Figure S3.  Alignment of Ostrinia nubilalis Lep1 Helitrons integrated within expressed sequences obtained by cDNA RACE.

>JG744036.1
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAAGTCGACATCTATACTAATATTATAAAGCTGAAGATTTTGTTTGTTTGTTT--------ACTTGAACGCGCTAATCTCGGGAACTACTGGTAAACGTCATACAGAGACTTCTACTTTGTATTGGAAGGTAGTAGCGAGAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
>JG744032.1
----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TAAAGTCGACATCTATACTGATATTATAAAGCTGAAGATTTTGTTTGTTTGTTT--------ACTTGAACGCGCTAATCTCTGGAACTACCGGTCCGATTTGAAAAATTCTTTCAGTGTTAGATAGCCCATTTATCGAGGAAGGCT--A---GGCTATA-TACCATCACGCTACAG------------------AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
>JG744033.1
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCATGCTCACCGGCCGCCATGGCCGCGGGATTAAAGTCGACATCTATACTGATATTATAAAGCTGAAGATTTTGTTTGTTTGTTT--------ACCTGAACGCGCTAATCTCTGGAACTACCGGTCCGATTTGAAAAATTCTTTCAGTGTTAGATAGCCCATTTATCGAGGATGGCT--A---GGCTATA-TACCGTCACGCTACT-------------------AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
>JG744031.1
----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TAAAGTCGACATCTATACTGATATTATAAAGCTGAAGATTTTGTTTGTTT------------ACTTGAACGACGTAATCTCAGGAACTACCGGTCCGATTTGAAAAATTCTTTCAGTGTTAGATAGCCCATTTATTTAGGAAGGCTATA---GGACTAT-ATAACCATCACGACTACGAATAATAGGTGTCGCTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
>JG732074.1
----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TAAAGTCGACATCTATACTGATATTATAAAGCTGAAGATTTTGTTTGTTTCTTT--------GGTTGAACGCGCTAATCTCAGGAACTACTGGACCGATTTGAAAAATTCTTCTTGTGTTGGATAGCCCGTTAGTTCCTGAAGGCTTTA---GGCTATT-TATCATCACGCTAAGACCAATAGGTCATTTGGCAAGATATAA-AGATAAGAGGTGGACCTATCAAACAACAAAATGGCAAGGCCCAAAAGATAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
>JG744027.1
----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TAAAGTCGACATCTATACTAATATTATAAAGCTGAAGATTTTGTTTGTTTGTTTGTTTGTTTGGTTGAACGCGCTAATCTCAGGAACTACTGGACCGATTTGAAAAATTATTTTTGTGTTGGATAGCCCGTTAGTTCCTGAAGGCTTTA---GGCTATT-TATCATCACGCTAAGACCAACAGGA-----GCGGAGCACCAA-TCAAGAA-TACTTCAAATCAATGAATTTTTACCTTCTGAGAGCTGATGCTGCGTAAACGGTTAAAGTTTCGCAAAAATCATGTATGACAGGATTGTTCCCCTTTAAAAGCTCTTTAAAAAAGTCCGCGGTAGCATATGTCTATCTTTTAAGGTTGGCTCATAGTAACCATTTTTATGCAAAAA-AAATCTGTTTTAAAATAATGCATTATTTGCGAAGGTGTTTCTATAAACATGATATTAATCCTTATCCAAATAAATAAATTATTCACCACAAGTATTTAATTTTAAACATTCTTGCCCTTTACACCATTCGATTTCAATAAATATCTTAGGAGATATCCCAGTTTTAAAATCACATCGCAGCAAAATAATGATCAAGTAGGTACTACGCGCGCTACTGATGGATCAATGCACAGCCTAAACCGCTGATCGTAAAGACCTGAAACTGGGACGGTGTGTTCTTTGTATGACGTAAGCATCTGATAAGAAAGGATTTTCCAAAATTCTACCCCTAAGGAAGTAAAAAGGAGGGGGCAAAGTTTGTATGAAAATAACGAGA
>JG744028.1
----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TAAAGTCGACATCTATACTAATATTATAAAGCTGAAGATTTTGTTTGTTTGTTTGTTT----GGTTGAACGCGCTAATCTCAGGAACTACTGGACCGATTTGAAAAATTCTTTTTGTGTTGGATAGCCCGTTAGTTCCTGAAGGCTTTA---GGCTAAA-TATCATCACGCTAAGACCAATAGGA-----GCGGAGCACCAA-TGAAGAA-TGTTTCAAATCAGTGATTTTTTTCCTTTTGAGAGCTGACGCTGTGTAAACGGTTAAAGTTTCGCAAAAATCATGTATGACAGGATTGTTCCCCTTTAAAAGTTCTAAAAAAAAGTCCGCGATAGTATATGTCTATCTTTTAAGGTTGGCTCATAGTAACCCTTTTTATGCAAAAAGAAATCTGTTTTATATTAATGCATTATTTGCGGAGGTTTTTTCATAAACATGATATTAATCCTTATCCATATAAATAAGTTATTCATCACAAGTATTTAATTTTAAACATACTTGGCCTTTACACCATTCGATTTCAATAAATATCTTAGGAGATATCGCAGTTTTAAAATATCCCCGGCCGTAATGGCCACTCTGCGTTGATACCACTGCTTA
>JG744030.1
----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TAAAGTCGACATCTATACTGATATTATAAAGCTGAAGATTTTGTTTGTTTGGTT--------GGTTGAACACGCTAATCTCAGGAACTACTGGACCGATTTGAAAAATTCTTTTTGTGTTGGATAGTCCGTTAGTTCCTGAAGGCTTTA---GGCTATA-TATCATCACGCTAAGACCAATAGGA-----GCGGAGCACCAA-TGAAGAA-TGTTTCAAATCAGTGATTTTTTTCCTTTTGAGAGCTGACGCTGCGTAAACGGTTAAAGTTTCGCAAAAATCATGTATCACAGGATTGTTCCCCTTTAAAAGTTTTAAAAAAAAGTCCGCGATAGTATATGTCTATCTTTTAAGGTTGGCTCATAGTAACCCTTTTTATGCAAAAAGAAATCTGTTTTATATTAATGCATTATTTGCGGAGGTTTTTTCATAAACATGATATTAATCCTTATCCAAATAAATAAGTTATTCAGTGAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
>JG732082.1
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATATGGTCGACCTGCAGGCGGCCGCACTAGTGATTAAAGTCGACATCTATACTGATATTATAAAGCTGAAGATTTTGTTTGTTTGGTT--------GGTTGAACACGCTAATCTCAGGAACTACTGGACCGATTTGAAAAATTCTTTTTGTGTTGGATAGTCCGTTAGTTCCTGAAGGCTTTA---GGCTATA-TATCATCACGCTAAGACCAATAGGA-----GCGGAGCACCAA-TGAAGAA-TGTTTCAAATCAGTGATTTTTTTCCTTTTGAGAGCTGACGCTGCGTAAACGGTTAAAGTTTCGCAAAAATCATGTATCACAGGATTGTTCCCCTTTAAAAGTTCTAAAAAAAAGTCCGCGATAGTATATGTCTATCTTTTAAGGTTGGCTCATAGTAACCCTTTTTATGCAAAAAGAAATCTGTTTTATATTAATGCATTATTTGCGGAGGTTTTTTCATAAACATGATATTAATCCTTATCCAAATAAATAAGTTATTCAGTGAAAAAAAAAAAAAAAAAAAAAAAAAAAA
>JG744029.1
----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TAAAGTCGACATCTATACTGATATTATAAAGCTGAAGATTTTGTTTGTTTGTTTGTTT----GGTTGAACGCGCTAATCTCAGGAACTACTGGACCGATCCGAAAAATTCTTTTTGTGTTGGATAGCCCGTTAGTTCCTGAAGGCTTTA---GGCTAAA-TATCATCACGCTAAGACCAATAGGA-----GCGGAGCACCAA-TGAAGAA-TGTTTCAAATCAGTGATTTTTTTCCTTTTGAGAGCTGACGCTGCGTAAACGGTTAAAGTTTCGCAAAAATCATGTATGACAGGATTGTTCCCCTTTAAAAGTTCTAAAAAAAAGTCCGCGATAGTATATGTCTATCTTTTAAGGTTGGCTCATAGTAACCCTTTTTATGCAAAAAGAA
>JG732081.1
GGCCAGGGTTATGGTATTCTTAAGAAAAACTTGGACCCGAAANTTGAAAAATTTTTAACTCGACTTGGGCGGTTGCACTACCGTGCCCCCNANATATTTTAGTTTTTCCTTGATTCATACACAAAACACTACTTATATTCCAAATTCGAAGCTTCTAGGTCTGCTAGAAGTGCCTTAGAGTTTTGATGATCGGTGAGTCAGTCAGTGAGTGACAAAATTAAGTAACTTTGACCCGTTATAATTCTTAAACTACTGGTTCAAATTGAATGAAATTTTAAATATACCGTGTCTTTACAATGCCTGCATAGCTAATGAAAATTCAGCCTTCTAGTTTTATCCACAACGAAGTTACAGGCAGTCGAAAATGGCCTGAATTGCTTCGAGAAAAGGATGGTACGGCCGTGCCGCTTTTTTGCTCGACTTGGTGGGGGCACTGCCGTGCCCCCAGATTTATACATATCTATACTAATATTATAAAGCTGAAGAGTTTGTTTGTTTGTTT--------ACTTGAACTCGCTAATCTCCGGAACTACTGGTCCGATTTGAAAAATTCTTTCAGTGTTAGACAGCCCATTTATCGAGGAAGGCTATA---GGCTATA-CAACATCAATCTACGATCAATAGGA-----GCAGAGCAATAA-TGAAAAA-TGTTGCGAAAACGGG-TTTTCACGCGTACGAAGTCGCGGG-CACAGCTAGTTACTGTACGCGTAAAAATCACTAGTGCGGCCGCCTGCAGGTCGACCATATGGGAGAGCTCCCAACGCGTTGGATGCATAGCT
>JG732072.1
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTAAAGTCGACATCTATACTAATATTATAAAGCTGAAGATTTTGTTTGTTT------------ACTTGAGCGCGCTAATCTCCGGAACTATTGGTCCGATTTGAAAAATTCTTTCAGTGTTAGATAGCCCATTTATTGAGGAA---------------------CATCACGTTATGATCAATAGGA-----GCAGAGCAACAA-TGAAAAA-TGTTGCGAAAACAAG-TTTTCACGCGTACGAAGTCGCGGG-CACAGCTAGTGTATCATAAAACAGTATAAATTATATTCTGTATATACATATTATAATGCTCAACGCAGCGGTCGGTATATAAATGGTTTTAAGTGCCATATAATACGGACTTGTTATATTGGTTTAGAAATAAATTGTGCCAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
>JG732080.1
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTATTTTGTGGTTAAAAGTCAAGGCTTTAGGTACTTATTAGATGTGGTCAGGTCCGGATATTTTAGTAAAATCTAATGTATTTTTTTAAACGGACTCAAGTCAAGTTGTATCATAGTAATGAGCAGTGCCTGGCAAATATACTTGACGATGGCTTATTGTTGCAAGCATAAATGTCTAGAAATGCTTGCAACGTCATTATTACCAATATCTACTTCGTAAGAAGATGTAATCTATAGTAACTAATATTATAAAGCTGAAGAGTTTGTTTGTTTGTTT--------ACTTGAACGCGCTAATCTCCGGAACTACTGGTCCGATTTGAAAAATTCTTTCAGTGTTAGATAGCCCATTTATCGAGAAAGGCTATA---GGCTATA-CAACATCACGCTACGATCAATAGGA-----GCAGAGCAATAA-TGAAAAA-GGCTGCGAAAACGGG-TTTTCACGCGTACGAAGTCACGGG-CACAGCTAGTTACTGTACGCGTAAAA
>JG732085.1
----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TAAAGTCGACATCTATACTGATATTATAAAGCTGAAGATTTTGTTTATTTGTTTGTTTGTTTACTTGAAAGCGCTAATCTCCGGAACTACTGGTCCGATTTGAAAAATTCTTCCAGTGTTAGATAGCCCATTTATCGAAGAAGGCTATA---GGCTATA-CAACATCATGCTACGATCAATAGGA-----GTAGAGCAATAA-TGAAAAA-TGTTGCGAAAACGGG-TTTTCACGCGTACGAAGTCGCGGG-AACAGCTAGTATCCTAATATAATAAAAACAGTAATAATGCTAAATAACAGGTGATAATAAAAAAATACATAAAATACTCAGAAAATGCAGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
>JG744035.1
----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TAAAGTCGACATCTATACTGATATTATAAAGCTGAAGATTTTGTTTGTTT------------ACTTGAACGCACTAATCTCCGGAACTATTGGTCCGATTTGAAAAATTCTTTCGGTGTTAGATAGCCCATTTATTGAGGAA---------------------CATCACGTTATGATCAATAGGA-----GCAGAGCAACAA-TGAAAAA-TGTTGCGAAAACAAG-TTTCCACGCGTACGAAGTCGCGGG-CACAGCTAGTGTATCATAAAACAGTATAAATTATATTCTGTATATACATATTATAATGCTCAACGCAGCGGTCGGTATATAAATGGTTTTAAGTGCCATATAATACGGACTTGTTATATAGGTTTAGAAATAAATTGTGTTACGAAAAAAAAAAAAAAAAAAAAAAAAAAAA
>JG732087.1
----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TAAAGTCGACATCTATACTAATATTATAAAGCTGAAGATTTTGTTTGTTT------------ACTTGAGCGCGCTAATCTCCGGAACTATTGGTCCGATTTGAAAAATTCTTTCAGTGTTAGATAGCCCATTTATTGAGGAA---------------------CATCACGTTATGATCAATAGGA-----GCAGAGCAACAA-TGAAAAA-TGTTGCGAAAACAAG-TTTTCACGCGTACGAAGTCGCGGG-CACAGCTAGTGTATCATAAAACAGTATAAATTATATTCTGTATATACATATTATAATGCTCAACGCAGCGGTCGGTATATAAATGGTTTTAAGTGCCATATAATACGGACTTGTTATATTGGTTTAGAAATAAATTGTGCCAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
>JG732084.1
----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TAAAGTCGACATCTATACTGATATTATAAAGCTGAAGATTTTGTTTTTTTGTTTGTTTGTTTACTTGAACGCGCTAATCTCCGGAACTACTGGTCCAATTTGAAAAATTCTTTCAGTGTTAGATAGCCCATTTATCGAGGAAGGCTTTATAGGGCTATG-CAACATCACGCTACGATC-----GAAAAA----------CAA-TGAAAAA-TGTCGTGAAAACGGG-TTTTCACGCGTACGAAGTCGCGGG-CACAGCTAGTAAATAATACAATTACCTGATCTCAACCACTAATGAGCACCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
>JG732083.1
----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TAAAGTCGACATCTATACTGATATTATAAAGCTGAAGATTTTGTTTTTTTGTTTGTTTGTTTACTTGAACGCGCTAATCTCCGGAACTACTGGTCCAATTTGAAAAATTCTTTCAGTGTTAGATAGCCCATTTATCGAGGAAGGCTTTATAGGGCTATG-CAACATCACGCTACGACC-----GAAAAA----------CAA-TGAAAAA-CGTCGTGAAAACGGG-TTTTCACGCGTACGAAGTCGCGGG-CACAGCTAGTAAATAATACAATTACCTGATCTCAACCACTAATGAGCTTGTAAAAATAAATAATAATCCATAATTCCAGTCATAACAAATAAGACATATTAATCACAGAACTAAACGTTCAAATAAATGTGCCACTAAATAAATAACGGAAATGCATTAAATAAACTATATTTTAATGATAGTTAAGATTCAGTCAATGATTCTATTACTTGGGTAGTTAGGTTAGTAGTTCAGTCTTTTTATATTTATATTTAAGAAACTAAGTTTAGATATAACAAGAACAAAAGTACAAGACAAACACTTAAAACTTTCGAGGGGACGTGAAAAACAGCACAAGCTAAAGACGTACGTAGTTCTAAAGGTGAGAATATACTTAGAGCATTTCCATGTATAATGTAACGTTCTTACGTGTAGTAAAACACTGGTAAATTGTAAGCCCAATGGTACGTGAAAGGCTGAGGTTCGTGGTTCTGTTACAAGTAAGTGCTCTAGCTAGTCTATAATCACCTGNATATGTTCAAAATCAAAATCAGAAATATTTATTCAGTTTAGAACGCGAAAAAAAAAAAAAAAAAAAAAAAAAA
>JG732086.1
----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TAAAGTCGACATCTATACTAATATTATAAAGCTGAAGATTTTGTTTGTTTGTTT--------ACTTGAACGCGCTAATCTCAGGAACTACCGGTCCGATTTGAAAAATTATTTCAGTGTTAGATAGCCCATTTATTGAGGAAGGCTATA---GGCTATA-CAACACGAGAGCAGCA-------GAAAAG--CAGAGCAATAA-TGTAAAA-TGTTGCGAAAACGGG-TTTTCACGCGTACGAAGTCGCGGG-CACAGCTAGTATATTATAAAGCTGAGGAGTTTGTTTGTTTGTTTACTTGAACGCTCTAATCTCAGGAACTCCCCGTCCGATTTGAAAAAATATTTCAGTGTTAGATAGCCCATTTATTGAGGAAGGCTATAGGCTGGTATACCATCACGCTACGAGTAATAGGTGTAGAGCAAAAATTAAAAATGTTGCGAAAACGGGTTTTCACGCGTACGAAGTCGCGGGCACAGCTAGTAACTAATAAAGGTAGCCGTTAAGATGTACTTTACATGTTTCCTTGACATTGCCAGCGCTTCAAGACAAGCATATTAAGGCAATTTAAAGTTTAATTGCAATAGGTACGTTCGTTTCAGCCAAATGACTTCTATTACTGGACAAAAGCCGCCCCCAAGGATTTCCATAACGATGGGTCCTGTGTTACCCGCGTTCAGGTAACTTCCGGGACCTTAAACACACCAGATCGTCGGTCCACCAAGTGGGCAGCCTTCCCACAATACGTACATAAGAGAACAAAATTTAAAATACTCAACAAAACNGCCTAATAATAACGATAAGAGTACAAGTTGCTATACATAGTTATTTTAAACTGACCGAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
>JG732075.1
--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TATTATTAATAAAGGCTGGGGAGTTTGGTTGTTTGTTT--------ACTTGAACGCTCTAATCTCAGGGACTCCCCGTCCGATTTTGAAAAAATTTTCAGTGTTAGATAGCCCCTTTATTGAGGAAGGCTATA---GGCTGGTATACCATCACGGCTACGAGGTAATAGGGGTA---GAGCAAAAAATTAAAAAATGTTGCGAAAACGGGGTTTTCACGCGTACGAAGTCGGCGGGCACAGCTAGGTAACTAATAAAGGTAGCCGTTAAGATGTACTTTACATGTTTCCTTGACATTGCCAGCGCTTCAAGACAAGCATATTAAGGCAATTTAAAGTTTAATTGCAATAGGTACGTTTGTTTCAGCCAAATGACTTTTATTACTGGACAAAAGCCGCCCCCAAGGATTTCCATAACGATTGGTCCTGTGTTACCCGGGTTCCAGGTAACTTCCGGGACCTTAAACACACCAGATTGTCGGTCCACCAAGTGGGCAGCCTTCCCACAATAAGTACATAAGAGAACAAAATTTTAAATACTCAACAAAACTGCCTAATAATAACGATAAGAGTACAAGTTGGCTAAACATAGTATTTTTAACTGACTGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAgnTNnatntnaatTngTNgtntnaGTnCGGTGTnCCcc
>JG744034.1
----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TAAAGTCGACATCTATACTGATATTATAAAGCTGAAGATTTTGTGTGTTTGTTT--------ACTTGAACGCGCTAGTCTCCGGAACTACTGGTCCGATTTGAAAAATTATTTCAGTGTTAGA--GCCCATTTATCGAGGAAGGCTATA--------------------------------------------------TTA-TGAAAAA-TGTTGTAAAAACGGG-TTTTCACGCGTACGAAGACGCGGG-CACAGCTAGTAATAAATATTTATATATGTAAAGTTTCAAACAGCACATTTTTTGCGTTCTCATTTTCTTGGGATCCTGTTATAATTTATTACACACTAAAAATTAAATAAAAACCTGCATTTAAAAAACCGACTTCAAAAACTATATTAGGTGGACATTCTTGCACTATTCACTTTTCAAAATCCCCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA