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


DroAna_CAF1_left   GTGTTTGTT--TTATTTTAGAATTCTTAGAGAGACTCTTGGTGTCTAAACA-AGACATCTTATTTAT-T-A-CATATTTAGGAA-TTAAATAAAAA-AATTAACCAGGTTTC--AACATT
DroEre_CAF1_left   AACTCTGGC--AATTTATAAATTTGAAAAATTCA-AAAAGCCTTTAGTTGGCGGCCATTACAATAAA-G-C-AAAACAAAATAA-CCCAACTCCGT-GACAATGCATATCGC--AGCATT
DroGri_CAF1_left   GCTTTGAAT--GATTCAATAAAATATATTCAACGTACAGACGATTTCGCATTAAGCAAAAAAACAAA-A-A-CCAACCCGGGAC-TCCGTCCGTGACAACATAGGCTCCAGC--AATATT
DroMel_CAF1_left   ATCAAACGC--TGGTGTTTTATACATTGAAAAGT-TCTCAAAGCCTTTTTGGGGCAAAAAAATGTAA-T-T-GGCGACTGTTCA-CCCAACTCCGT-GACAATGCATATTGC--AGCATT
DroMoj_CAF1_left   ATTTAATTT--AAGAGTTCCTCATATATTCAGCT-TGGCGCTTTTATGAAATTAAACACAATAGAAAGA-A-AGAAAAAAG-AACCCAGACTCCGT-GACAATGCCTTCCTTTGGGCATT
DroPer_CAF1_left   TTCATTCCG--TATACTGAAATGATCACGAAACTTTTAAAGGTAAATATAT-GGAAAGGTGGCGGCG-GAA-ACAAAAGAAAAG-CCCAA-TCCGT-GACAATGCGTAATGC--AGCATT
DroPse_CAF1_left   TTCATTCCG--TATACTGAAATGAGCACGAAACTTTTAAAGGTAAATATAT-GGAAAGGTGGCGGCG-GAG-ACAAAAGAAAAG-CCCAA-TCCGT-GACAATGCGTAATGC--AGCATT
DroSec_CAF1_left   ATACATTGA--AATGTTCTTAAAGCCTTGTTGGG-ACTAAAAAAAATGTAATTGCCGACTGTTGCAA-T-A-ACAAAAAACTAA-CCCAACTCCGT-GACAATGCATATCGC--AGCATT
DroVir_CAF1_left   TC-GCACCA--AACTTTTTTAAGTAAAGCGCAGATTGACTCCGATAAAGCA-AAAGAGAATTCAAAT-T-TATAAAATAATAAGCCTCGACTCCGT-GACAGTGAGTTA--C--ATCACT
DroWil_CAF1_left   CATGCGGCA--TTTAAAAAAATACTTTAACTTGGTGTGTAGGGACCATGGA-CGATTCAAATCGTGG-A-A-AGAAAAAAAAAA-CCGAACTCCGT-GACAATGCGTATTGC--AGCATT
DroYak_CAF1_left   CTTAGAAATTGAAAAGATCTTAAAGCTTTCTGGG-ATAAAAAAGTAGCTGGCGGCTATTGCAATG---T-A-CCAAAAAATAAA-CCCAACTCCGT-GACAATGCATATCGC--AGCATT
DroSim_CAF1_left   NNNNNNNNN--NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-NNNNNNNNNNNNNNN-N-N-NNNNNNNNNNNN-NNNNNNNNNNN-NNNNNNNNNNNNNNN--NNNNNN

DroAna_CAF1_left   GCCGTGACCAGGATTCGAACCTGGGTTACCACGGCCACAACGTGGGGTCCTAACCACTAGACGATCACGGCTACGCCCGGCTGTTGAA-AGATGCCGTCTCCGAACCCAGCTCGTCACCT
DroEre_CAF1_left   GCCGTGACCAGGATTCGAACCTGGGTTACCACGGCCACAACGTGGGGTCCTAACCACTAGACGATCACGGCTACGTCGGGTTGTAGGA-TGAGGCTTTCCCAAATCCGAGCTGGTCACCT
DroGri_CAF1_left   GCCGTGACCAGGATTCGAACCTGGGTTACCACGGCCACAACGTGGGGTCCTAACCACTAGACGATCACGGCTATGCCTGGGCGATGCAAGCCGACATTCAAAGCTCT--AAACATTAGCA
DroMel_CAF1_left   GCCGTGACCAGGATTCGAACCTGGGTTACCACGGCCACAACGTGGGGTCCTAACCACTAGACGATCACGGCTACGTCGGGTTGTTGGG-TGGA-GCTTCCCAAATCCCAGCTCGCTACCT
DroMoj_CAF1_left   GTCGTGACCAGGATTCGAACCTGGGTTACCACGGCCACAACGTGGGGTCCTAACCACTAGACGATCACGGCTACGCCGGGTTATTAAT-AATATCGAGACTAACTACCAAAGATGTACAA
DroPer_CAF1_left   GCCGTGACCAGGATTCGAACCTGGGTTACCACGGCCACAACGTGGGGTCCTAACCACTAGACGATCACGGCTACCTCGGGCTGTTGGAACTCGGCGTCCGGGAACGCAAGCTGTTCGGTT
DroPse_CAF1_left   GCCGTGACCAGGATTCGAACCTGGGTTACCACGGCCACAACGTGGGGTCCTAACCACTAGACGATCACGGCTACCTCGGGCTGTTGGAACTCGGCGTCCGGGAACGCAAGCTGTTCGGTT
DroSec_CAF1_left   GCCGTGACCAGGATTCGAACCTGGGTTACCACGGCCACAACGTGGGGTCCTAACCACTAGACGATCACGGCTACGTCGGGTTGTTGGA-TGGAGGTTTCCCAAATCCCAGCTGGTCACCT
DroVir_CAF1_left   GCCGTGACCAGGATTCGAACCTGGGTTACCACGGCCACAACGTGGGGTCCTAACCACTAGACGATCACGGCTACGTCTGGCTGTTGAAACGCATCGTCAAAATATCTAAACAA-ATACAA
DroWil_CAF1_left   GCCGTGACCAGGATTCGAACCTGGGTTACCACGGCCACAACGTGGGGTCCTAACCACTAGACGATCACGGCTACGTCGGGTGCTTAATAAACAGCGTCTAAGCAGCCAAGCAG-T--TTG
DroYak_CAF1_left   GCCGTGACCAGGATTCGAACCTGGGTTACCACGGCCACAACGTGGGGTCCTAACCACTAGACGATCACGGCTACGTCGGGTTGACGGA-CGAAGCTTTCCCAAATCCCAGCTGGTCACCT
DroSim_CAF1_left   NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

DroAna_CAF1_left   AACGGTCC-TCTTTA--CCAACAATAT-CTATACTCTATAAATTATT--T--AAAATATATTTT-CCTAGATAAGAAAGAACTTTGATAACAATT
DroEre_CAF1_left   AATGGTCA-TCATGA-ATTAAATAAAG-AGTTAGGT-CTAAAGTGAT--T--AAAATAATTCTT-TCAAAGTAAGCGAGGTGTAAAATAAAACAA
DroGri_CAF1_left   GGGCGACA-AACCCATGAAATATACATTAATTAGCA-AATGTTCACC-TG--TACGTTTTTTTA-AACTGAAG-TGTGTATAATCCAAATTAAAA
DroMel_CAF1_left   AATGGTCA-TCATTG-ATTAACTAAAG-TCTTAGTA-TCAACTAGAT--C--CTTTCATGCGAG-TTGTAAAATAAAGTCAGAAGTTAGAAAATA
DroMoj_CAF1_left   AGCTGAT------------CGAATAAT-TTATTTTC--AATTTATATACA--TACATTACATAT-CTTTTGGA--AAAATAAATGAAGACAGAAT
DroPer_CAF1_left   ACACTCAA-AGATAA-TGCAAATTCAT-TAATAATT-TGAAATTAAG-TT--GTCAATCCAGAG-TCCAAATT-GAACTTTATTTGGTGAAAAAC
DroPse_CAF1_left   ATACTCAA-AGATAA-TGCAAATTCAT-TAATAATT-TGCAATTAAG-TT--GTCAATCCAGAG-TCCAAATT-AAACTTTATTTGGTGAAAAAA
DroSec_CAF1_left   AATGATCA-TCATTG-ATTAACTAAAC-ACAGATCT-ATAGTAATTG--AAAGTATCAAC-TAG-ATCCTT-TCATGCGATATAAATAAAGTCAG
DroVir_CAF1_left   AACATACAAACTTTT-TTTCAAGTTTA-AATGTTTT-AAATCTTTCT-AT--AAATTATGACAA-TCACTAAT-TCTTATGGTGCGGCCTATACA
DroWil_CAF1_left   GCTATTATTGGAGAAATTGGCTTTAAT-TACAGTTA-CTTACGCTCA-TT--TAGGGTGTTCCTTTTTCGAGT-GGTAAAAAATGATCTAGTAAT
DroYak_CAF1_left   TATGGTCA-TCAATG-GTTAAAGAGTT-TAGTCCGA-AATAAGTAAA-AG--TATCATCTAGAT-TCTTTGAAAGTTAGCGG-GGTGTAATTAAT
DroSim_CAF1_left   NNNNNNNN-NNNNNN-NNNNNNNNNNN-NNNNNNNN-NNNNNNNNNN-NN--NNNNNNNNNNNN-NNNNNNNN-NNNNNNNNNNNNNNNNNNNNN