fragments are runs of matching sites with penalties.) # (Sim and BC KA P-values are corrected for multiple comparisons.) # (Fragments are listed only if Sim P-value <= 0.05.) # See earlier in the file for the full restrictions on fragments. # # BC KA means Bonferroni-corrected KA (BLAST-like) Pvalues. # KA Pvalues are NOT corrected for multiple pairwise comparisons. # In the following table, BC Pvalues are KA Pvalues multiplied by 12. # Num Poly is the number of polymorphic sites in the fragment. # Num Dif is the number of mismatches within the fragment. # Tot Difs is the total number of mismatches between two sequences. # MisM Pen is the penalty per mismatch for these two sequences. # # Seq Sim BC KA Aligned Offsets Num Num Tot MisM # Names Pvalue Pvalue Begin End Len Poly Dif Difs Pen. GI Hum_EIF3C;Cat_EIF3C 0.0106 0.04018 3652 3768 117 37 4 228 3 GI Hor_EIF3CY;Prz_EIF3C 0.0115 0.04330 641 2463 1823 298 11 55 10 GI Hor_EIF3C;Prz_EIF3C 0.0175 0.06927 744 3694 2951 362 1 33 16 GI Ctl_EIF3C;Cat_EIF3C 0.0301 0.10688 3741 3826 86 24 1 222 3 GI Dog_EIF3C;Ctl_EIF3C 0.0425 0.16886 3684 3768 85 30 4 251 2 GI Prz_EIF3C;Don_EIF3C 0.0467 0.17065 685 3694 3010 373 11 43 12 # # 6 inner fragments listed. # 1437 overlapping fragments discarded. # # ADDITIONAL PAIRWISE FRAGMENTS with BC Pairwise SimPval < 0.05 # OR LISTED GLOBAL FRAGMENTS with significantly better BC SimPval # Here BC SimPval is the Pairwise Sim Pvalue multiplied by 12. # # Seq BC Sim BC KA Aligned Offsets Num Num Tot MisM # Names Pvalue Pvalue Begin End Len Poly Dif Difs Pen. AI Hor_EIF3CY;Prz_EIF3C 0.0012 0.04330 641 2463 1823 298 11 55 10 AI Hor_EIF3C;Prz_EIF3C 0.0012 0.06927 744 3694 2951 362 1 33 16 AI Prz_EIF3C;Don_EIF3C 0.0012 0.17065 685 3694 3010 373 11 43 12 # # 3 inner fragments listed. # # # Global outer-sequence fragments (502 polymorphisms, 4267 aligned bases): # (Outer-sequence fragments are runs of sites that are unique in that group.) # (Sim and BC KA P-values are corrected for multiple comparisons.) # (Fragments are listed only if Sim P-value <= 0.05.) # See earlier in the file for the full restrictions on fragments. # # BC KA means Bonferroni-corrected KA (BLAST-like) Pvalues. # KA Pvalues are NOT corrected for multiple pairwise comparisons. # In the following table, BC Pvalues are KA Pvalues multiplied by 8. # Num Poly is the number of polymorphic sites in the fragment. # Num Mat is the number of nonunique sites within the fragment. # Tot Mats is the total number of nonunique sites for that sequence. # MisM Pen is the penalty per nonunique site for this sequence. # # Seq Sim BC KA Aligned Offsets Num Num Tot MisM # Name Pvalue Pvalue Begin End Len Poly Mat Mats Pen. GO Prz_EIF3C 0.0000 0.00000 3690 3787 98 30 1 471 2 # # One outer-sequence fragment listed. # 20 overlapping fragments discarded. # # # Pairwise inner fragments (502 polymorphisms, 4267 aligned bases): # (Inner fragments are runs of matching sites with penalties.) # (P-values are not corrected for multiple comparisons.) # (Fragments are listed only if Sim P-value <= 0.05.) # See earlier in the file for the full restrictions on fragments. # # KA Pvalues are NOT corrected for multiple pairwise comparisons. # Multiply by 12 for Bonferroni-corrected KA Pvalues. # Num Poly is the number of polymorphic sites in the fragment. # Num Dif is the number of mismatches within the fragment. # Tot Difs is the total number of mismatches between two sequences. # MisM Pen is the penalty per mismatch for these two sequences. # # Seq Sim KA Aligned Offsets Num Num Tot MisM # Names Pvalue Pvalue Begin End Len Poly Dif Difs Pen. Group EQUIDS: PI Hor_EIF3CY;Prz_EIF3C 0.0000 0.00361 641 2463 1823 298 11 55 10 PI Hor_EIF3CY;Prz_EIF3C 0.0480 0.14470 3804 4132 329 80 0 55 10 PI Hor_EIF3C;Prz_EIF3C 0.0000 0.00577 744 3694 2951 362 1 33 16 PI Hor_EIF3C;Don_EIF3C 0.0045 0.03084 1938 4267 2330 275 1 15 34 PI Prz_EIF3C;Don_EIF3C 0.0000 0.01422 685 3694 3010 373 11 43 12 Group OUT: PI Hum_EIF3C;Dog_EIF3C 0.0186 0.02585 3654 3768 115 36 7 263 2 PI Hum_EIF3C;Cat_EIF3C 0.0022 0.00335 3652 3768 117 37 4 228 3 PI Dog_EIF3C;Ctl_EIF3C 0.0084 0.01407 3684 3768 85 30 4 251 2 PI Dog_EIF3C;Cat_EIF3C 0.0385 0.05417 2933 3768 836 46 7 209 3 PI Ctl_EIF3C;Cat_EIF3C 0.0064 0.00891 3741 3826 86 24 1 222 3 # # 10 inner fragments listed. # 1437 overlapping fragments discarded. # # # Pairwise outer-sequence fragments (502 polymorphisms, 4267 aligned bases): # (Outer-sequence fragments are runs of sites that are unique in that group.) # (P-values are not corrected for multiple comparisons.) # (Fragments are listed only if Sim P-value <= 0.05.) # See earlier in the file for the full restrictions on fragments. # # KA Pvalues are NOT corrected for multiple pairwise comparisons. # Multiply by 8 for Bonferroni-corrected KA Pvalues. # Num Poly is the number of polymorphic sites in the fragment. # Num Mat is the number of nonunique sites within the fragment. # Tot Mats is the total number of nonunique sites for that sequence. # MisM Pen is the penalty per nonunique site for this sequence. # # Seq Sim KA Aligned Offsets Num Num Tot MisM # Name Pvalue Pvalue Begin End Len Poly Mat Mats Pen. Group EQUIDS: PO Prz_EIF3C 0.0000 0.00000 3690 3787 98 30 1 471 2 Group OUT: PO Ctl_EIF3C 0.0250 0.03224 1528 1561 34 6 0 399 2 # # 2 outer-sequence fragments listed. # 20 overlapping fragments discarded. ################################################################################### # Output of GENECONV for sequence file HTRA3Y.fas # GENECONV version 1.81 # Command line: GENECONV HTRA3Y.fas htra3ygroup.cfg htra3ygroupoutg1 /lp # /g1 # Contents of parameter configuration file: # htra3ygroup.cfg: -Startseed=123 -MaxSimGlobalPval=0.05 # -group EQUIDS Ho_HTRA3Y1 Hor_HTRA3 Don_HTRA3 # -group OUT Rhi_HTRA3 Cat_HTRA3 Pig_HTRA3 Hum_HTRA3 Chi_HTRA3 # Mac_HTRA3 Dog_HTRA3 Mou_HTRA3 Rat_HTRA3 Opo_HTRA3 # # HTRA3Y.fas: 13 sequences. # # Options and features: Using 13 DNA sequences, 3270 aligned bases, # 130 polymorphisms, FASTA format, gscale=1 for mismatches, # 2 groups defined, maxSimPairPval=0.05, maxSimGlobPval=0.05, # no maxKAPairPval limits, no maxKAGlobPval limits, # simPvals based on 10,000 permutations, # global P-values based on BLAST-like global scores, # fragment limits: minlength=1, minnpolys=2, minscore=2, # pairwise max lists=2000, at most one overlapping fragment, # starting seed=123, contiguous sites with indels are one polymorphism, # 3 indel blocks with up to 1539 sites each, # no match (replacement) char in source file. # Groups: # EQUIDS (3): Ho_HTRA3Y1 Hor_HTRA3 Don_HTRA3 # OUT (10): Rhi_HTRA3 Cat_HTRA3 Pig_HTRA3 Hum_HTRA3 Chi_HTRA3 # Mac_HTRA3 Dog_HTRA3 Mou_HTRA3 Rat_HTRA3 Opo_HTRA3 # Looking at within-group fragments only (2 groups) # # Mismatch penalty: 1 * npolys / num_ppen # where `num_ppen' is the number of ``potential penalties'': # sequence differences for inner fragments, # local monomorphisms for outer fragments. # Nucleotide codes in data: T(5162) C(8788) A(5285) G(8056) # Other(15,219) CG/TCAG ratio: 61.72% # Non-nucleotide characters in data: -(2DH)(n=15,219) # 2897 sites with missing data or unrecognized characters. # (These characters are treated as indels for the # purpose of creating indel blocks.) # No sites with all gap or unrecognized characters. # 127 polymorphic and 246 monomorphic sites with no indels. # No single polymorphic sites with indels. # 3 indel blocks with more than one site # (each block is treated as a single polymorphism). # 130 polymorphisms to be permuted. # # The starting random number seed is 123. # Simulated P-values are based on 10,000 permutations. # Maximum BLAST-like scores (2 groups): # Inner Max Sim S.D.s above S.D. of # frags Score P-value sim. mean sims # SCORE 4.921 0.2038 0.07 0.1496 # OuterSeq # frags 2.631 0.2203 1.01 1.0976 # # Global lists: no I and no O significant fragments # Pairwise lists: 1 I and no O significant fragments # where I means inner pair, O is outer seq, A is outer pair, and # G means outer group (fragments). # Global P-values are based on BLAST-like global scores. # # Fragment offsets and lengths are in nucleotides. # Note: A polymorphism can be at a run of sites with indels, # which here have up to 1539 sites. # Bases other than `TCAGU' are treated as indels # for the purpose of generating polymorphisms. # # # Global inner fragments (130 polymorphisms, 3270 aligned bases): # (Inner fragments are runs of matching sites with penalties.) # (Sim and BC KA P-values are corrected for multiple comparisons.) # (Fragments are listed only if Sim P-value <= 0.05.) # See earlier in the file for the full restrictions on fragments. # # # No inner fragments listed. # # # Global outer-sequence fragments (130 polymorphisms, 3270 aligned bases): # (Outer-sequence fragments are runs of sites that are unique in that group.) # (Sim and BC KA P-values are corrected for multiple comparisons.) # (Fragments are listed only if Sim P-value <= 0.05.) # See earlier in the file for the full restrictions on fragments. # # # No outer-sequence fragments listed. # # # Pairwise inner fragments (130 polymorphisms, 3270 aligned bases): # (Inner fragments are runs of matching sites with penalties.) # (P-values are not corrected for multiple comparisons.) # (Fragments are listed only if Sim P-value <= 0.05.) # See earlier in the file for the full restrictions on fragments. # # KA Pvalues are NOT corrected for multiple pairwise comparisons. # Multiply by 48 for Bonferroni-corrected KA Pvalues. # Num Poly is the number of polymorphic sites in the fragment. # Num Dif is the number of mismatches within the fragment. # Tot Difs is the total number of mismatches between two sequences. # MisM Pen is the penalty per mismatch for these two sequences. # # Seq Sim KA Aligned Offsets Num Num Tot MisM # Names Pvalue Pvalue Begin End Len Poly Dif Difs Pen. Group EQUIDS: PI Hor_HTRA3;Don_HTRA3 0.0099 0.03912 1164 1388 225 80 0 7 19 # # One inner fragment listed. # 1374 overlapping fragments discarded. # # # Pairwise outer-sequence fragments (130 polymorphisms, 3270 aligned bases): # (Outer-sequence fragments are runs of sites that are unique in that group.) # (P-values are not corrected for multiple comparisons.) # (Fragments are listed only if Sim P-value <= 0.05.) # See earlier in the file for the full restrictions on fragments. # # No outer-sequence fragments listed. ##################################################################################### # Output of GENECONV for sequence file MYL9Y.fas # GENECONV version 1.81 # Command line: GENECONV MYL9Y.fas myl9ygroup.cfg myl9ygroupoutg1 /lp /g1 # Contents of parameter configuration file: # myl9ygroup.cfg: -Startseed=123 -MaxSimGlobalPval=0.05 # -group EQUIDS Horse_MYL9Y Horse_MYL9 Donkey_MYL9 Przewalski_MYL9 # -group OUT Rhino_MYL9 Cat_MYL9 Dog_MYL9 Cow_MYL9 Pig_MYL9 # Human_MYL9 Chimpanzee_MYL9 Macaque_MYL9 Mouse_MYL9 Rat_MYL9 # Rabbit_MYL9 Platypus_MYL9 Chicken_MYL9 # # MYL9Y.fas: 17 sequences. # # Options and features: Using 17 DNA sequences, 1505 aligned bases, # 112 polymorphisms, FASTA format, gscale=1 for mismatches, # 2 groups defined, maxSimPairPval=0.05, maxSimGlobPval=0.05, # no maxKAPairPval limits, no maxKAGlobPval limits, # simPvals based on 10,000 permutations, # global P-values based on BLAST-like global scores, # fragment limits: minlength=1, minnpolys=2, minscore=2, # pairwise max lists=2000, at most one overlapping fragment, # starting seed=123, contiguous sites with indels are one polymorphism, # 2 indel blocks with up to 748 sites each, # no match (replacement) char in source file. # Groups: # EQUIDS (4): Horse_MYL9Y Horse_MYL9 Donkey_MYL9 Przewalski_MYL9 # OUT (13): Rhino_MYL9 Cat_MYL9 Dog_MYL9 Cow_MYL9 Pig_MYL9 # Human_MYL9 Chimpanzee_MYL9 Macaque_MYL9 Mouse_MYL9 Rat_MYL9 # Rabbit_MYL9 Platypus_MYL9 Chicken_MYL9 # Looking at within-group fragments only (2 groups) # # Mismatch penalty: 1 * npolys / num_ppen # where `num_ppen' is the number of ``potential penalties'': # sequence differences for inner fragments, # local monomorphisms for outer fragments. # Nucleotide codes in data: T(2976) C(6239) A(4469) G(5058) # Other(6843) CG/TCAG ratio: 60.28% # Non-nucleotide characters in data: -(2DH)(n=6843) # 1047 sites with missing data or unrecognized characters. # (These characters are treated as indels for the # purpose of creating indel blocks.) # No sites with all gap or unrecognized characters. # 109 polymorphic and 349 monomorphic sites with no indels. # One single polymorphic site with indels. # 2 indel blocks with more than one site # (each block is treated as a single polymorphism). # 112 polymorphisms to be permuted. # # The starting random number seed is 123. # Simulated P-values are based on 10,000 permutations. # Maximum BLAST-like scores (2 groups): # Inner Max Sim S.D.s above S.D. of # frags Score P-value sim. mean sims # SCORE 6.752 0.0022 0.84 0.0310 # OuterSeq # frags 4.045 0.0445 2.19 1.0708 # # Global lists: 1 I and 1 O significant fragments # Pairwise lists: 10 I and 1 O significant fragments # where I means inner pair, O is outer seq, A is outer pair, and # G means outer group (fragments). # Global P-values are based on BLAST-like global scores. # # Fragment offsets and lengths are in nucleotides. # Note: A polymorphism can be at a run of sites with indels, # which here have up to 748 sites. # Bases other than `TCAGU' are treated as indels # for the purpose of generating polymorphisms. # # # Global inner fragments (112 polymorphisms, 1505 aligned bases): # (Inner fragments are runs of matching sites with penalties.) # (Sim and BC KA P-values are corrected for multiple comparisons.) # (Fragments are listed only if Sim P-value <= 0.05.) # See earlier in the file for the full restrictions on fragments. # # BC KA means Bonferroni-corrected KA (BLAST-like) Pvalues. # KA Pvalues are NOT corrected for multiple pairwise comparisons. # In the following table, BC Pvalues are KA Pvalues multiplied by 84. # Num Poly is the number of polymorphic sites in the fragment. # Num Dif is the number of mismatches within the fragment. # Tot Difs is the total number of mismatches between two sequences. # MisM Pen is the penalty per mismatch for these two sequences. # # Seq Sim BC KA Aligned Offsets Num Num Tot MisM # Names Pvalue Pvalue Begin End Len Poly Dif Difs Pen. GI Horse_MYL9;Przewalski_MYL9 0.0022 0.09811 299 757 459 110 0 2 56 # # One inner fragment listed. # 2423 overlapping fragments discarded. # # # Global outer-sequence fragments (112 polymorphisms, 1505 aligned bases): # (Outer-sequence fragments are runs of sites that are unique in that group.) # (Sim and BC KA P-values are corrected for multiple comparisons.) # (Fragments are listed only if Sim P-value <= 0.05.) # See earlier in the file for the full restrictions on fragments. # # BC KA means Bonferroni-corrected KA (BLAST-like) Pvalues. # KA Pvalues are NOT corrected for multiple pairwise comparisons. # In the following table, BC Pvalues are KA Pvalues multiplied by 17. # Num Poly is the number of polymorphic sites in the fragment. # Num Mat is the number of nonunique sites within the fragment. # Tot Mats is the total number of nonunique sites for that sequence. # MisM Pen is the penalty per nonunique site for this sequence. # # Seq Sim BC KA Aligned Offsets Num Num Tot MisM # Name Pvalue Pvalue Begin End Len Poly Mat Mats Pen. GO Chicken_MYL9 0.0445 0.29521 618 648 31 5 0 92 2 # # One outer-sequence fragment listed. # One overlapping fragment discarded. # # # Pairwise inner fragments (112 polymorphisms, 1505 aligned bases): # (Inner fragments are runs of matching sites with penalties.) # (P-values are not corrected for multiple comparisons.) # (Fragments are listed only if Sim P-value <= 0.05.) # See earlier in the file for the full restrictions on fragments. # # KA Pvalues are NOT corrected for multiple pairwise comparisons. # Multiply by 84 for Bonferroni-corrected KA Pvalues. # Num Poly is the number of polymorphic sites in the fragment. # Num Dif is the number of mismatches within the fragment. # Tot Difs is the total number of mismatches between two sequences. # MisM Pen is the penalty per mismatch for these two sequences. # # Seq Sim KA Aligned Offsets Num Num Tot MisM # Names Pvalue Pvalue Begin End Len Poly Dif Difs Pen. Group EQUIDS: PI Horse_MYL9Y;Horse_MYL9 0.0137 0.03273 299 693 395 91 1 6 19 PI Horse_MYL9Y;Donkey_MYL9 0.0168 0.03273 299 693 395 91 1 6 19 PI Horse_MYL9Y;Przewalski_MYL9 0.0137 0.03273 299 693 395 91 1 6 19 PI Horse_MYL9;Przewalski_MYL9 0.0009 0.00117 299 757 459 110 0 2 56 Group OUT: PI Human_MYL9;Chimpanzee_MYL9 0.0443 0.00917 299 678 380 86 0 3 38 PI Human_MYL9;Macaque_MYL9 0.0098 0.03900 299 645 347 80 1 8 14 PI Human_MYL9;Platypus_MYL9 0.0369 0.06027 377 423 47 11 0 54 3 PI Chimpanzee_MYL9;Macaque_MYL9 0.0273 0.03124 299 645 347 80 1 7 16 PI Chimpanzee_MYL9;Platypus_MYL9 0.0369 0.06027 377 423 47 11 0 54 3 PI Macaque_MYL9;Platypus_MYL9 0.0445 0.07195 377 423 47 11 0 53 3 # # 10 inner fragments listed. # 2423 overlapping fragments discarded. # # # Pairwise outer-sequence fragments (112 polymorphisms, 1505 aligned bases): # (Outer-sequence fragments are runs of sites that are unique in that group.) # (P-values are not corrected for multiple comparisons.) # (Fragments are listed only if Sim P-value <= 0.05.) # See earlier in the file for the full restrictions on fragments. # # KA Pvalues are NOT corrected for multiple pairwise comparisons. # Multiply by 17 for Bonferroni-corrected KA Pvalues. # Num Poly is the number of polymorphic sites in the fragment. # Num Mat is the number of nonunique sites within the fragment. # Tot Mats is the total number of nonunique sites for that sequence. # MisM Pen is the penalty per nonunique site for this sequence. # # Seq Sim KA Aligned Offsets Num Num Tot MisM # Name Pvalue Pvalue Begin End Len Poly Mat Mats Pen. Group OUT: PO Chicken_MYL9 0.0114 0.01737 618 648 31 5 0 92 2 # # One outer-sequence fragment listed. # One overlapping fragment discarded. ###################################################################################### # Output of GENECONV for sequence file NLGN4Y.fas # GENECONV version 1.81 # Command line: GENECONV NLGN4Y.fas nlgn4ygroup.cfg nlgn4ygroupoutg1 /lp # /g1 # Contents of parameter configuration file: # nlgn4ygroup.cfg: -Startseed=123 -MaxSimGlobalPval=0.05 # -group EQUIDS Hor_NLGN4Y Don_NLGN4Y Ona_NLGN4Y Hor_NLGN4X # Prz_NLGN4X Pr_NLGN4XL Don_NLGN4X # -group OUT Rhi_NLGN4X Ctl_NLGN4X Pig_NLGN4X Cat_NLGN4X # Dog_NLGN4X Hum_NLGN4X Hum_NLGN4Y Chi_NLGN4X Chi_NLGN4Y Mac_NLGN4X # Mac_NLGN4Y Opo_NLGN4X Pla_NLGN4X # # NLGN4Y.fas: 20 sequences. # # Options and features: Using 20 DNA sequences, 6689 aligned bases, # 1976 polymorphisms, FASTA format, gscale=1 for mismatches, # 2 groups defined, maxSimPairPval=0.05, maxSimGlobPval=0.05, # no maxKAPairPval limits, no maxKAGlobPval limits, # simPvals based on 10,000 permutations, # global P-values based on BLAST-like global scores, # fragment limits: minlength=1, minnpolys=2, minscore=2, # pairwise max lists=2000, at most one overlapping fragment, # starting seed=123, contiguous sites with indels are one polymorphism, # one indel block with up to 4714 sites each, # no match (replacement) char in source file. # Groups: # EQUIDS (7): Hor_NLGN4Y Don_NLGN4Y Ona_NLGN4Y Hor_NLGN4X Prz_NLGN4X # Pr_NLGN4XL Don_NLGN4X # OUT (13): Rhi_NLGN4X Ctl_NLGN4X Pig_NLGN4X Cat_NLGN4X Dog_NLGN4X # Hum_NLGN4X Hum_NLGN4Y Chi_NLGN4X Chi_NLGN4Y Mac_NLGN4X # Mac_NLGN4Y Opo_NLGN4X Pla_NLGN4X # Looking at within-group fragments only (2 groups) # # Mismatch penalty: 1 * npolys / num_ppen # where `num_ppen' is the number of ``potential penalties'': # sequence differences for inner fragments, # local monomorphisms for outer fragments. # Nucleotide codes in data: T(24,873) C(22,780) A(26,745) G(20,559) # Other(38,823) CG/TCAG ratio: 45.64% # Non-nucleotide characters in data: ?(3FH)(n=38,823) # 4714 sites with missing data or unrecognized characters. # (These characters are treated as indels for the # purpose of creating indel blocks.) # No sites with all gap or unrecognized characters. # 1975 polymorphic and 0 monomorphic sites with no indels. # No single polymorphic sites with indels. # One indel block with more than one site # (each block is treated as a single polymorphism). # 1976 polymorphisms to be permuted. # # The starting random number seed is 123. # Simulated P-values are based on 10,000 permutations. # Maximum BLAST-like scores (2 groups): # Inner Max Sim S.D.s above S.D. of # frags Score P-value sim. mean sims # SCORE 286.088 0.0000 217.25 1.2963 # OuterSeq # frags 5.534 0.0388 2.45 1.2486 # # Global lists: 7 I and 1 O significant fragments # Pairwise lists: 18 I and 2 O significant fragments # where I means inner pair, O is outer seq, A is outer pair, and # G means outer group (fragments). # Global P-values are based on BLAST-like global scores. # # Fragment offsets and lengths are in nucleotides. # Note: A polymorphism can be at a run of sites with indels, # which here have up to 4714 sites. # Bases other than `TCAGU' are treated as indels # for the purpose of generating polymorphisms. # # # Global inner fragments (1976 polymorphisms, 6689 aligned bases): # (Inner fragments are runs of matching sites with penalties.) # (Sim and BC KA P-values are corrected for multiple comparisons.) # (Fragments are listed only if Sim P-value <= 0.05.) # See earlier in the file for the full restrictions on fragments. # # BC KA means Bonferroni-corrected KA (BLAST-like) Pvalues. # KA Pvalues are NOT corrected for multiple pairwise comparisons. # In the following table, BC Pvalues are KA Pvalues multiplied by 99. # Num Poly is the number of polymorphic sites in the fragment. # Num Dif is the number of mismatches within the fragment. # Tot Difs is the total number of mismatches between two sequences. # MisM Pen is the penalty per mismatch for these two sequences. # # Seq Sim BC KA Aligned Offsets Num Num Tot MisM # Names Pvalue Pvalue Begin End Len Poly Dif Difs Pen. GI Pr_NLGN4XL;Don_NLGN4X 0.0000 0.00000 1 417 417 417 2 1141 2 GI Hor_NLGN4Y;Don_NLGN4Y 0.0000 0.00000 1 360 360 360 1 1201 2 GI Prz_NLGN4X;Pr_NLGN4XL 0.0000 0.00000 1 417 417 417 25 1152 2 GI Hor_NLGN4Y;Ona_NLGN4Y 0.0000 0.00000 1 95 95 95 1 1401 2 GI Don_NLGN4Y;Ona_NLGN4Y 0.0000 0.00000 1 95 95 95 1 1374 2 GI Hor_NLGN4Y;Pr_NLGN4XL 0.0167 0.03325 827 838 12 12 0 1446 2 GI Don_NLGN4Y;Ona_NLGN4Y 0.0301 0.05482 361 373 13 13 0 1374 2 # # 7 inner fragments listed. # 5837 overlapping fragments discarded. # # ADDITIONAL PAIRWISE FRAGMENTS with BC Pairwise SimPval < 0.05 # OR LISTED GLOBAL FRAGMENTS with significantly better BC SimPval # Here BC SimPval is the Pairwise Sim Pvalue multiplied by 99. # # Seq BC Sim BC KA Aligned Offsets Num Num Tot MisM # Names Pvalue Pvalue Begin End Len Poly Dif Difs Pen. AI Prz_NLGN4X;Don_NLGN4X 0.0099 > 1.0 424 1941 1518 1518 38 83 24 # # One inner fragment listed. # # # Global outer-sequence fragments (1976 polymorphisms, 6689 aligned bases): # (Outer-sequence fragments are runs of sites that are unique in that group.) # (Sim and BC KA P-values are corrected for multiple comparisons.) # (Fragments are listed only if Sim P-value <= 0.05.) # See earlier in the file for the full restrictions on fragments. # # BC KA means Bonferroni-corrected KA (BLAST-like) Pvalues. # KA Pvalues are NOT corrected for multiple pairwise comparisons. # In the following table, BC Pvalues are KA Pvalues multiplied by 20. # Num Poly is the number of polymorphic sites in the fragment. # Num Mat is the number of nonunique sites within the fragment. # Tot Mats is the total number of nonunique sites for that sequence. # MisM Pen is the penalty per nonunique site for this sequence. # # Seq Sim BC KA Aligned Offsets Num Num Tot MisM # Name Pvalue Pvalue Begin End Len Poly Mat Mats Pen. GO Don_NLGN4X 0.0388 0.07887 1974 6689 4716 3 0 1951 2 # # One outer-sequence fragment listed. # 158 overlapping fragments discarded. # # # Pairwise inner fragments (1976 polymorphisms, 6689 aligned bases): # (Inner fragments are runs of matching sites with penalties.) # (P-values are not corrected for multiple comparisons.) # (Fragments are listed only if Sim P-value <= 0.05.) # See earlier in the file for the full restrictions on fragments. # # KA Pvalues are NOT corrected for multiple pairwise comparisons. # Multiply by 99 for Bonferroni-corrected KA Pvalues. # Num Poly is the number of polymorphic sites in the fragment. # Num Dif is the number of mismatches within the fragment. # Tot Difs is the total number of mismatches between two sequences. # MisM Pen is the penalty per mismatch for these two sequences. # # Seq Sim KA Aligned Offsets Num Num Tot MisM # Names Pvalue Pvalue Begin End Len Poly Dif Difs Pen. Group EQUIDS: PI Hor_NLGN4Y;Don_NLGN4Y 0.0000 0.00000 1 360 360 360 1 1201 2 PI Hor_NLGN4Y;Ona_NLGN4Y 0.0000 0.00000 1 95 95 95 1 1401 2 PI Hor_NLGN4Y;Prz_NLGN4X 0.0383 0.04006 470 477 8 8 0 1460 2 PI Hor_NLGN4Y;Pr_NLGN4XL 0.0007 0.00034 827 838 12 12 0 1446 2 PI Hor_NLGN4Y;Don_NLGN4X 0.0294 0.03170 470 477 8 8 0 1475 2 PI Don_NLGN4Y;Ona_NLGN4Y 0.0000 0.00000 1 95 95 95 1 1374 2 PI Don_NLGN4Y;Ona_NLGN4Y 0.0005 0.00055 361 373 13 13 0 1374 2 PI Don_NLGN4Y;Prz_NLGN4X 0.0040 0.00386 1674 1682 9 9 0 1517 2 PI Don_NLGN4Y;Don_NLGN4X 0.0044 0.00349 1674 1682 9 9 0 1522 2 PI Prz_NLGN4X;Pr_NLGN4XL 0.0000 0.00000 1 417 417 417 25 1152 2 PI Prz_NLGN4X;Don_NLGN4X 0.0000 0.03739 424 1941 1518 1518 38 83 24 PI Pr_NLGN4XL;Don_NLGN4X 0.0000 0.00000 1 417 417 417 2 1141 2 Group OUT: PI Rhi_NLGN4X;Pla_NLGN4X 0.0420 0.04525 857 864 8 8 0 1452 2 PI Pig_NLGN4X;Pla_NLGN4X 0.0173 0.01825 903 917 15 15 2 1432 2 PI Cat_NLGN4X;Hum_NLGN4Y 0.0021 0.00180 1710 1720 11 11 0 1426 2 PI Dog_NLGN4X;Pla_NLGN4X 0.0231 0.02107 191 201 11 11 1 1500 2 PI Chi_NLGN4X;Opo_NLGN4X 0.0227 0.02571 497 504 8 8 0 1488 2 PI Chi_NLGN4Y;Pla_NLGN4X 0.0274 0.02656 944 954 11 11 1 1486 2 # # 18 inner fragments listed. # 5837 overlapping fragments discarded. # # # Pairwise outer-sequence fragments (1976 polymorphisms, 6689 aligned bases): # (Outer-sequence fragments are runs of sites that are unique in that group.) # (P-values are not corrected for multiple comparisons.) # (Fragments are listed only if Sim P-value <= 0.05.) # See earlier in the file for the full restrictions on fragments. # # KA Pvalues are NOT corrected for multiple pairwise comparisons. # Multiply by 20 for Bonferroni-corrected KA Pvalues. # Num Poly is the number of polymorphic sites in the fragment. # Num Mat is the number of nonunique sites within the fragment. # Tot Mats is the total number of nonunique sites for that sequence. # MisM Pen is the penalty per nonunique site for this sequence. # # Seq Sim KA Aligned Offsets Num Num Tot MisM # Name Pvalue Pvalue Begin End Len Poly Mat Mats Pen. Group EQUIDS: PO Pr_NLGN4XL 0.0441 0.04455 460 468 9 9 1 1636 2 PO Don_NLGN4X 0.0033 0.00394 1974 6689 4716 3 0 1951 2 # # 2 outer-sequence fragments listed. # 158 overlapping fragments discarded. ################################################################################ # Output of GENECONV for sequence file OFD1Y.fas # GENECONV version 1.81 # Command line: GENECONV OFD1Y.fas ofd1ygroup.cfg ofd1ygroupoutg1 /lp /g1 # Contents of parameter configuration file: # ofd1ygroup.cfg: -Startseed=123 -MaxSimGlobalPval=0.05 # -group EQUIDS Horse_OFD1Y Horse_OFD1 Donkey_OFD1 # -group LAUR Cattle_OFD1Y Pig1_OFD1Y Pig2_OFD1Y Dog_OFD1Y # Cattle_OFD1 Cat_OFD1 Dog_OFD1 Pig_OFD1 # -group PRIM Human_OFD1P1Y Human_OFD1P2Y Human_OFD1P3Y # Human_OFD1P4Y Human_OFD1P5Y Human1_OFD1P6Y Human2_OFD1P6Y # Human_OFD1P7Y Human_OFD1P8Y Human_OFD1P9Y Human_OFD1P10Y # Human_OFD1P11Y Human_OFD1P12Y Human_OFD1P13Y Human_OFD1P15Y # Human_OFD1P16Y Human_OFD1P18Y Human_OFD1 Macaque_OFD1 Chimp_OFD1 # Rat_OFD1 Mouse_OFD1 # -group OUT Opossum_OFD1 Platypus_OFD1 Chicken_OFD1 # # OFD1Y.fas: 36 sequences. # # Options and features: Using 36 DNA sequences, 7274 aligned bases, # 6 polymorphisms, FASTA format, gscale=1 for mismatches, # 4 groups defined, maxSimPairPval=0.05, maxSimGlobPval=0.05, # no maxKAPairPval limits, no maxKAGlobPval limits, # simPvals based on 10,000 permutations, # global P-values based on BLAST-like global scores, # fragment limits: minlength=1, minnpolys=2, minscore=2, # pairwise max lists=2000, at most one overlapping fragment, # starting seed=123, contiguous sites with indels are one polymorphism, # 2 indel blocks with up to 5311 sites each, # no match (replacement) char in source file. # Groups: # EQUIDS (3): Horse_OFD1Y Horse_OFD1 Donkey_OFD1 # LAUR (8): Cattle_OFD1Y Pig1_OFD1Y Pig2_OFD1Y Dog_OFD1Y Cattle_OFD1 # Cat_OFD1 Dog_OFD1 Pig_OFD1 # PRIM (22): Human_OFD1P1Y Human_OFD1P2Y Human_OFD1P3Y Human_OFD1P4Y # Human_OFD1P5Y Human1_OFD1P6Y Human2_OFD1P6Y Human_OFD1P7Y # Human_OFD1P8Y Human_OFD1P9Y Human_OFD1P10Y Human_OFD1P11Y # Human_OFD1P12Y Human_OFD1P13Y Human_OFD1P15Y Human_OFD1P16Y # Human_OFD1P18Y Human_OFD1 Macaque_OFD1 Chimp_OFD1 Rat_OFD1 # Mouse_OFD1 # OUT (3): Opossum_OFD1 Platypus_OFD1 Chicken_OFD1 # Looking at within-group fragments only (4 groups) # # Mismatch penalty: 1 * npolys / num_ppen # where `num_ppen' is the number of ``potential penalties'': # sequence differences for inner fragments, # local monomorphisms for outer fragments. # Nucleotide codes in data: T(21,440) C(18,037) A(30,040) G(20,234) # Other(172,113) CG/TCAG ratio: 42.64% # Non-nucleotide characters in data: -(2DH)(n=172,000) N(4EH)(n=113) # 7270 sites with missing data or unrecognized characters. # (These characters are treated as indels for the # purpose of creating indel blocks.) # No sites with all gap or unrecognized characters. # 4 polymorphic and 0 monomorphic sites with no indels. # No single polymorphic sites with indels. # 2 indel blocks with more than one site # (each block is treated as a single polymorphism). # 6 polymorphisms to be permuted. # # The starting random number seed is 123. # Simulated P-values are based on 10,000 permutations. # Maximum BLAST-like scores (4 groups): # Inner Max Sim S.D.s above S.D. of # frags Score P-value sim. mean sims # SCORE 3.314 0.3330 1.22 0.0433 # OuterSeq # frags 3.261 0.6600 0.01 0.0437 # # Global lists: no I and no O significant fragments # Pairwise lists: no I and no O significant fragments # where I means inner pair, O is outer seq, A is outer pair, and # G means outer group (fragments). # Global P-values are based on BLAST-like global scores. # # Fragment offsets and lengths are in nucleotides. # Note: A polymorphism can be at a run of sites with indels, # which here have up to 5311 sites. # Bases other than `TCAGU' are treated as indels # for the purpose of generating polymorphisms. # # # Global inner fragments (6 polymorphisms, 7274 aligned bases): # (Inner fragments are runs of matching sites with penalties.) # (Sim and BC KA P-values are corrected for multiple comparisons.) # (Fragments are listed only if Sim P-value <= 0.05.) # See earlier in the file for the full restrictions on fragments. # # # No inner fragments listed. # # # Global outer-sequence fragments (6 polymorphisms, 7274 aligned bases): # (Outer-sequence fragments are runs of sites that are unique in that group.) # (Sim and BC KA P-values are corrected for multiple comparisons.) # (Fragments are listed only if Sim P-value <= 0.05.) # See earlier in the file for the full restrictions on fragments. # # # No outer-sequence fragments listed. # # # Pairwise inner fragments (6 polymorphisms, 7274 aligned bases): # (Inner fragments are runs of matching sites with penalties.) # (P-values are not corrected for multiple comparisons.) # (Fragments are listed only if Sim P-value <= 0.05.) # See earlier in the file for the full restrictions on fragments. # # No inner fragments listed. # # # Pairwise outer-sequence fragments (6 polymorphisms, 7274 aligned bases): # (Outer-sequence fragments are runs of sites that are unique in that group.) # (P-values are not corrected for multiple comparisons.) # (Fragments are listed only if Sim P-value <= 0.05.) # See earlier in the file for the full restrictions on fragments. # # No outer-sequence fragments listed. # ##################################################################################### # Output of GENECONV for sequence file SH3TC1Y.fas # GENECONV version 1.81 # Command line: GENECONV SH3TC1Y.fas sh3tc1ygroup.cfg sh3tc1ygroupoutg1 # /lp /g1 # Contents of parameter configuration file: # sh3tc1ygroup.cfg: -Startseed=123 -MaxSimGlobalPval=0.05 # -group EQUIDS Ho_SH3C1Y1 Ho_SH3C1Y2 Ho_SH3C1Y3 Hor_SH3TC1 # Don_SH3TC1 # -group OUT Hum_SH3TC1 Chi_SH3TC1 Dog_SH3TC1 Ctl_SH3TC1 # Mou_SH3TC1 Rat_SH3TC1 Opo_SH3TC1 Cat_SH3TC1 Pig_SH3TC1 Mac_SH3TC1 # Rhi_SH3TC1 # # SH3TC1Y.fas: 16 sequences. # # Options and features: Using 16 DNA sequences, 10,088 aligned bases, # 1372 polymorphisms, FASTA format, gscale=1 for mismatches, # 2 groups defined, maxSimPairPval=0.05, maxSimGlobPval=0.05, # no maxKAPairPval limits, no maxKAGlobPval limits, # simPvals based on 10,000 permutations, # global P-values based on BLAST-like global scores, # fragment limits: minlength=1, minnpolys=2, minscore=2, # pairwise max lists=2000, at most one overlapping fragment, # starting seed=123, contiguous sites with indels are one polymorphism, # 91 indel blocks with up to 5237 sites each, # no match (replacement) char in source file. # Groups: # EQUIDS (5): Ho_SH3C1Y1 Ho_SH3C1Y2 Ho_SH3C1Y3 Hor_SH3TC1 Don_SH3TC1 # OUT (11): Hum_SH3TC1 Chi_SH3TC1 Dog_SH3TC1 Ctl_SH3TC1 Mou_SH3TC1 # Rat_SH3TC1 Opo_SH3TC1 Cat_SH3TC1 Pig_SH3TC1 Mac_SH3TC1 # Rhi_SH3TC1 # Looking at within-group fragments only (2 groups) # # Mismatch penalty: 1 * npolys / num_ppen # where `num_ppen' is the number of ``potential penalties'': # sequence differences for inner fragments, # local monomorphisms for outer fragments. # Nucleotide codes in data: T(12,990) C(22,615) A(13,212) G(23,122) # Other(89,469) CG/TCAG ratio: 63.58% # Non-nucleotide characters in data: -(2DH)(n=89,467) ?(3FH)(n=2) # 8589 sites with missing data or unrecognized characters. # (These characters are treated as indels for the # purpose of creating indel blocks.) # No sites with all gap or unrecognized characters. # 1275 polymorphic and 224 monomorphic sites with no indels. # 6 single polymorphic sites with indels. # 91 indel blocks with more than one site # (each block is treated as a single polymorphism). # 1372 polymorphisms to be permuted. # # Comparisons without any fragments (NUCLEOTIDES): # Ho_SH3C1Y2 (outer sequence frags): No sites are unique. # # The starting random number seed is 123. # Simulated P-values are based on 10,000 permutations. # Maximum BLAST-like scores (2 groups): # Inner Max Sim S.D.s above S.D. of # frags Score P-value sim. mean sims # SCORE 243.304 0.0000 1087486.17 0.0002 # OuterSeq # frags 63.505 0.0000 47.67 1.2877 # # Global lists: 29 I and 3 O significant fragments # Pairwise lists: 72 I and 6 O significant fragments # where I means inner pair, O is outer seq, A is outer pair, and # G means outer group (fragments). # Global P-values are based on BLAST-like global scores. # # Fragment offsets and lengths are in nucleotides. # Note: A polymorphism can be at a run of sites with indels, # which here have up to 5237 sites. # Bases other than `TCAGU' are treated as indels # for the purpose of generating polymorphisms. # # # Global inner fragments (1372 polymorphisms, 10,088 aligned bases): # (Inner fragments are runs of matching sites with penalties.) # (Sim and BC KA P-values are corrected for multiple comparisons.) # (Fragments are listed only if Sim P-value <= 0.05.) # See earlier in the file for the full restrictions on fragments. # # BC KA means Bonferroni-corrected KA (BLAST-like) Pvalues. # KA Pvalues are NOT corrected for multiple pairwise comparisons. # In the following table, BC Pvalues are KA Pvalues multiplied by 65. # Num Poly is the number of polymorphic sites in the fragment. # Num Dif is the number of mismatches within the fragment. # Tot Difs is the total number of mismatches between two sequences. # MisM Pen is the penalty per mismatch for these two sequences. # # Seq Sim BC KA Aligned Offsets Num Num Tot MisM # Names Pvalue Pvalue Begin End Len Poly Dif Difs Pen. GI Ho_SH3C1Y1;Hor_SH3TC1 0.0000 0.00000 2031 2590 560 318 7 848 2 GI Ho_SH3C1Y2;Hor_SH3TC1 0.0000 0.00000 2031 2590 560 318 8 849 2 GI Ho_SH3C1Y3;Hor_SH3TC1 0.0000 0.00000 2031 2590 560 318 8 849 2 GI Hor_SH3TC1;Don_SH3TC1 0.0000 0.00000 2031 2590 560 318 10 852 2 GI Hum_SH3TC1;Mac_SH3TC1 0.0000 0.00000 2031 4053 2023 909 55 402 4 GI Chi_SH3TC1;Mac_SH3TC1 0.0000 0.00000 2031 4053 2023 909 50 396 4 GI Cat_SH3TC1;Mac_SH3TC1 0.0000 0.00000 3843 4053 211 169 16 669 3 GI Dog_SH3TC1;Mac_SH3TC1 0.0000 0.00000 2512 4053 1542 627 122 553 3 GI Pig_SH3TC1;Rhi_SH3TC1 0.0000 0.00000 2145 3733 1589 702 128 477 3 GI Mac_SH3TC1;Rhi_SH3TC1 0.0000 0.00000 2323 4053 1731 757 159 553 3 GI Dog_SH3TC1;Pig_SH3TC1 0.0000 0.00000 2310 3733 1424 590 107 487 3 GI Rat_SH3TC1;Cat_SH3TC1 0.0000 0.00000 3872 4847 976 597 107 478 3 GI Mou_SH3TC1;Cat_SH3TC1 0.0000 0.00000 3980 4851 872 523 91 484 3 GI Hum_SH3TC1;Cat_SH3TC1 0.0000 0.00000 3843 4851 1009 630 82 383 4 GI Cat_SH3TC1;Rhi_SH3TC1 0.0000 0.00000 3843 4851 1009 630 69 341 5 GI Chi_SH3TC1;Cat_SH3TC1 0.0000 0.00000 3843 4847 1005 626 86 391 4 GI Dog_SH3TC1;Cat_SH3TC1 0.0000 0.00000 3842 4847 1006 627 65 346 4 GI Ctl_SH3TC1;Mac_SH3TC1 0.0000 0.00000 3295 4052 758 257 42 578 3 GI Ctl_SH3TC1;Cat_SH3TC1 0.0000 0.00000 3843 4802 960 599 86 403 4 GI Ctl_SH3TC1;Pig_SH3TC1 0.0000 0.00000 2512 3732 1221 446 78 493 3 GI Opo_SH3TC1;Mac_SH3TC1 0.0000 0.00000 3858 4034 177 137 30 788 2 GI Rat_SH3TC1;Mac_SH3TC1 0.0000 0.00000 3865 4053 189 147 23 634 3 GI Chi_SH3TC1;Rat_SH3TC1 0.0000 0.00002 3979 4493 515 305 37 369 4 GI Dog_SH3TC1;Rat_SH3TC1 0.0000 0.00003 3979 4850 872 523 78 355 4 GI Dog_SH3TC1;Mou_SH3TC1 0.0000 0.00004 3980 4851 872 523 80 361 4 GI Pig_SH3TC1;Mac_SH3TC1 0.0000 0.00005 2701 2915 215 143 26 629 3 GI Hum_SH3TC1;Pig_SH3TC1 0.0000 0.00006 2701 2915 215 143 22 536 3 GI Mou_SH3TC1;Mac_SH3TC1 0.0000 0.00006 3976 4053 78 66 7 635 3 GI Ho_SH3C1Y2;Ho_SH3C1Y3 0.0010 0.00007 2031 10088 8058 1371 0 1 1372 # # 29 inner fragments listed. # 187,086 overlapping fragments discarded. # # ADDITIONAL PAIRWISE FRAGMENTS with BC Pairwise SimPval < 0.05 # OR LISTED GLOBAL FRAGMENTS with significantly better BC SimPval # Here BC SimPval is the Pairwise Sim Pvalue multiplied by 65. # # Seq BC Sim BC KA Aligned Offsets Num Num Tot MisM # Names Pvalue Pvalue Begin End Len Poly Dif Difs Pen. AI Hum_SH3TC1;Dog_SH3TC1 0.0065 0.05669 3885 4847 963 584 68 258 6 AI Hum_SH3TC1;Mou_SH3TC1 0.0065 0.00023 3980 4493 514 304 41 374 4 AI Hum_SH3TC1;Rat_SH3TC1 0.0065 0.00013 3979 4493 515 305 40 371 4 AI Hum_SH3TC1;Opo_SH3TC1 0.0390 0.06595 3858 4028 171 131 25 565 3 AI Chi_SH3TC1;Dog_SH3TC1 0.0065 0.03831 3885 4851 967 588 68 258 6 AI Chi_SH3TC1;Mou_SH3TC1 0.0065 0.00011 3980 4493 514 304 40 373 4 AI Chi_SH3TC1;Pig_SH3TC1 0.0065 0.00097 2701 2915 215 143 24 536 3 AI Dog_SH3TC1;Ctl_SH3TC1 0.0065 0.01469 3909 4825 917 543 68 280 5 AI Ctl_SH3TC1;Mou_SH3TC1 0.0065 0.00513 3980 4224 245 144 17 420 4 AI Ctl_SH3TC1;Rat_SH3TC1 0.0065 0.00017 3979 4485 507 298 45 420 4 AI Ctl_SH3TC1;Mac_SH3TC1 0.0065 0.00670 2613 2749 137 99 16 578 3 AI Mou_SH3TC1;Pig_SH3TC1 0.0260 0.02964 2825 2898 74 44 4 612 3 AI Mou_SH3TC1;Mac_SH3TC1 0.0065 0.00017 2825 2898 74 44 2 635 3 AI Mou_SH3TC1;Rhi_SH3TC1 0.0065 0.00851 4014 4847 834 492 83 375 4 AI Rat_SH3TC1;Mac_SH3TC1 0.0065 0.01132 2825 2898 74 44 4 634 3 AI Rat_SH3TC1;Rhi_SH3TC1 0.0065 0.00072 3992 4492 501 295 41 377 4 AI Cat_SH3TC1;Pig_SH3TC1 0.0065 0.00036 2315 2381 67 56 5 622 3 AI Cat_SH3TC1;Mac_SH3TC1 0.0065 0.00748 2317 2381 65 54 7 669 3 # # 18 inner fragments listed. # # # Global outer-sequence fragments (1372 polymorphisms, 10,088 aligned bases): # (Outer-sequence fragments are runs of sites that are unique in that group.) # (Sim and BC KA P-values are corrected for multiple comparisons.) # (Fragments are listed only if Sim P-value <= 0.05.) # See earlier in the file for the full restrictions on fragments. # # BC KA means Bonferroni-corrected KA (BLAST-like) Pvalues. # KA Pvalues are NOT corrected for multiple pairwise comparisons. # In the following table, BC Pvalues are KA Pvalues multiplied by 16. # Num Poly is the number of polymorphic sites in the fragment. # Num Mat is the number of nonunique sites within the fragment. # Tot Mats is the total number of nonunique sites for that sequence. # MisM Pen is the penalty per nonunique site for this sequence. # # Seq Sim BC KA Aligned Offsets Num Num Tot MisM # Name Pvalue Pvalue Begin End Len Poly Mat Mats Pen. GO Hor_SH3TC1 0.0000 0.00000 2607 4850 2244 1041 209 529 3 GO Mac_SH3TC1 0.0000 0.00039 4232 4285 54 35 8 1102 2 GO Mac_SH3TC1 0.0179 0.04634 4721 4780 60 17 3 1102 2 # # 3 outer-sequence fragments listed. # 16,851 overlapping fragments discarded. # # # Pairwise inner fragments (1372 polymorphisms, 10,088 aligned bases): # (Inner fragments are runs of matching sites with penalties.) # (P-values are not corrected for multiple comparisons.) # (Fragments are listed only if Sim P-value <= 0.05.) # See earlier in the file for the full restrictions on fragments. # # KA Pvalues are NOT corrected for multiple pairwise comparisons. # Multiply by 65 for Bonferroni-corrected KA Pvalues. # Num Poly is the number of polymorphic sites in the fragment. # Num Dif is the number of mismatches within the fragment. # Tot Difs is the total number of mismatches between two sequences. # MisM Pen is the penalty per mismatch for these two sequences. # # Seq Sim KA Aligned Offsets Num Num Tot MisM # Names Pvalue Pvalue Begin End Len Poly Dif Difs Pen. Group EQUIDS: PI Ho_SH3C1Y1;Ho_SH3C1Y2 0.0278 0.00671 3924 10088 6165 557 0 15 92 PI Ho_SH3C1Y1;Ho_SH3C1Y3 0.0217 0.00552 3924 10088 6165 557 0 16 86 PI Ho_SH3C1Y1;Hor_SH3TC1 0.0000 0.00000 2031 2590 560 318 7 848 2 PI Ho_SH3C1Y2;Ho_SH3C1Y3 0.0010 0.00000 2031 10088 8058 1371 0 1 1372 PI Ho_SH3C1Y2;Hor_SH3TC1 0.0000 0.00000 2031 2590 560 318 8 849 2 PI Ho_SH3C1Y3;Hor_SH3TC1 0.0000 0.00000 2031 2590 560 318 8 849 2 PI Hor_SH3TC1;Don_SH3TC1 0.0000 0.00000 2031 2590 560 318 10 852 2 Group OUT: PI Hum_SH3TC1;Dog_SH3TC1 0.0001 0.00087 3885 4847 963 584 68 258 6 PI Hum_SH3TC1;Ctl_SH3TC1 0.0035 0.00996 3978 4268 291 186 19 299 5 PI Hum_SH3TC1;Mou_SH3TC1 0.0000 0.00000 3980 4493 514 304 41 374 4 PI Hum_SH3TC1;Rat_SH3TC1 0.0000 0.00000 3979 4493 515 305 40 371 4 PI Hum_SH3TC1;Opo_SH3TC1 0.0006 0.00101 3858 4028 171 131 25 565 3 PI Hum_SH3TC1;Cat_SH3TC1 0.0000 0.00000 3843 4851 1009 630 82 383 4 PI Hum_SH3TC1;Pig_SH3TC1 0.0000 0.00000 2701 2915 215 143 22 536 3 PI Hum_SH3TC1;Mac_SH3TC1 0.0000 0.00000 2031 4053 2023 909 55 402 4 PI Chi_SH3TC1;Dog_SH3TC1 0.0001 0.00059 3885 4851 967 588 68 258 6 PI Chi_SH3TC1;Ctl_SH3TC1 0.0068 0.01453 3978 4268 291 186 20 303 5 PI Chi_SH3TC1;Mou_SH3TC1 0.0000 0.00000 3980 4493 514 304 40 373 4 PI Chi_SH3TC1;Rat_SH3TC1 0.0000 0.00000 3979 4493 515 305 37 369 4 PI Chi_SH3TC1;Opo_SH3TC1 0.0031 0.00516 3858 4028 171 131 26 564 3 PI Chi_SH3TC1;Cat_SH3TC1 0.0000 0.00000 3843 4847 1005 626 86 391 4 PI Chi_SH3TC1;Pig_SH3TC1 0.0000 0.00001 2701 2915 215 143 24 536 3 PI Chi_SH3TC1;Mac_SH3TC1 0.0000 0.00000 2031 4053 2023 909 50 396 4 PI Dog_SH3TC1;Ctl_SH3TC1 0.0000 0.00023 3909 4825 917 543 68 280 5 PI Dog_SH3TC1;Mou_SH3TC1 0.0000 0.00000 3980 4851 872 523 80 361 4 PI Dog_SH3TC1;Rat_SH3TC1 0.0000 0.00000 3979 4850 872 523 78 355 4 PI Dog_SH3TC1;Cat_SH3TC1 0.0000 0.00000 3842 4847 1006 627 65 346 4 PI Dog_SH3TC1;Pig_SH3TC1 0.0000 0.00000 2310 3733 1424 590 107 487 3 PI Dog_SH3TC1;Mac_SH3TC1 0.0000 0.00000 2512 4053 1542 627 122 553 3 PI Dog_SH3TC1;Mac_SH3TC1 0.0312 0.03527 2318 2394 77 59 9 553 3 PI Dog_SH3TC1;Rhi_SH3TC1 0.0242 0.07850 4206 4746 541 336 29 200 7 PI Ctl_SH3TC1;Mou_SH3TC1 0.0000 0.00008 3980 4224 245 144 17 420 4 PI Ctl_SH3TC1;Mou_SH3TC1 0.0320 0.04144 4354 4485 132 63 6 420 4 PI Ctl_SH3TC1;Rat_SH3TC1 0.0000 0.00000 3979 4485 507 298 45 420 4 PI Ctl_SH3TC1;Cat_SH3TC1 0.0000 0.00000 3843 4802 960 599 86 403 4 PI Ctl_SH3TC1;Pig_SH3TC1 0.0000 0.00000 2512 3732 1221 446 78 493 3 PI Ctl_SH3TC1;Pig_SH3TC1 0.0300 0.04329 2161 2355 195 137 27 493 3 PI Ctl_SH3TC1;Mac_SH3TC1 0.0000 0.00000 3295 4052 758 257 42 578 3 PI Ctl_SH3TC1;Mac_SH3TC1 0.0001 0.00010 2613 2749 137 99 16 578 3 PI Mou_SH3TC1;Rat_SH3TC1 0.0043 0.05052 4007 4546 540 329 10 114 13 PI Mou_SH3TC1;Cat_SH3TC1 0.0000 0.00000 3980 4851 872 523 91 484 3 PI Mou_SH3TC1;Pig_SH3TC1 0.0004 0.00046 2825 2898 74 44 4 612 3 PI Mou_SH3TC1;Mac_SH3TC1 0.0000 0.00000 3976 4053 78 66 7 635 3 PI Mou_SH3TC1;Mac_SH3TC1 0.0000 0.00000 2825 2898 74 44 2 635 3 PI Mou_SH3TC1;Mac_SH3TC1 0.0258 0.02939 2722 2749 28 26 2 635 3 PI Mou_SH3TC1;Rhi_SH3TC1 0.0000 0.00013 4014 4847 834 492 83 375 4 PI Rat_SH3TC1;Cat_SH3TC1 0.0000 0.00000 3872 4847 976 597 107 478 3 PI Rat_SH3TC1;Pig_SH3TC1 0.0187 0.02075 2825 2898 74 44 6 612 3 PI Rat_SH3TC1;Pig_SH3TC1 0.0300 0.03326 3002 3023 22 19 0 612 3 PI Rat_SH3TC1;Mac_SH3TC1 0.0000 0.00000 3865 4053 189 147 23 634 3 PI Rat_SH3TC1;Mac_SH3TC1 0.0000 0.00017 2825 2898 74 44 4 634 3 PI Rat_SH3TC1;Mac_SH3TC1 0.0255 0.03017 2726 2749 24 22 1 634 3 PI Rat_SH3TC1;Rhi_SH3TC1 0.0000 0.00001 3992 4492 501 295 41 377 4 PI Opo_SH3TC1;Cat_SH3TC1 0.0062 0.00628 3869 4028 160 120 25 652 3 PI Opo_SH3TC1;Pig_SH3TC1 0.0041 0.00560 2842 2913 72 43 9 786 2 PI Opo_SH3TC1;Mac_SH3TC1 0.0000 0.00000 3858 4034 177 137 30 788 2 PI Opo_SH3TC1;Rhi_SH3TC1 0.0117 0.01567 3995 4028 34 28 1 566 3 PI Cat_SH3TC1;Pig_SH3TC1 0.0000 0.00001 2315 2381 67 56 5 622 3 PI Cat_SH3TC1;Pig_SH3TC1 0.0206 0.02529 2440 2494 55 35 4 622 3 PI Cat_SH3TC1;Mac_SH3TC1 0.0000 0.00000 3843 4053 211 169 16 669 3 PI Cat_SH3TC1;Mac_SH3TC1 0.0000 0.00012 2317 2381 65 54 7 669 3 PI Cat_SH3TC1;Mac_SH3TC1 0.0051 0.00660 2199 2240 42 27 2 669 3 PI Cat_SH3TC1;Mac_SH3TC1 0.0169 0.02085 2126 2178 53 37 5 669 3 PI Cat_SH3TC1;Rhi_SH3TC1 0.0000 0.00000 3843 4851 1009 630 69 341 5 PI Pig_SH3TC1;Mac_SH3TC1 0.0000 0.00000 2701 2915 215 143 26 629 3 PI Pig_SH3TC1;Mac_SH3TC1 0.0056 0.00759 2304 2391 88 69 12 629 3 PI Pig_SH3TC1;Mac_SH3TC1 0.0180 0.02082 2553 2662 110 67 12 629 3 PI Pig_SH3TC1;Mac_SH3TC1 0.0180 0.02082 3001 3094 94 47 7 629 3 PI Pig_SH3TC1;Mac_SH3TC1 0.0295 0.03438 3529 3555 27 22 1 629 3 PI Pig_SH3TC1;Rhi_SH3TC1 0.0000 0.00000 2145 3733 1589 702 128 477 3 PI Mac_SH3TC1;Rhi_SH3TC1 0.0000 0.00000 2323 4053 1731 757 159 553 3 PI Mac_SH3TC1;Rhi_SH3TC1 0.0008 0.00121 2146 2238 93 60 7 553 3 # # 72 inner fragments listed. # 187,086 overlapping fragments discarded. # # # Pairwise outer-sequence fragments (1372 polymorphisms, 10,088 aligned bases): # (Outer-sequence fragments are runs of sites that are unique in that group.) # (P-values are not corrected for multiple comparisons.) # (Fragments are listed only if Sim P-value <= 0.05.) # See earlier in the file for the full restrictions on fragments. # # KA Pvalues are NOT corrected for multiple pairwise comparisons. # Multiply by 16 for Bonferroni-corrected KA Pvalues. # Num Poly is the number of polymorphic sites in the fragment. # Num Mat is the number of nonunique sites within the fragment. # Tot Mats is the total number of nonunique sites for that sequence. # MisM Pen is the penalty per nonunique site for this sequence. # # Seq Sim KA Aligned Offsets Num Num Tot MisM # Name Pvalue Pvalue Begin End Len Poly Mat Mats Pen. Group EQUIDS: PO Hor_SH3TC1 0.0000 0.00000 2607 4850 2244 1041 209 529 3 Group OUT: PO Opo_SH3TC1 0.0451 0.04752 2323 2336 14 10 1 1050 2 PO Cat_SH3TC1 0.0341 0.03536 2646 2650 5 5 0 1202 2 PO Mac_SH3TC1 0.0000 0.00002 4232 4285 54 35 8 1102 2 PO Mac_SH3TC1 0.0034 0.00290 4721 4780 60 17 3 1102 2 PO Mac_SH3TC1 0.0134 0.01415 4392 4449 58 37 10 1102 2 # # 6 outer-sequence fragments listed. # 16,851 overlapping fragments discarded. # ######################################################################################## # Output of GENECONV for sequence file STSY.fas # GENECONV version 1.81 # Command line: GENECONV STSY.fas stsygroup.cfg stsygroupoutg1 /lp /g1 # Contents of parameter configuration file: # stsygroup.cfg: -Startseed=123 -MaxSimGlobalPval=0.05 # -group EQUIDS Hor_STSY Don_STSY Ona_STSY Prz_STSY Hor_STS # Don_STS # -group OUT Hum_STS Chi_STS Mac_STS Dog_STS Ctl_STS Rhi_STS # Cat_STS Pig_STS Opossum Hum_STSYP1 # # STSY.fas: 16 sequences. # # Options and features: Using 16 DNA sequences, 7336 aligned bases, # 1152 polymorphisms, FASTA format, gscale=1 for mismatches, # 2 groups defined, maxSimPairPval=0.05, maxSimGlobPval=0.05, # no maxKAPairPval limits, no maxKAGlobPval limits, # simPvals based on 10,000 permutations, # global P-values based on BLAST-like global scores, # fragment limits: minlength=1, minnpolys=2, minscore=2, # pairwise max lists=2000, at most one overlapping fragment, # starting seed=123, contiguous sites with indels are one polymorphism, # one indel block with up to 6185 sites each, # no match (replacement) char in source file. # Groups: # EQUIDS (6): Hor_STSY Don_STSY Ona_STSY Prz_STSY Hor_STS Don_STS # OUT (10): Hum_STS Chi_STS Mac_STS Dog_STS Ctl_STS Rhi_STS # Cat_STS Pig_STS Opossum Hum_STSYP1 # Looking at within-group fragments only (2 groups) # # Mismatch penalty: 1 * npolys / num_ppen # where `num_ppen' is the number of ``potential penalties'': # sequence differences for inner fragments, # local monomorphisms for outer fragments. # Nucleotide codes in data: T(14,382) C(13,572) A(14,449) G(12,538) # Other(62,435) CG/TCAG ratio: 47.52% # Non-nucleotide characters in data: ?(3FH)(n=62,435) # 6185 sites with missing data or unrecognized characters. # (These characters are treated as indels for the # purpose of creating indel blocks.) # No sites with all gap or unrecognized characters. # 1151 polymorphic and 0 monomorphic sites with no indels. # No single polymorphic sites with indels. # One indel block with more than one site # (each block is treated as a single polymorphism). # 1152 polymorphisms to be permuted. # # The starting random number seed is 123. # Simulated P-values are based on 10,000 permutations. # Maximum BLAST-like scores (2 groups): # Inner Max Sim S.D.s above S.D. of # frags Score P-value sim. mean sims # SCORE 128.011 0.0000 98.44 1.2598 # OuterSeq # frags 6.129 0.0115 2.89 1.2956 # # Global lists: 3 I and 1 O significant fragments # Pairwise lists: 6 I and 2 O significant fragments # where I means inner pair, O is outer seq, A is outer pair, and # G means outer group (fragments). # Global P-values are based on BLAST-like global scores. # # Fragment offsets and lengths are in nucleotides. # Note: A polymorphism can be at a run of sites with indels, # which here have up to 6185 sites. # Bases other than `TCAGU' are treated as indels # for the purpose of generating polymorphisms. # # # Global inner fragments (1152 polymorphisms, 7336 aligned bases): # (Inner fragments are runs of matching sites with penalties.) # (Sim and BC KA P-values are corrected for multiple comparisons.) # (Fragments are listed only if Sim P-value <= 0.05.) # See earlier in the file for the full restrictions on fragments. # # BC KA means Bonferroni-corrected KA (BLAST-like) Pvalues. # KA Pvalues are NOT corrected for multiple pairwise comparisons. # In the following table, BC Pvalues are KA Pvalues multiplied by 60. # Num Poly is the number of polymorphic sites in the fragment. # Num Dif is the number of mismatches within the fragment. # Tot Difs is the total number of mismatches between two sequences. # MisM Pen is the penalty per mismatch for these two sequences. # # Seq Sim BC KA Aligned Offsets Num Num Tot MisM # Names Pvalue Pvalue Begin End Len Poly Dif Difs Pen. GI Don_STSY;Ona_STSY 0.0000 0.00000 1 146 146 146 1 746 2 GI Don_STSY;Prz_STSY 0.0000 0.00000 1 38 38 38 0 831 2 GI Ona_STSY;Prz_STSY 0.0000 0.00000 1 38 38 38 0 819 2 # # 3 inner fragments listed. # 1024 overlapping fragments discarded. # # # Global outer-sequence fragments (1152 polymorphisms, 7336 aligned bases): # (Outer-sequence fragments are runs of sites that are unique in that group.) # (Sim and BC KA P-values are corrected for multiple comparisons.) # (Fragments are listed only if Sim P-value <= 0.05.) # See earlier in the file for the full restrictions on fragments. # # BC KA means Bonferroni-corrected KA (BLAST-like) Pvalues. # KA Pvalues are NOT corrected for multiple pairwise comparisons. # In the following table, BC Pvalues are KA Pvalues multiplied by 16. # Num Poly is the number of polymorphic sites in the fragment. # Num Mat is the number of nonunique sites within the fragment. # Tot Mats is the total number of nonunique sites for that sequence. # MisM Pen is the penalty per nonunique site for this sequence. # # Seq Sim BC KA Aligned Offsets Num Num Tot MisM # Name Pvalue Pvalue Begin End Len Poly Mat Mats Pen. GO Don_STS 0.0115 0.03481 93 105 13 13 1 846 2 # # One outer-sequence fragment listed. # 112 overlapping fragments discarded. # # # Pairwise inner fragments (1152 polymorphisms, 7336 aligned bases): # (Inner fragments are runs of matching sites with penalties.) # (P-values are not corrected for multiple comparisons.) # (Fragments are listed only if Sim P-value <= 0.05.) # See earlier in the file for the full restrictions on fragments. # # KA Pvalues are NOT corrected for multiple pairwise comparisons. # Multiply by 60 for Bonferroni-corrected KA Pvalues. # Num Poly is the number of polymorphic sites in the fragment. # Num Dif is the number of mismatches within the fragment. # Tot Difs is the total number of mismatches between two sequences. # MisM Pen is the penalty per mismatch for these two sequences. # # Seq Sim KA Aligned Offsets Num Num Tot MisM # Names Pvalue Pvalue Begin End Len Poly Dif Difs Pen. Group EQUIDS: PI Hor_STSY;Don_STSY 0.0470 0.05468 82 88 7 7 0 869 2 PI Hor_STSY;Prz_STSY 0.0196 0.02070 233 240 8 8 0 856 2 PI Don_STSY;Ona_STSY 0.0000 0.00000 1 146 146 146 1 746 2 PI Don_STSY;Prz_STSY 0.0000 0.00000 1 38 38 38 0 831 2 PI Ona_STSY;Prz_STSY 0.0000 0.00000 1 38 38 38 0 819 2 Group OUT: PI Cat_STS;Opossum 0.0454 0.04844 581 587 7 7 0 874 2 # # 6 inner fragments listed. # 1024 overlapping fragments discarded. # # # Pairwise outer-sequence fragments (1152 polymorphisms, 7336 aligned bases): # (Outer-sequence fragments are runs of sites that are unique in that group.) # (P-values are not corrected for multiple comparisons.) # (Fragments are listed only if Sim P-value <= 0.05.) # See earlier in the file for the full restrictions on fragments. # # KA Pvalues are NOT corrected for multiple pairwise comparisons. # Multiply by 16 for Bonferroni-corrected KA Pvalues. # Num Poly is the number of polymorphic sites in the fragment. # Num Mat is the number of nonunique sites within the fragment. # Tot Mats is the total number of nonunique sites for that sequence. # MisM Pen is the penalty per nonunique site for this sequence. # # Seq Sim KA Aligned Offsets Num Num Tot MisM # Name Pvalue Pvalue Begin End Len Poly Mat Mats Pen. Group EQUIDS: PO Don_STS 0.0019 0.00218 93 105 13 13 1 846 2 PO Don_STS 0.0280 0.02699 57 67 11 11 1 846 2 # # 2 outer-sequence fragments listed. # 112 overlapping fragments discarded. ################################################################################ # Output of GENECONV for sequence file TBL1Y.fas # GENECONV version 1.81 # Command line: GENECONV TBL1Y.fas tbl1ygroup.cfg tbl1ygroupoutg1 /lp /g1 # Contents of parameter configuration file: # tbl1ygroup.cfg: -Startseed=123 -MaxSimGlobalPval=0.05 # -group EQUIDS Hor_TBL1Y Don_TBL1Y Ona_TBL1Y Hor_TBL1X Prz1_TBL1X # Don1_TBL1X Don2_TBL1X # -group OUT Hum_TBL1Y Chi_TBL1Y Mac_TBL1Y Cam_TBL1Y Hum_TBL1X # Chi_TBL1X Dog_TBL1X Ctl_TBL1X Mou_TBL1X Rat_TBL1X Cam_TBL1X # Cat_TBL1X Pig_TBL1X Opo_TBL1X Mac_TBL1X Rhi_TBL1X # # TBL1Y.fas: 23 sequences. # # Options and features: Using 23 DNA sequences, 5768 aligned bases, # 980 polymorphisms, FASTA format, gscale=1 for mismatches, # 2 groups defined, maxSimPairPval=0.05, maxSimGlobPval=0.05, # no maxKAPairPval limits, no maxKAGlobPval limits, # simPvals based on 10,000 permutations, # global P-values based on BLAST-like global scores, # fragment limits: minlength=1, minnpolys=2, minscore=2, # pairwise max lists=2000, at most one overlapping fragment, # starting seed=123, contiguous sites with indels are one polymorphism, # one indel block with up to 4789 sites each, # no match (replacement) char in source file. # Groups: # EQUIDS (7): Hor_TBL1Y Don_TBL1Y Ona_TBL1Y Hor_TBL1X Prz1_TBL1X # Don1_TBL1X Don2_TBL1X # OUT (16): Hum_TBL1Y Chi_TBL1Y Mac_TBL1Y Cam_TBL1Y Hum_TBL1X # Chi_TBL1X Dog_TBL1X Ctl_TBL1X Mou_TBL1X Rat_TBL1X Cam_TBL1X # Cat_TBL1X Pig_TBL1X Opo_TBL1X Mac_TBL1X Rhi_TBL1X # Looking at within-group fragments only (2 groups) # # Mismatch penalty: 1 * npolys / num_ppen # where `num_ppen' is the number of ``potential penalties'': # sequence differences for inner fragments, # local monomorphisms for outer fragments. # Nucleotide codes in data: T(17,696) C(18,826) A(19,494) G(19,180) # Other(57,468) CG/TCAG ratio: 50.54% # Non-nucleotide characters in data: ?(3FH)(n=57,468) # 4789 sites with missing data or unrecognized characters. # (These characters are treated as indels for the # purpose of creating indel blocks.) # No sites with all gap or unrecognized characters. # 979 polymorphic and 0 monomorphic sites with no indels. # No single polymorphic sites with indels. # One indel block with more than one site # (each block is treated as a single polymorphism). # 980 polymorphisms to be permuted. # # The starting random number seed is 123. # Simulated P-values are based on 10,000 permutations. # Maximum BLAST-like scores (2 groups): # Inner Max Sim S.D.s above S.D. of # frags Score P-value sim. mean sims # SCORE 116.940 0.0000 89.12 1.2581 # OuterSeq # frags 1.553 0.7585 -0.67 1.2115 # # Global lists: 4 I and no O significant fragments # Pairwise lists: 8 I and no O significant fragments # where I means inner pair, O is outer seq, A is outer pair, and # G means outer group (fragments). # Global P-values are based on BLAST-like global scores. # # Fragment offsets and lengths are in nucleotides. # Note: A polymorphism can be at a run of sites with indels, # which here have up to 4789 sites. # Bases other than `TCAGU' are treated as indels # for the purpose of generating polymorphisms. # # # Global inner fragments (980 polymorphisms, 5768 aligned bases): # (Inner fragments are runs of matching sites with penalties.) # (Sim and BC KA P-values are corrected for multiple comparisons.) # (Fragments are listed only if Sim P-value <= 0.05.) # See earlier in the file for the full restrictions on fragments. # # BC KA means Bonferroni-corrected KA (BLAST-like) Pvalues. # KA Pvalues are NOT corrected for multiple pairwise comparisons. # In the following table, BC Pvalues are KA Pvalues multiplied by 141. # Num Poly is the number of polymorphic sites in the fragment. # Num Dif is the number of mismatches within the fragment. # Tot Difs is the total number of mismatches between two sequences. # MisM Pen is the penalty per mismatch for these two sequences. # # Seq Sim BC KA Aligned Offsets Num Num Tot MisM # Names Pvalue Pvalue Begin End Len Poly Dif Difs Pen. GI Chi_TBL1X;Ctl_TBL1X 0.0000 0.00000 257 603 347 347 31 466 3 GI Hor_TBL1Y;Ona_TBL1Y 0.0000 0.00000 1 83 83 83 1 666 2 GI Don_TBL1Y;Ona_TBL1Y 0.0000 0.00000 84 123 40 40 0 707 2 GI Dog_TBL1X;Cat_TBL1X 0.0051 0.01241 714 730 17 17 1 682 2 # # 4 inner fragments listed. # 4683 overlapping fragments discarded. # # # Global outer-sequence fragments (980 polymorphisms, 5768 aligned bases): # (Outer-sequence fragments are runs of sites that are unique in that group.) # (Sim and BC KA P-values are corrected for multiple comparisons.) # (Fragments are listed only if Sim P-value <= 0.05.) # See earlier in the file for the full restrictions on fragments. # # # No outer-sequence fragments listed. # # # Pairwise inner fragments (980 polymorphisms, 5768 aligned bases): # (Inner fragments are runs of matching sites with penalties.) # (P-values are not corrected for multiple comparisons.) # (Fragments are listed only if Sim P-value <= 0.05.) # See earlier in the file for the full restrictions on fragments. # # KA Pvalues are NOT corrected for multiple pairwise comparisons. # Multiply by 141 for Bonferroni-corrected KA Pvalues. # Num Poly is the number of polymorphic sites in the fragment. # Num Dif is the number of mismatches within the fragment. # Tot Difs is the total number of mismatches between two sequences. # MisM Pen is the penalty per mismatch for these two sequences. # # Seq Sim KA Aligned Offsets Num Num Tot MisM # Names Pvalue Pvalue Begin End Len Poly Dif Difs Pen. Group EQUIDS: PI Hor_TBL1Y;Ona_TBL1Y 0.0000 0.00000 1 83 83 83 1 666 2 PI Don_TBL1Y;Ona_TBL1Y 0.0000 0.00000 84 123 40 40 0 707 2 PI Ona_TBL1Y;Don2_TBL1X 0.0463 0.04704 766 775 10 10 1 739 2 Group OUT: PI Hum_TBL1X;Dog_TBL1X 0.0376 0.03847 730 742 13 13 2 746 2 PI Chi_TBL1X;Ctl_TBL1X 0.0000 0.00000 257 603 347 347 31 466 3 PI Dog_TBL1X;Cat_TBL1X 0.0000 0.00009 714 730 17 17 1 682 2 PI Dog_TBL1X;Pig_TBL1X 0.0188 0.01951 767 777 11 11 1 725 2 PI Cat_TBL1X;Pig_TBL1X 0.0332 0.03317 665 671 7 7 0 751 2 # # 8 inner fragments listed. # 4683 overlapping fragments discarded. # # # Pairwise outer-sequence fragments (980 polymorphisms, 5768 aligned bases): # (Outer-sequence fragments are runs of sites that are unique in that group.) # (P-values are not corrected for multiple comparisons.) # (Fragments are listed only if Sim P-value <= 0.05.) # See earlier in the file for the full restrictions on fragments. # # No outer-sequence fragments listed. ######################################################################################### # Output of GENECONV for sequence file TMSB4Y.fas # GENECONV version 1.81 # Command line: GENECONV TMSB4Y.fas tmsb4ygroup.cfg tmsb4ygroupoutg1 /lp # /g1 # Contents of parameter configuration file: # tmsb4ygroup.cfg: -Startseed=123 -MaxSimGlobalPval=0.05 # -group EQUIDS Hor_TMSB4Y Don_TMSB4Y Ona_TMSB4Y Prz_TMSB4Y # Hor_TMSB4 Prz_TMSB4 Prz_ncRNA Don_TMSB4 # -group OUT Hum_TMSB4 Mou_TMSB4 Rhi2_TMSB4 Rhi1_TMSB4 Dog_TMSB4 # Cat_TMSB4 Rat_TMSB4 Chi_TMSB4 Mac_TMSB4 Pig_TMSB4 Ctl_TMSB4 # Opo_TMSB4 Ckn_TMSB4 Hum_TMSB4Y Chi_TMSB4Y Mac_TMSB4Y # # TMSB4Y.fas: 24 sequences. # # Options and features: Using 24 DNA sequences, 4128 aligned bases, # 128 polymorphisms, FASTA format, gscale=1 for mismatches, # 2 groups defined, maxSimPairPval=0.05, maxSimGlobPval=0.05, # no maxKAPairPval limits, no maxKAGlobPval limits, # simPvals based on 10,000 permutations, # global P-values based on BLAST-like global scores, # fragment limits: minlength=1, minnpolys=2, minscore=2, # pairwise max lists=2000, at most one overlapping fragment, # starting seed=123, contiguous sites with indels are one polymorphism, # one indel block with up to 4001 sites each, # no match (replacement) char in source file. # Groups: # EQUIDS (8): Hor_TMSB4Y Don_TMSB4Y Ona_TMSB4Y Prz_TMSB4Y Hor_TMSB4 # Prz_TMSB4 Prz_ncRNA Don_TMSB4 # OUT (16): Hum_TMSB4 Mou_TMSB4 Rhi2_TMSB4 Rhi1_TMSB4 Dog_TMSB4 # Cat_TMSB4 Rat_TMSB4 Chi_TMSB4 Mac_TMSB4 Pig_TMSB4 Ctl_TMSB4 # Opo_TMSB4 Ckn_TMSB4 Hum_TMSB4Y Chi_TMSB4Y Mac_TMSB4Y # Looking at within-group fragments only (2 groups) # # Mismatch penalty: 1 * npolys / num_ppen # where `num_ppen' is the number of ``potential penalties'': # sequence differences for inner fragments, # local monomorphisms for outer fragments. # Nucleotide codes in data: T(5130) C(4176) A(5607) G(4593) # Other(79,566) CG/TCAG ratio: 44.96% # Non-nucleotide characters in data: ?(3FH)(n=79,566) # 4001 sites with missing data or unrecognized characters. # (These characters are treated as indels for the # purpose of creating indel blocks.) # No sites with all gap or unrecognized characters. # 127 polymorphic and 0 monomorphic sites with no indels. # No single polymorphic sites with indels. # One indel block with more than one site # (each block is treated as a single polymorphism). # 128 polymorphisms to be permuted. # # Comparisons without any fragments (NUCLEOTIDES): # Hor_TMSB4Y (outer sequence frags): No sites are unique. # # The starting random number seed is 123. # Simulated P-values are based on 10,000 permutations. # Maximum BLAST-like scores (2 groups): # Inner Max Sim S.D.s above S.D. of # frags Score P-value sim. mean sims # SCORE 18.330 0.0000 268.91 0.0346 # OuterSeq # frags 1.675 0.7199 -0.39 1.0478 # # Global lists: 4 I and no O significant fragments # Pairwise lists: 15 I and no O significant fragments # where I means inner pair, O is outer seq, A is outer pair, and # G means outer group (fragments). # Global P-values are based on BLAST-like global scores. # # Fragment offsets and lengths are in nucleotides. # Note: A polymorphism can be at a run of sites with indels, # which here have up to 4001 sites. # Bases other than `TCAGU' are treated as indels # for the purpose of generating polymorphisms. # # # Global inner fragments (128 polymorphisms, 4128 aligned bases): # (Inner fragments are runs of matching sites with penalties.) # (Sim and BC KA P-values are corrected for multiple comparisons.) # (Fragments are listed only if Sim P-value <= 0.05.) # See earlier in the file for the full restrictions on fragments. # # BC KA means Bonferroni-corrected KA (BLAST-like) Pvalues. # KA Pvalues are NOT corrected for multiple pairwise comparisons. # In the following table, BC Pvalues are KA Pvalues multiplied by 148. # Num Poly is the number of polymorphic sites in the fragment. # Num Dif is the number of mismatches within the fragment. # Tot Difs is the total number of mismatches between two sequences. # MisM Pen is the penalty per mismatch for these two sequences. # # Seq Sim BC KA Aligned Offsets Num Num Tot MisM # Names Pvalue Pvalue Begin End Len Poly Dif Difs Pen. GI Ona_TMSB4Y;Prz_TMSB4Y 0.0000 0.00000 1 53 53 53 1 55 3 GI Hor_TMSB4Y;Ona_TMSB4Y 0.0000 0.00005 1 53 53 53 1 51 3 GI Don_TMSB4Y;Ona_TMSB4Y 0.0000 0.00005 1 53 53 53 1 51 3 GI Mac_TMSB4;Pig_TMSB4 0.0006 0.01088 95 108 14 14 0 84 2 # # 4 inner fragments listed. # 416 overlapping fragments discarded. # # ADDITIONAL PAIRWISE FRAGMENTS with BC Pairwise SimPval < 0.05 # OR LISTED GLOBAL FRAGMENTS with significantly better BC SimPval # Here BC SimPval is the Pairwise Sim Pvalue multiplied by 148. # # Seq BC Sim BC KA Aligned Offsets Num Num Tot MisM # Names Pvalue Pvalue Begin End Len Poly Dif Difs Pen. AI Hor_TMSB4Y;Prz_TMSB4Y 0.0148 > 1.0 1 109 109 109 0 12 11 AI Don_TMSB4Y;Prz_TMSB4Y 0.0148 > 1.0 1 109 109 109 1 13 10 # # 2 inner fragments listed. # # # Global outer-sequence fragments (128 polymorphisms, 4128 aligned bases): # (Outer-sequence fragments are runs of sites that are unique in that group.) # (Sim and BC KA P-values are corrected for multiple comparisons.) # (Fragments are listed only if Sim P-value <= 0.05.) # See earlier in the file for the full restrictions on fragments. # # # No outer-sequence fragments listed. # # # Pairwise inner fragments (128 polymorphisms, 4128 aligned bases): # (Inner fragments are runs of matching sites with penalties.) # (P-values are not corrected for multiple comparisons.) # (Fragments are listed only if Sim P-value <= 0.05.) # See earlier in the file for the full restrictions on fragments. # # KA Pvalues are NOT corrected for multiple pairwise comparisons. # Multiply by 148 for Bonferroni-corrected KA Pvalues. # Num Poly is the number of polymorphic sites in the fragment. # Num Dif is the number of mismatches within the fragment. # Tot Difs is the total number of mismatches between two sequences. # MisM Pen is the penalty per mismatch for these two sequences. # # Seq Sim KA Aligned Offsets Num Num Tot MisM # Names Pvalue Pvalue Begin End Len Poly Dif Difs Pen. Group EQUIDS: PI Hor_TMSB4Y;Ona_TMSB4Y 0.0000 0.00000 1 53 53 53 1 51 3 PI Hor_TMSB4Y;Prz_TMSB4Y 0.0000 0.02911 1 109 109 109 0 12 11 PI Don_TMSB4Y;Ona_TMSB4Y 0.0000 0.00000 1 53 53 53 1 51 3 PI Don_TMSB4Y;Prz_TMSB4Y 0.0000 0.03347 1 109 109 109 1 13 10 PI Ona_TMSB4Y;Prz_TMSB4Y 0.0000 0.00000 1 53 53 53 1 55 3 PI Ona_TMSB4Y;Hor_TMSB4 0.0130 0.01814 97 102 6 6 0 98 2 Group OUT: PI Rhi2_TMSB4;Mac_TMSB4 0.0165 0.02313 81 87 7 7 0 90 2 PI Rhi1_TMSB4;Opo_TMSB4 0.0115 0.01814 119 124 6 6 0 98 2 PI Rhi1_TMSB4;Mac_TMSB4Y 0.0122 0.01814 89 94 6 6 0 98 2 PI Mac_TMSB4;Pig_TMSB4 0.0000 0.00007 95 108 14 14 0 84 2 PI Pig_TMSB4;Ckn_TMSB4 0.0063 0.01128 59 66 8 8 0 88 2 PI Ckn_TMSB4;Hum_TMSB4Y 0.0190 0.02641 81 86 6 6 0 96 2 PI Ckn_TMSB4;Chi_TMSB4Y 0.0238 0.03156 81 86 6 6 0 95 2 PI Hum_TMSB4Y;Mac_TMSB4Y 0.0377 0.05207 5 9 5 5 0 100 2 PI Chi_TMSB4Y;Mac_TMSB4Y 0.0483 0.06135 5 9 5 5 0 99 2 # # 15 inner fragments listed. # 416 overlapping fragments discarded. # # # Pairwise outer-sequence fragments (128 polymorphisms, 4128 aligned bases): # (Outer-sequence fragments are runs of sites that are unique in that group.) # (P-values are not corrected for multiple comparisons.) # (Fragments are listed only if Sim P-value <= 0.05.) # See earlier in the file for the full restrictions on fragments. # # No outer-sequence fragments listed. #################################################################################### # Output of GENECONV for sequence file XKR3Y.fas # GENECONV version 1.81 # Command line: GENECONV XKR3Y.fas xkr3ygroup.cfg xkr3ygroupoutg1 /lp /g1 # Contents of parameter configuration file: # xkr3ygroup.cfg: -Startseed=123 -MaxSimGlobalPval=0.05 # -group EQUIDS Hor_XKR3Y Hor_XKR3 Prz_XKR3 Don_XKR3 # -group OUT Hum_XKR3 Chi_XKR3 Ora_XKR3 Mac_XKR3 Hum_XKRY # Opo_XKRX # # XKR3Y.fas: 10 sequences. # # Options and features: Using 10 DNA sequences, 675 aligned bases, # 388 polymorphisms, FASTA format, gscale=1 for mismatches, # 2 groups defined, maxSimPairPval=0.05, maxSimGlobPval=0.05, # no maxKAPairPval limits, no maxKAGlobPval limits, # simPvals based on 10,000 permutations, # global P-values based on BLAST-like global scores, # fragment limits: minlength=1, minnpolys=2, minscore=2, # pairwise max lists=2000, at most one overlapping fragment, # starting seed=123, contiguous sites with indels are one polymorphism, # 3 indel blocks with up to 4 sites each, # no match (replacement) char in source file. # Groups: # EQUIDS (4): Hor_XKR3Y Hor_XKR3 Prz_XKR3 Don_XKR3 # OUT (6): Hum_XKR3 Chi_XKR3 Ora_XKR3 Mac_XKR3 Hum_XKRY Opo_XKRX # Looking at within-group fragments only (2 groups) # # Mismatch penalty: 1 * npolys / num_ppen # where `num_ppen' is the number of ``potential penalties'': # sequence differences for inner fragments, # local monomorphisms for outer fragments. # Nucleotide codes in data: T(2098) C(1429) A(1800) G(1399) Other(24) # CG/TCAG ratio: 42.05% # Non-nucleotide characters in data: -(2DH)(n=24) # 15 sites with missing data or unrecognized characters. # (These characters are treated as indels for the # purpose of creating indel blocks.) # No sites with all gap or unrecognized characters. # 381 polymorphic and 279 monomorphic sites with no indels. # 4 single polymorphic sites with indels. # 3 indel blocks with more than one site # (each block is treated as a single polymorphism). # 388 polymorphisms to be permuted. # # The starting random number seed is 123. # Simulated P-values are based on 10,000 permutations. # Maximum BLAST-like scores (2 groups): # Inner Max Sim S.D.s above S.D. of # frags Score P-value sim. mean sims # SCORE 5.854 0.1012 0.18 0.1174 # OuterSeq # frags 2.045 0.3474 0.47 1.2533 # # Global lists: no I and no O significant fragments # Pairwise lists: no I and no O significant fragments # where I means inner pair, O is outer seq, A is outer pair, and # G means outer group (fragments). # Global P-values are based on BLAST-like global scores. # # Fragment offsets and lengths are in nucleotides. # Note: A polymorphism can be at a run of sites with indels, # which here have up to 4 sites. # Bases other than `TCAGU' are treated as indels # for the purpose of generating polymorphisms. # # # Global inner fragments (388 polymorphisms, 675 aligned bases): # (Inner fragments are runs of matching sites with penalties.) # (Sim and BC KA P-values are corrected for multiple comparisons.) # (Fragments are listed only if Sim P-value <= 0.05.) # See earlier in the file for the full restrictions on fragments. # # # No inner fragments listed. # # # Global outer-sequence fragments (388 polymorphisms, 675 aligned bases): # (Outer-sequence fragments are runs of sites that are unique in that group.) # (Sim and BC KA P-values are corrected for multiple comparisons.) # (Fragments are listed only if Sim P-value <= 0.05.) # See earlier in the file for the full restrictions on fragments. # # # No outer-sequence fragments listed. # # # Pairwise inner fragments (388 polymorphisms, 675 aligned bases): # (Inner fragments are runs of matching sites with penalties.) # (P-values are not corrected for multiple comparisons.) # (Fragments are listed only if Sim P-value <= 0.05.) # See earlier in the file for the full restrictions on fragments. # # No inner fragments listed. # # # Pairwise outer-sequence fragments (388 polymorphisms, 675 aligned bases): # (Outer-sequence fragments are runs of sites that are unique in that group.) # (P-values are not corrected for multiple comparisons.) # (Fragments are listed only if Sim P-value <= 0.05.) # See earlier in the file for the full restrictions on fragments. # # No outer-sequence fragments listed. # ############################################################################### # Output of GENECONV for sequence file ZFY.fas # GENECONV version 1.81 # Command line: GENECONV ZFY.fas zfygroup.cfg zfygroupoutg1 /lp /g1 # Contents of parameter configuration file: # zfygroup.cfg: -Startseed=123 -MaxSimGlobalPval=0.05 # -group EQUIDS Donkey_ZFX Donkey_ZFY Horse_ZFX Horse_ZFY # Przewalski_ZFX Przewalski_ZFY # -group OUT Cat_ZFX Cat_ZFY Cattle_ZFX Cattle_ZFY Chicken_ZFX # Chimpanzee_ZFX Chimpanzee_ZFY Dog_ZFX Dog_ZFY Human_ZFX Human_ZFY # Macaque_ZFX Macaque_ZFY Mouse_ZFX Mouse_ZFY1 Mouse_ZFY2 # Opossum_ZFX Pig_ZFX Pig_ZFY1 Rat_ZFX Rat_ZFY Rhinoceros_ZFX # # ZFY.fas: 28 sequences. # # Options and features: Using 28 DNA sequences, 8687 aligned bases, # 396 polymorphisms, FASTA format, gscale=1 for mismatches, # 2 groups defined, maxSimPairPval=0.05, maxSimGlobPval=0.05, # no maxKAPairPval limits, no maxKAGlobPval limits, # simPvals based on 10,000 permutations, # global P-values based on BLAST-like global scores, # fragment limits: minlength=1, minnpolys=2, minscore=2, # pairwise max lists=2000, at most one overlapping fragment, # starting seed=123, contiguous sites with indels are one polymorphism, # 19 indel blocks with up to 6141 sites each, # no match (replacement) char in source file. # Groups: # EQUIDS (6): Donkey_ZFX Donkey_ZFY Horse_ZFX Horse_ZFY # Przewalski_ZFX Przewalski_ZFY # OUT (22): Cat_ZFX Cat_ZFY Cattle_ZFX Cattle_ZFY Chicken_ZFX # Chimpanzee_ZFX Chimpanzee_ZFY Dog_ZFX Dog_ZFY Human_ZFX # Human_ZFY Macaque_ZFX Macaque_ZFY Mouse_ZFX Mouse_ZFY1 # Mouse_ZFY2 Opossum_ZFX Pig_ZFX Pig_ZFY1 Rat_ZFX Rat_ZFY # Rhinoceros_ZFX # Looking at within-group fragments only (2 groups) # # Mismatch penalty: 1 * npolys / num_ppen # where `num_ppen' is the number of ``potential penalties'': # sequence differences for inner fragments, # local monomorphisms for outer fragments. # Nucleotide codes in data: T(41,626) C(24,606) A(43,232) G(28,499) # Other(105,273) CG/TCAG ratio: 38.49% # Non-nucleotide characters in data: -(2DH)(n=105,273) # 7880 sites with missing data or unrecognized characters. # (These characters are treated as indels for the # purpose of creating indel blocks.) # No sites with all gap or unrecognized characters. # 376 polymorphic and 431 monomorphic sites with no indels. # One single polymorphic site with indels. # 19 indel blocks with more than one site # (each block is treated as a single polymorphism). # 396 polymorphisms to be permuted. # # The starting random number seed is 123. # Simulated P-values are based on 10,000 permutations. # Maximum BLAST-like scores (2 groups): # Inner Max Sim S.D.s above S.D. of # frags Score P-value sim. mean sims # SCORE 6.305 0.0312 1.20 0.2389 # OuterSeq # frags 3.877 0.0949 1.42 1.2736 # # Global lists: 1 I and no O significant fragments # Pairwise lists: 51 I and 1 O significant fragments # where I means inner pair, O is outer seq, A is outer pair, and # G means outer group (fragments). # Global P-values are based on BLAST-like global scores. # # Fragment offsets and lengths are in nucleotides. # Note: A polymorphism can be at a run of sites with indels, # which here have up to 6141 sites. # Bases other than `TCAGU' are treated as indels # for the purpose of generating polymorphisms. # # # Global inner fragments (396 polymorphisms, 8687 aligned bases): # (Inner fragments are runs of matching sites with penalties.) # (Sim and BC KA P-values are corrected for multiple comparisons.) # (Fragments are listed only if Sim P-value <= 0.05.) # See earlier in the file for the full restrictions on fragments. # # BC KA means Bonferroni-corrected KA (BLAST-like) Pvalues. # KA Pvalues are NOT corrected for multiple pairwise comparisons. # In the following table, BC Pvalues are KA Pvalues multiplied by 246. # Num Poly is the number of polymorphic sites in the fragment. # Num Dif is the number of mismatches within the fragment. # Tot Difs is the total number of mismatches between two sequences. # MisM Pen is the penalty per mismatch for these two sequences. # # Seq Sim BC KA Aligned Offsets Num Num Tot MisM # Names Pvalue Pvalue Begin End Len Poly Dif Difs Pen. GI Chimpanzee_ZFX;Opossum_ZFX 0.0312 0.44922 1195 1449 255 108 9 98 5 # # One inner fragment listed. # 42,253 overlapping fragments discarded. # # ADDITIONAL PAIRWISE FRAGMENTS with BC Pairwise SimPval < 0.05 # OR LISTED GLOBAL FRAGMENTS with significantly better BC SimPval # Here BC SimPval is the Pairwise Sim Pvalue multiplied by 246. # # Seq BC Sim BC KA Aligned Offsets Num Num Tot MisM # Names Pvalue Pvalue Begin End Len Poly Dif Difs Pen. AI Donkey_ZFX;Przewalski_ZFX 0.0246 > 1.0 1191 1785 595 268 2 25 16 AI Donkey_ZFY;Przewalski_ZFY 0.0246 > 1.0 1191 1785 595 268 2 24 17 AI Horse_ZFX;Przewalski_ZFX 0.0246 > 1.0 1191 1785 595 268 0 23 18 AI Horse_ZFY;Przewalski_ZFY 0.0246 > 1.0 1191 1785 595 268 0 23 18 AI Dog_ZFX;Dog_ZFY 0.0246 > 1.0 1211 1527 317 143 1 53 8 AI Human_ZFX;Opossum_ZFX 0.0246 0.92532 1195 1467 273 119 11 100 4 AI Macaque_ZFX;Opossum_ZFX 0.0246 > 1.0 1195 1467 273 119 12 101 4 # # 7 inner fragments listed. # # # Global outer-sequence fragments (396 polymorphisms, 8687 aligned bases): # (Outer-sequence fragments are runs of sites that are unique in that group.) # (Sim and BC KA P-values are corrected for multiple comparisons.) # (Fragments are listed only if Sim P-value <= 0.05.) # See earlier in the file for the full restrictions on fragments. # # # No outer-sequence fragments listed. # # # Pairwise inner fragments (396 polymorphisms, 8687 aligned bases): # (Inner fragments are runs of matching sites with penalties.) # (P-values are not corrected for multiple comparisons.) # (Fragments are listed only if Sim P-value <= 0.05.) # See earlier in the file for the full restrictions on fragments. # # KA Pvalues are NOT corrected for multiple pairwise comparisons. # Multiply by 246 for Bonferroni-corrected KA Pvalues. # Num Poly is the number of polymorphic sites in the fragment. # Num Dif is the number of mismatches within the fragment. # Tot Difs is the total number of mismatches between two sequences. # MisM Pen is the penalty per mismatch for these two sequences. # # Seq Sim KA Aligned Offsets Num Num Tot MisM # Names Pvalue Pvalue Begin End Len Poly Dif Difs Pen. Group EQUIDS: PI Donkey_ZFX;Przewalski_ZFX 0.0000 0.02995 1191 1785 595 268 2 25 16 PI Donkey_ZFX;Przewalski_ZFY 0.0019 0.06424 1753 2546 794 138 3 42 10 PI Donkey_ZFY;Przewalski_ZFX 0.0066 0.09233 1753 2546 794 138 3 38 11 PI Donkey_ZFY;Przewalski_ZFY 0.0000 0.03103 1191 1785 595 268 2 24 17 PI Horse_ZFX;Przewalski_ZFX 0.0000 0.02126 1191 1785 595 268 0 23 18 PI Horse_ZFX;Przewalski_ZFY 0.0013 0.05418 1753 2546 794 138 2 39 11 PI Horse_ZFY;Przewalski_ZFX 0.0012 0.05418 1753 2546 794 138 2 39 11 PI Horse_ZFY;Przewalski_ZFY 0.0000 0.02126 1191 1785 595 268 0 23 18 Group OUT: PI Cat_ZFX;Dog_ZFY 0.0110 0.07580 1202 1530 329 147 12 68 6 PI Cat_ZFX;Macaque_ZFX 0.0351 0.09785 1195 1521 327 149 12 65 7 PI Cat_ZFX;Opossum_ZFX 0.0061 0.02169 1191 1440 250 109 14 109 4 PI Cattle_ZFX;Human_ZFX 0.0389 0.13429 1195 1537 343 157 12 59 7 PI Cattle_ZFX;Opossum_ZFX 0.0004 0.00257 1191 1440 250 109 11 107 4 PI Cattle_ZFY;Chicken_ZFX 0.0268 0.04047 1247 1374 128 51 8 161 3 PI Cattle_ZFY;Opossum_ZFX 0.0166 0.03767 1191 1258 68 31 0 116 4 PI Chicken_ZFX;Mouse_ZFY1 0.0299 0.04188 1268 1299 32 13 1 241 2 PI Chicken_ZFX;Rat_ZFY 0.0294 0.03750 1268 1308 41 18 2 222 2 PI Chimpanzee_ZFX;Dog_ZFX 0.0064 0.07041 1211 1537 327 150 9 58 7 PI Chimpanzee_ZFX;Dog_ZFY 0.0087 0.05591 1202 1527 326 145 10 63 7 PI Chimpanzee_ZFX;Human_ZFY 0.0318 0.07732 1403 1527 125 64 3 79 6 PI Chimpanzee_ZFX;Macaque_ZFY 0.0435 0.11717 1403 1527 125 64 2 71 6 PI Chimpanzee_ZFX;Opossum_ZFX 0.0001 0.00183 1195 1449 255 108 9 98 5 PI Chimpanzee_ZFX;Pig_ZFX 0.0027 0.04895 1195 1494 300 133 7 60 7 PI Chimpanzee_ZFX;Rhinoceros_ZFX 0.0368 0.13379 1195 1527 333 150 8 48 9 PI Dog_ZFX;Dog_ZFY 0.0000 0.00515 1211 1527 317 143 1 53 8 PI Dog_ZFX;Human_ZFX 0.0013 0.03835 1211 1537 327 150 8 59 7 PI Dog_ZFX;Human_ZFY 0.0334 0.06742 1403 1527 125 64 5 97 5 PI Dog_ZFX;Macaque_ZFX 0.0021 0.03659 1211 1537 327 150 9 61 7 PI Dog_ZFX;Macaque_ZFY 0.0219 0.05877 1403 1527 125 64 4 91 5 PI Dog_ZFX;Opossum_ZFX 0.0369 0.07103 1191 1311 121 51 3 98 5 PI Dog_ZFX;Pig_ZFX 0.0258 0.11969 1191 1491 301 133 8 57 7 PI Dog_ZFY;Human_ZFX 0.0018 0.02485 1202 1527 326 145 9 64 7 PI Dog_ZFY;Macaque_ZFX 0.0029 0.03396 1202 1521 320 144 9 63 7 PI Dog_ZFY;Macaque_ZFY 0.0470 0.11627 1403 1530 128 66 4 84 5 PI Dog_ZFY;Pig_ZFX 0.0120 0.06211 1202 1491 290 125 8 64 7 PI Human_ZFX;Human_ZFY 0.0441 0.11792 1403 1527 125 64 3 81 5 PI Human_ZFX;Macaque_ZFY 0.0294 0.08888 1403 1527 125 64 2 73 6 PI Human_ZFX;Opossum_ZFX 0.0000 0.00376 1195 1467 273 119 11 100 4 PI Human_ZFX;Pig_ZFX 0.0004 0.03120 1195 1494 300 133 6 60 7 PI Human_ZFX;Rhinoceros_ZFX 0.0121 0.08788 1195 1527 333 150 7 48 9 PI Human_ZFY;Macaque_ZFX 0.0443 0.11315 1403 1521 119 63 3 82 5 PI Macaque_ZFX;Macaque_ZFY 0.0270 0.08398 1403 1521 119 63 2 74 6 PI Macaque_ZFX;Opossum_ZFX 0.0001 0.00543 1195 1467 273 119 12 101 4 PI Macaque_ZFX;Pig_ZFX 0.0007 0.03120 1195 1494 300 133 6 60 7 PI Macaque_ZFX;Rhinoceros_ZFX 0.0103 0.07625 1195 1521 327 149 7 49 9 PI Mouse_ZFX;Pig_ZFX 0.0323 0.07699 1418 1644 227 110 12 91 5 PI Mouse_ZFX;Rhinoceros_ZFX 0.0229 0.07057 1430 1644 215 103 10 87 5 PI Mouse_ZFY1;Rat_ZFX 0.0251 0.03657 1515 1560 46 23 3 207 2 PI Opossum_ZFX;Pig_ZFX 0.0128 0.03379 1191 1311 121 51 2 96 5 PI Opossum_ZFX;Rhinoceros_ZFX 0.0140 0.04476 1191 1392 202 84 7 91 5 PI Pig_ZFX;Rhinoceros_ZFX 0.0255 0.12193 1191 1503 313 141 4 37 11 # # 51 inner fragments listed. # 42,253 overlapping fragments discarded. # # # Pairwise outer-sequence fragments (396 polymorphisms, 8687 aligned bases): # (Outer-sequence fragments are runs of sites that are unique in that group.) # (P-values are not corrected for multiple comparisons.) # (Fragments are listed only if Sim P-value <= 0.05.) # See earlier in the file for the full restrictions on fragments. # # KA Pvalues are NOT corrected for multiple pairwise comparisons. # Multiply by 28 for Bonferroni-corrected KA Pvalues. # Num Poly is the number of polymorphic sites in the fragment. # Num Mat is the number of nonunique sites within the fragment. # Tot Mats is the total number of nonunique sites for that sequence. # MisM Pen is the penalty per nonunique site for this sequence. # # Seq Sim KA Aligned Offsets Num Num Tot MisM # Name Pvalue Pvalue Begin End Len Poly Mat Mats Pen. Group OUT: PO Mouse_ZFY2 0.0156 0.02049 1220 1231 12 3 0 381 2 # # One outer-sequence fragment listed. # 4 overlapping fragments discarded. # # ########################################################################################## # Output of GENECONV for sequence file ZRSR2Y.fas # GENECONV version 1.81 # Command line: GENECONV ZRSR2Y.fas zrsr2ygroup.cfg zrsr2ygroupoutg1 /lp # /g1 # Contents of parameter configuration file: # zrsr2ygroup.cfg: -Startseed=123 -MaxSimGlobalPval=0.05 # -group EQUIDS Horse_ZRSR2Y Horse_ZRSR2 Donkey_ZRSR2 # -group OUT Human_ZRSR2 Mouse1_ZRSR2 Mouse2_ZRSR2 Rat_ZRSR2 # Macaque_ZRSR2 Chimpanzee_ZRSR2 Chicken_ZRSR2 Opossum_ZRSR2 # Platypus_ZRSR2 Cat_ZRSR2 Dog_ZRSR2 Pig_ZRSR2 Cattle_ZRSR2Y # Cattle_ZRSR2 Pig_ZRSR2Y # # ZRSR2Y.fas: 18 sequences. # # Options and features: Using 18 DNA sequences, 4490 aligned bases, # 118 polymorphisms, FASTA format, gscale=1 for mismatches, # 2 groups defined, maxSimPairPval=0.05, maxSimGlobPval=0.05, # no maxKAPairPval limits, no maxKAGlobPval limits, # simPvals based on 10,000 permutations, # global P-values based on BLAST-like global scores, # fragment limits: minlength=1, minnpolys=2, minscore=2, # pairwise max lists=2000, at most one overlapping fragment, # starting seed=123, contiguous sites with indels are one polymorphism, # 3 indel blocks with up to 3168 sites each, # no match (replacement) char in source file. # Groups: # EQUIDS (3): Horse_ZRSR2Y Horse_ZRSR2 Donkey_ZRSR2 # OUT (15): Human_ZRSR2 Mouse1_ZRSR2 Mouse2_ZRSR2 Rat_ZRSR2 # Macaque_ZRSR2 Chimpanzee_ZRSR2 Chicken_ZRSR2 Opossum_ZRSR2 # Platypus_ZRSR2 Cat_ZRSR2 Dog_ZRSR2 Pig_ZRSR2 Cattle_ZRSR2Y # Cattle_ZRSR2 Pig_ZRSR2Y # Looking at within-group fragments only (2 groups) # # Mismatch penalty: 1 * npolys / num_ppen # where `num_ppen' is the number of ``potential penalties'': # sequence differences for inner fragments, # local monomorphisms for outer fragments. # Nucleotide codes in data: T(7271) C(7238) A(11,083) G(9960) # Other(45,268) CG/TCAG ratio: 48.37% # Non-nucleotide characters in data: -(2DH)(n=44,684) N(4EH)(n=584) # 4247 sites with missing data or unrecognized characters. # (These characters are treated as indels for the # purpose of creating indel blocks.) # No sites with all gap or unrecognized characters. # 115 polymorphic and 128 monomorphic sites with no indels. # No single polymorphic sites with indels. # 3 indel blocks with more than one site # (each block is treated as a single polymorphism). # 118 polymorphisms to be permuted. # # The starting random number seed is 123. # Simulated P-values are based on 10,000 permutations. # Maximum BLAST-like scores (2 groups): # Inner Max Sim S.D.s above S.D. of # frags Score P-value sim. mean sims # SCORE 6.852 0.0020 0.62 0.0392 # OuterSeq # frags 2.034 0.4303 0.39 1.1194 # # Global lists: 2 I and no O significant fragments # Pairwise lists: 5 I and no O significant fragments # where I means inner pair, O is outer seq, A is outer pair, and # G means outer group (fragments). # Global P-values are based on BLAST-like global scores. # # Fragment offsets and lengths are in nucleotides. # Note: A polymorphism can be at a run of sites with indels, # which here have up to 3168 sites. # Bases other than `TCAGU' are treated as indels # for the purpose of generating polymorphisms. # # # Global inner fragments (118 polymorphisms, 4490 aligned bases): # (Inner fragments are runs of matching sites with penalties.) # (Sim and BC KA P-values are corrected for multiple comparisons.) # (Fragments are listed only if Sim P-value <= 0.05.) # See earlier in the file for the full restrictions on fragments. # # BC KA means Bonferroni-corrected KA (BLAST-like) Pvalues. # KA Pvalues are NOT corrected for multiple pairwise comparisons. # In the following table, BC Pvalues are KA Pvalues multiplied by 108. # Num Poly is the number of polymorphic sites in the fragment. # Num Dif is the number of mismatches within the fragment. # Tot Difs is the total number of mismatches between two sequences. # MisM Pen is the penalty per mismatch for these two sequences. # # Seq Sim BC KA Aligned Offsets Num Num Tot MisM # Names Pvalue Pvalue Begin End Len Poly Dif Difs Pen. GI Horse_ZRSR2;Donkey_ZRSR2 0.0020 0.11414 1052 1322 271 116 0 2 59 GI Mouse1_ZRSR2;Mouse2_ZRSR2 0.0020 0.11414 1052 1322 271 116 0 2 59 # # 2 inner fragments listed. # 3508 overlapping fragments discarded. # # ADDITIONAL PAIRWISE FRAGMENTS with BC Pairwise SimPval < 0.05 # OR LISTED GLOBAL FRAGMENTS with significantly better BC SimPval # Here BC SimPval is the Pairwise Sim Pvalue multiplied by 108. # # Seq BC Sim BC KA Aligned Offsets Num Num Tot MisM # Names Pvalue Pvalue Begin End Len Poly Dif Difs Pen. AI Human_ZRSR2;Chimpanzee_ZRSR2 0.0216 0.86302 1052 1291 240 113 0 3 40 # # One inner fragment listed. # # # Global outer-sequence fragments (118 polymorphisms, 4490 aligned bases): # (Outer-sequence fragments are runs of sites that are unique in that group.) # (Sim and BC KA P-values are corrected for multiple comparisons.) # (Fragments are listed only if Sim P-value <= 0.05.) # See earlier in the file for the full restrictions on fragments. # # # No outer-sequence fragments listed. # # # Pairwise inner fragments (118 polymorphisms, 4490 aligned bases): # (Inner fragments are runs of matching sites with penalties.) # (P-values are not corrected for multiple comparisons.) # (Fragments are listed only if Sim P-value <= 0.05.) # See earlier in the file for the full restrictions on fragments. # # KA Pvalues are NOT corrected for multiple pairwise comparisons. # Multiply by 108 for Bonferroni-corrected KA Pvalues. # Num Poly is the number of polymorphic sites in the fragment. # Num Dif is the number of mismatches within the fragment. # Tot Difs is the total number of mismatches between two sequences. # MisM Pen is the penalty per mismatch for these two sequences. # # Seq Sim KA Aligned Offsets Num Num Tot MisM # Names Pvalue Pvalue Begin End Len Poly Dif Difs Pen. Group EQUIDS: PI Horse_ZRSR2;Donkey_ZRSR2 0.0004 0.00106 1052 1322 271 116 0 2 59 Group OUT: PI Human_ZRSR2;Chimpanzee_ZRSR2 0.0002 0.00799 1052 1291 240 113 0 3 40 PI Mouse1_ZRSR2;Mouse2_ZRSR2 0.0004 0.00106 1052 1322 271 116 0 2 59 PI Macaque_ZRSR2;Platypus_ZRSR2 0.0398 0.09072 1117 1191 75 32 4 44 3 PI Pig_ZRSR2;Pig_ZRSR2Y 0.0145 0.03018 1072 1279 208 97 1 6 20 # # 5 inner fragments listed. # 3508 overlapping fragments discarded. # # # Pairwise outer-sequence fragments (118 polymorphisms, 4490 aligned bases): # (Outer-sequence fragments are runs of sites that are unique in that group.) # (P-values are not corrected for multiple comparisons.) # (Fragments are listed only if Sim P-value <= 0.05.) # See earlier in the file for the full restrictions on fragments. # # No outer-sequence fragments listed. #