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


DroAna_CAF1_left   CGTC-TATGTGGA---TGTGGCCACCC--TTCGTCC-------TTGGATAGTTAAGG-CTGCCAATGCTATTTAAAACATC-TG----T---AAGGA-TT---CAAATAAATGCTTTAAA
DroEre_CAF1_left   ATG-TGGCCTTTC---TGCGACCATGGATAGTGAAGGC-GGCCAATGCCATATGAAC-AGATTCTGCAAAATAAAG--ACC-AT----G---TTTAA-AA---ATTTCAAAAACCAATAT
DroMel_CAF1_left   ---T-GGCGATTC---TGCGACCTTGGATAGTCAAGGC-GGCCAATGCCATATGAAC-AGATTTTGGAAAATAAAG--ACC-ATGCT-T---AAAAA-AGTTTAAGAATG---CAACTCC
DroMoj_CAF1_left   CGCATTCTTATCA---AGTGTACCCCAAGAAAAATGAATTGACATTTTCACAGGAGTGATATACATGAATACAATA--AAATAA-AATA---ATGGA-AA---ATGAAACTAGTTTAAAT
DroPer_CAF1_left   C--T-TGGA--TA---GTTAACGCAGCAAATGCAATTT-AAATAGTTATGGAAGAAA-AATAAAGCACACTTCTTC--ACA-TTTTA-CAAAAGTTTTCGACTATAATAGCTCCTCCTCT
DroPse_CAF1_left   ACCT-TGGA--TA---GTTAACGCAGCAAATGCAATTT-AAATTGTTATGGAAGAAA-AATAAAGCACACTTCTAC--ACA-TTTTT-CA--AGTTTTCGACTTAAATAGTTTCTCCTCT
DroSec_CAF1_left   G--T-GGCCATTC---TGCGTCCTTGGATAGTCAAGGC-GGCCAATGCCATATGAAC-AGATTTTGGAAAATAAAG--ACC-ATGAT-C---AAAAA--GTTTAAGAATACAGCTCCATC
DroSim_CAF1_left   NNNN-NNNNNNNN---NNNNNNNNN--NNNNNNNNNNN-NNNNNNNNNNNNNNNNNN-NNNNNNNNNNNNNNNNNN--NNN-NNNNN-N---NNNNN--NNNNNNTTATACAGCTCCATC
DroVir_CAF1_left   TTTA-AGCAAATT---GCTTACTCT--TTTGGCATATT-TTAAGACATTTTTGTGTC-TCTCTTCTTCCGTGTATT--ACC-TCTAT-A---TTCGC-CG-CAAAAAACCAACTGACATC
DroYak_CAF1_left   ATGT-GGCCATTT---TGCGACCTTGGATAGTCAAGGC-GGCCAATGCCATATGAAT-ACATTCAGCAAAATAAAG--AGC-ATCTT-T---AAAGA-TTTGGAATACCAA--TATATGT
DroGri_CAF1_left   TATA-CATTGAATATTTGTGTTTATGTACATATTAATT-ATTCTTCTATAAAT--TT-ATAAAATATATATCTAAA--AAT-AA-AT-AA--ACGAATTTATAAAATAATAATTAAACAT

DroAna_CAF1_left   AAAAAACATCGCCCCCCAGGTGGAATCGAACCACTTCGACGCTAATCGACTACGGATTTGAAGTCCGCACCCCGGACCACCGAAGCTCAGTGGGGCACTTCTATT-GTTCA-TGATTCAC
DroEre_CAF1_left   ATTTATATTCGCCCCCCAGGTGGAATCGAACCACTTCGACGCTAATCGACTACGGATTTGAAGTCCGCACCCCGGACCACCGAAGCTCAGTGGGGCATTTAGCAT-GTTAG-AATTTCCT
DroMel_CAF1_left   ATTAATATTCGCCCCCCAGGTGGAATCGAACCACTTCGACGCAAATCGACTACGGATTTGAAGTCCGCACCCCGGACCACCGAAGTTCAGTGGGGCATTTAGTGT-GCTAG-AGTTTCCC
DroMoj_CAF1_left   TGCAGTTTACGCCCCCCAGGTGGAATCGAACCACTTCGACGTTAATCGACTACGGATTTGAAGTCCGCACCCCGGACCACCGAAGCTCAGTGGGGCAGATTTTTA-CTACA-ATTAGTTG
DroPer_CAF1_left   TCTGTAAGTCGCCCCACAGGTGGAATCGAACCACTTCGACGCTAATCGACTACGGATTTGAAGTCCGCACCCCGGACCACCGAAGCTCAGTGAGGCAACATTGCA-GCCCG-AGCTGCCG
DroPse_CAF1_left   TCTGTAAGTCGCCCCACAGGTGGAATCGAACCACTTCGACGCTAATCGACTACGGATTTGAAGTCCGCACCCCGGACCACCGAAGCTCAGTGAGGCAACATTGCA-GCCCG-AGCTGCCG
DroSec_CAF1_left   ATTTATATTCGCCCCCCAGGTGGAATCGAACCACTTCGACGCAAATCGACTACGGATTTGAAGTCCGCACCCCGGACCACCGAAGCTCAGTGGGGCATTTAGCAT-GCTAG-AGTTTCCC
DroSim_CAF1_left   ATTTATATTCGCCCCCCAGGTGGAATCGAACCACTTCGACGCAAATCGACTACGGATTTGAAGTCCGCACCCCGGACCACCGAAGCTCAGTGGGGCATTTAGCAT-GCTAG-AGTTTCCC
DroVir_CAF1_left   AAATAGAATCGCCCCCCAGGTGGAATCGAACCACTTCGACGTTAATCGACTGCGGATTTGAAGTCCGCACCCCGGACCACCGAAGCTCAGTGGGGCATCATTCGT-TCACA-AAAAGCTG
DroYak_CAF1_left   ATTTATATTCGCCCCCCAGGTGGAATCGAACCACTTCGACGCTAATCGACTACGGATTTGAAGTCCGCACCCCGGACCACCGAAGCTCAGTGGGGCATTGAGCTT-GATAG-AATTTCCT
DroGri_CAF1_left   GCCGCTGATCGCCCCCCAGGTGGAATCGAACCACTTCGACGTTAATCGACTACGGATTTGAAGTCCGCACCCCGGACCACCGAAGCTCAGTGGGGCGGCAGTCCTCATTCTAAATAGGCG

DroAna_CAF1_left   CTTTTAAATAAAGAGTTGGCTGAAAAAGCACTTGAGAATTATTAAAATTTCTAACGCAGTAAAAAGATGTTGGAAATCT-T-G------TTTAA-AC
DroEre_CAF1_left   TACTTATATGCACGTTGTGCTGAATAAGCACTTGG-GAATTTTAAGAGTACGTGTGGGGCAGATTCCAGAAGATCTGACGG-C------AATAA-AG
DroMel_CAF1_left   TAATTATATACACGTTGTGCTGAATAAGCACTTGG-GAATTTTAAGAGTACGTGTAGAGCAAATTCCAGTAGATCTGAGGG-C------AATAT-AG
DroMoj_CAF1_left   TATTTATACGAGTAACAGTCACAAAAAGCACTTGG-GAATTCTAAAAGTGATACCAATTTTTATCACCACGGAATATCAAA-G------ATTTG-TA
DroPer_CAF1_left   CTTTTATATGCCGATTGTCCCGAAAAAGCACTTGG-GAATTACAAGGGCATTGGTCACTTTTCCTACATCTTCCAATCTAC-C------CAGAT-TT
DroPse_CAF1_left   CTTTTATATGCCGATTGTCCCGAAAAAGCACTTGG-GAATTACAAGGGCATTGGTCACTTTTCCTACATCTTCCAATCTAC-C------CAGAT-TT
DroSec_CAF1_left   TACTTATATGCACGTGGTGCTGAATAAGCACTTGG-GAATTTTAAGACTACGTGTAGAGCAGATTCCAGTAGATCTGAGGG-C------AATAA-AG
DroSim_CAF1_left   TACTTATATGCACGTGGTGCTGAAAAAGCACTTGG-GAATTTTACG------TGTAGAGCAGATTCCAGTAGATCTGAGGG-CATAAAGATAAC-AT
DroVir_CAF1_left   TATTTGTAAGCAGTGTTGGCTAAAAAAGCACTTGG-GAATTTCAACCAGAAAAATTCATCTCTTATCTTTAACCACTTTCA-A------ATATT-TT
DroYak_CAF1_left   TACTTATATGCACGTTGTGCTGAATAAGAACTTGG-GAATTTTAAGAGTACGTGTG-GGCAGATTCCAGTAAATCTGAGGG-C------AATAAAGA
DroGri_CAF1_left   TATTTACGAGCACAAATGCGGGAAAAAGAACTTGG-GAATTCTAAGTAAAATGTCATAACGA-TTGCAACATATTACAAATTA------CAACG-AA