CLUSTAL W --- LocARNA 1.4.8 - Local Alignment of RNA


DroMoj_CAF1_left   ACATGTGCACATTTATATCATATATAAAAGCTTAA-AGCTTTCTTA-CTGAAAGCTTAAATATTCG-ATGTA-CGTTTTGTTACTGTTTATTTTTAGTCGGCGATTGAATCACCGGCTCG
DroWil_CAF1_left   ACTCATCGGTTCGATGTTCGATTCCTCGGTGCGAT-GTTAGCATCA-ATCGTTGCGGTTGCATTAAAAAGCT-CGTTCATTTAAA-TTAGCTTTTGGCCATTAATGTGGCAACTGGCTCG
DroMel_CAF1_left   GTTTTCCTGGAAAGCTTATGCCAGATTTAGAC-AGCGCC-AAAGCTCTC-TTCGCACTTGCGTATGAAGTGCCCGCCATAGCAAA-GCGGATTTTTAGCGCTTGTTTACCAACTGGCTCG
DroPer_CAF1_left   CTACGATTTTCCTGGAAA-GCTTGCGTCTTCC-GCAGTCAAAAGCT-TTATATGCACTTGCGCGTGGAGTGGCGGCCATAACAAA-ACGTATTTTAACCGCCCATACGTCAACTGGCTCG
DroPse_CAF1_left   CTACGATTTTCCTGGAAA-GCTTGCAAAAACC-GCAGTCAAAAGCT-TTAAATGCACTTGCGCATGGAGTGGCGGCCATAACAAA-ACGTATTTTAACCGCCCATACGTCAACTGGCTCG
DroSec_CAF1_left   GTTTTCCTGGAAAGCTTATGCCAGATTTAGAC-AGCGCC-AAAGCT-CTCTTCGCACTTGCATATGGAGTGCCCGCCATAACAAA-ACGGATTTTAAGCACGCAGTGAGCAACTGGCTCG
DroSim_CAF1_left   GTTTTCCTGGAAAGCTTATGCCAGATTTAGAC-AGCGCC-AAAGCT-CTCTTCGCACTTGCGTATGGAGTGCCCGCCATAACAAA-ACGGATTTTAAGCGCGCAATGAACAACTGGCTCG
DroYak_CAF1_left   GTTTTCCTGGAAAGCTTACGCCAAATTTAGAC-AGCGCT-AAAGCT-TTATTTGCACTTGCGCATGGAGTGGCCGCCATAACAAA-ACGGATTATTAGCAGTCGCTGTTCAACTGGCTCG

DroMoj_CAF1_left   TTGGTCTAGGGGTATGATTTCCGCTTAGGGTGCGGGAGGTCCCGGGTTCAAATCCCGGACGAGCCCAAGTAATATGTTTTTTATTT------AA-ATTTTT-TTTTATTTTATTTATTTT
DroWil_CAF1_left   TTGGTCTAGGGGTATGATTTCCGCTTAGGGTGCGGGAGGTCCCGGGTTCAAATCCCGGACGAGCCCAAGTGAAGTTGAATTA-TTT------TG-TTTTTT-TATAATGAATTTTTCATA
DroMel_CAF1_left   TTGGTCTAGGGGTATGATTTCCGCTTAGGGTGCGGGAGGTCCCGGGTTCAAATCCCGGACGAGCCCAAGATGGAGTAGTTTTTTTGTGTTTATT-T-TTTATTTCCTTTAA-CTTCCCAG
DroPer_CAF1_left   TTGGTCTAGGGGTATGATTTCCGCTTAGGGTGCGGGAGGTCCCGGGTTCAAATCCCGGACGAGCCCAAGTAA--AATAACTTTTTT---------T-TCTCTTCTTATATTTTTTGAATA
DroPse_CAF1_left   TTGGTCTAGGGGTATGATTTCCGCTTAGGGTGCGGGAGGTCCCGGGTTCAAATCCCGGACGAGCCCAAGTCAATNNNNNNNNNNNN------NN-NNNNNNNNNNNNNNNNNNNNNNNNN
DroSec_CAF1_left   TTGGTCTAGGGGTATGATTTCCGCTTAGGGTGCGGGAGGTCCCGGGTTCAAATCCCGGACGAGCCCAAGAAGAAGTAGTTTTTTTA------TT-GTGTTTATTTTTTATTTCCTTTAAC
DroSim_CAF1_left   TTGGTCTAGGGGTATGATTTCCGCTTAGGGTGCGGGAGGTCCCGGGTTCAAATCCCGGACGAGCCCAAGAAAGAGTAGTTTTTTTA------TT-GTGTTTATTTTTTATTTCCTTTAAC
DroYak_CAF1_left   TTGGTCTAGGGGTATGATTTCCGCTTAGGGTGCGGGAGGTCCCGGGTTCAAATCCCGGACGAGCCCAAGAAG-GTTATCTTTTT-T------GCCAATCTTTTGATCTTC-TAC-----T

DroMoj_CAF1_left   TTTTT-TTATCATTA-----ATAGG-TGTAAAT-AAGTATGCGACAGAA--GA--GAAT-TAGTTTTATGGCATTAAAATTATT--A--GTCAGAGCATAT
DroWil_CAF1_left   AAGTA-GTCTATTAT-----GAAAC-AAATCGG-AGACATCGGAGTTGC--AA--CCTA-AACTTACAATTGATTTAGAAAATT--T--GTTTGGACATTC
DroMel_CAF1_left   AAATTGAGACATAAC-----AA-TTGCTAGTAC-AATTATAGA--GGATG-TAAG--AAAAACAGCAAGACTAAAATTCATCTT--C--------GGCAAT
DroPer_CAF1_left   ATTAAATTGCATTTA-----AA-AATTATTAAT-GAAGAAAAT--GAGAA-GAAATAGAGAATATTAACTTGCAATGAAGCCAGAATGAATATCATATCCC
DroPse_CAF1_left   NNNNN-NNNNNNNNN-----NN-NNNNNNNNNN-NNNNNNNNN--NNNNN-NNNNNNNNNNNNNNNNNNNNNNNNN----NNNNNNNNNNNNNNNNNNNNN
DroSec_CAF1_left   TGTAA-CAATTGCTA-----GT-ATAATTATAG-AGGATGTAA--GAAGA-AAA-GAAGAAACAGCTAAACTAAAATTCATCTC--TGGCAATCTCA-ACA
DroSim_CAF1_left   TGTAA-CAATTGCTA-----GT-ATAATTATAG-AGGATGTAA--GAAAA-AAAAGAAGAAACTGCAACACTAAAATTTATCTC--TGGCAATCTCA--AC
DroYak_CAF1_left   TACATATTATGTATGCACACTC-ATATC-GAGGATTTA-GAAG--ATACTAGCA-AATTGAAAAAACACGTTTCGCGATTCACAAAATCACACCAATTTTG