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


DroEre_CAF1_left   AGGATCACTTTTCCCCATT--A-AAGAGGAGGTGGAA--GACGAAGACAACCTTAAGATCCACA-AATATGGTAAGT--AAAATATAAAGTCCGACTAT----CTGCACT------GCAA
DroMel_CAF1_left   CGGATTAAAACACCTTTTG--G-TTAAAAA-----AA--TGGCCC-AAATAGTGCACAGTAAAGTGTAATTTGTGCC--TTGATTTCTTAGTTTATAAAA--TTAGGATCACACCAAAAA
DroSec_CAF1_left   CCAAACACGCGGATTGAAG--A-CTAACACAT-CCAT--GAGTTCCATACCTATAGTACTTAAACTATAGAGCAAGA--TAGTCTGCACTGCAAACAAAA--TAGTGAGC------AAAA
DroSim_CAF1_left   CCAAACACGCGGATTGAAG--A-CTAACACAT-CCAT--GAGTTCTATAACTAGAGTACTTAAACTATAGAGCCAGA--TAGTCTGCACTGCAAACAAAA--TAGTGAGC------AAAA
DroYak_CAF1_left   AATTCTT-AAAAAGTGAGG--ATCACACCTAT-TCTGGTTTTATATATATTC-CACATAGTATAGTGCC-TAATATATGAAGTCAG--CTGCAAACAAAA--TAGTGAGC-------AAA
DroPer_CAF1_left   CAATAAACCA-TACACAAC--C-CATAGTA-----GC--TAATCTCAGTAAAAG-ATTTAAAAGTGTAACTATTATA--AACCATCAGAAAGTAATACAAAAAAAAAACG------AAAC
DroPse_CAF1_left   AGTAGCTAAT-CTCAGAGGCAG-CTCAGAA-----AA--GAAAACGACTAAAAG-ATTTAAAAGTGTAAGTATTATA--AACCATCAGAAAGTAATAAAA--AAAAAACG------AAAC

DroEre_CAF1_left   AAAAAGCAGGTCCTTCTCCGTGACAATGCGT--ATCTCAGCATTGCCGTGACCAGGATTCGAACCTGGGTTACCACGGCCACAACGTGGGGTCCTAACCACTAGACGATCACGGCTACGA
DroMel_CAF1_left   AAAAAGTAGATCCTTCTCCGTGACAATGCAT--ATTGCAGCATTGCCGTGACCAGGATTCGAACCTGGGTTACCACGGCCACAACGTGGGGTCCTAACCACTAGACGATCACGGCTATGA
DroSec_CAF1_left   AAAAAGTATATCCTTCTCCGTGACAATGCAT--ATTGCAGCATTGCCGTGACCAGGATTCGAACCTGGGTTACCACGGCCACAACGTGGGGTCCTAACCACTAGACGATCACGGCTATGA
DroSim_CAF1_left   AAAAAGCAGATCCTTCTCCGTGACAATGCAT--ATTGCAGCATTGCCGTGACCAGGATTCGAACCTGGGTTACCACGGCCACAACGTGGGGTCCTAACCACTAGACGATCACGGCTATGA
DroYak_CAF1_left   AAAAAGCAGATCCTTCTCCGTGACAATGCGT--ATCTCAGCATTGCCGTGACCAGGATTCGAACCTGGGTTACCACGGCCACAACGTGGGGTCCTAACCACTAGACGATCACGGCTACGA
DroPer_CAF1_left   GAAAAAAGATGTCCTCTCCGTGACAATGCGTTAATTGCAGCATTGCCGTGACCAGGATTCGAACCTGGGTTACCACGGCCACAACGTGGGGTCCTAACCACTAGACGATCACGGCTACGA
DroPse_CAF1_left   GAAAAAAGATGTCCTCTCCGTGACAATGCGTTA-TTGCAGCATTGCCGTGACCAGGATTCGAACCTGGGTTACCACGGCCACAACGTGGGGTCCTAACCACTAGACGATCACGGCTACGA

DroEre_CAF1_left   AGGCACTTGAATCTGCGAGCGTTAATCGCGTGCATAAGCAGCGCAC--ATACA-TGTAAGTAAGAGTGA-ATGGGTAGCTAAGACTAAACTGGGGCCATTTGCTGCAT-TTCTTTGCTC
DroMel_CAF1_left   AGGCACTTGAATTTACGAGCGTCAATCGCGTTCATAAGTAGCTATAGTATATG-TGTGGCTAAGACT-A-AAGCTTAAGCTGGCGCTATTTGCCTGCATTTCTTTGCT-CGAAAACA-A
DroSec_CAF1_left   AGGCACTTGAATTTACGAGCGCCAATCGCGTTCATAAGTAGCTAGT--ATATG-AGTGGCTAAGACTTC-AAGCTGAAGCTGGGGCTATTTGCCTACATTTCTTTGCT-CCAAAACAAC
DroSim_CAF1_left   AGGCACTTGAATTTACGAGCGCCAATCGCGTTCATAAGTAGCTAGT--ATATG-AGTGGCTAAGACTTC-AAGCTGAAGCTGGGGCTATTTGCCTGCATTTCTTTGCT-CCAAAACAAC
DroYak_CAF1_left   AGGCACTTGAATCTACGAGCGATAATCGCGTTCATAAGCAGCGCAC--ATATTTATACGTTTGTGTGTG-TTTGTGTAGCTAAGACTAAA-GCTGGGACTGGAGGCAA-TTTGCCTGCA
DroPer_CAF1_left   AGACACTTGAAAGTACCGCTGTAAATAGCGCACAAGAGCCGCATAT--GTA-G-AGCGGCGGCCCCACTTGC-TTGCAGTTCTTGCTCTCCGAAAAGTTTATGGAGCAACGACTCCTCT
DroPse_CAF1_left   AGACACTTGAAAGTACCGCTGCAAATAGCGCACAAGAGCCGCATAT--GTA-G-AGCGGCGACCCCACTTAC-TTGCAGTTCTTGCTCTCCGAAAAGTTTATGGAGCAACGACTCCTCT