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


DroAna_CAF1_left   CCCCCCCAATGGAGTTCTATGTGGAATCGAAGCCATAAGTGGTGGTGATGTGATAAAATTTAATT-TATGCAAAGAATTATTA-TTATTGAGAAGTA-GTGCTGTT--GAGAACCAAACT
DroEre_CAF1_left   ATTAAAGAATCCCAATCGAACTGCACCACTTGC-TCCACCCAAT-CCCAGCCATACAAAAGTTGGTGGTGCAACAAATTTTGATTGTGGGCAACAAA-AAAGTGCT--CTGAGCCGGACT
DroGri_CAF1_left   TCCCAGCCA-TACAATGTGTGTGCGTGTGTG-T-GTATGTGTTGCTTGTGCGTGTGTGTAAAAGTGATTTATTGAAATTGAAAAATAGAAAAGAAAAAAAAGTATATATATATTTATATA
DroMel_CAF1_left   AA--AAGAATCCCAATCGAACTGCACCACTTAA-TAAACCCAATCCCCAGCCATACAAAAGTTGGTGGTGCAACAAATTTTGATTGTGGACAACAAAGAAAGTGTT--CTGAGCCAAACT
DroSec_CAF1_left   TA--AAGAACCCCAATCGAACTGCACCACTTAC-TAAACCCAATCCCCAGCCATACAAAAGTTGCTGGTGCAACAAATTTTGATTGTGGGCAACAAAGAAAGTGTT--CCGAGCCAGACT
DroSim_CAF1_left   TA--AAGAACCCCAATCGAACTGCACCACTTAC-TAAACCCAATCCCCAGCCATACAAAAGTTGGTGGTGCAACAAATTTTGATTGTGGGCATCAAAGAAAGTGTT--CCGAGCCAGACT
DroYak_CAF1_left   ATTAAAGAATCCCAATCGAACCGCACCACTTAC-TCCACTTAAT-CCCAGCCATACAAAAGTTGGTGGTGCAACAAATTTTGATTGTGGGCAACAAA-AAAGTGTT--CCGAGCCGGACT
DroWil_CAF1_left   TA--ATTAT--TCAATCATACTATACAATGTGC-TAG---CTTT-CTTTGCTTGACTATAAGCCACAG-ATATGATCTAAATAGACAGTTGACACCA-GCCATATA--TACATTTATCAA

DroAna_CAF1_left   CCGTCCAGCTCGATCGAGAGCCGACATTCGCCA-A-------GCAAATGCATCCGCCGGGCGCATGTAAATATTGGTATTGGTGACATGTGCAAATGTTTGTATGGCTGATTCCCTGAGA
DroEre_CAF1_left   ------CTCGTTCATTTTCAT-TACAAATGCCTTAAGT--ATGTAAATGCAA---CCGGGCATATGTAAATATTGGCATTGGTGACATGTGCAAATGTTTGTATGGCTGATTCCCTGAGA
DroGri_CAF1_left   ------TACAGGCAAATATAT-ATCATAATC---GATC--TCATATGAAATT---CACTGCATATTTACACATTGGTATTAGTGACATGTGCAAATGTTTGTATGGCTGATTCCCTGAGA
DroMel_CAF1_left   ------ATTGTTAAATATCAT-TACGAATGCCA-AAGT--ATGTAAATGCAA---CCGGGCATATGTAAATATTGGCATTGGTGACATGTGCAAATGTTTGTATGGCTGATTCCCTGAGA
DroSec_CAF1_left   ------ATTGTTAAATTTCAT-TACGAATGCCTAATGCCTATGTAAATGCAA---CCGGGCATATGTAAATATTGGCATTGGTGACATGTGCAAATGTTTGTATGGCTGATTCCCTGAGA
DroSim_CAF1_left   ------ATTGTTAAATTTCAT-TACGAATGCCTAA-GT--ATGTAAATGCAA---CCGGGCGTATGTAAATATTGGCATTGGTGACATGTGCAAATGTTTGTATGGCTGATTCCCTGAGA
DroYak_CAF1_left   ------TTTGTTCAATTTCAT-TACGAATGCCTTAAGT--ATGTAAATGCAA---CCGGGCATATGTAAATATTGGCATTGGTGACATGTGCAAATGTTTGTATGGCTGATTCCCTGAGA
DroWil_CAF1_left   ------TTGTGAAAAGT-------------------------GCATATGATA---CAGTTCAAATAATATTATTGGTATTAGTGACATGTGCAAATGTTTGTATGGCTGATTCCCTGAGA

DroAna_CAF1_left   CCCTAACTTGTGACTTTTAATACCAGTTTCACAAGTTTTGATCTCCGGTATTGGACGCAAACTTGCTGATGTTAATACAAAAA-AGATAAAGCAAAC-TGAGAGCC-AAGG-GTCCACTG
DroEre_CAF1_left   CCCTAACTTGTGACTTTTAATACCAGTTTCACAAGTTTTGATCTCCGGTATTGGACGCAAACTTGCTGATGTTAGTA----AA-AAATAAGGCAAAAACAAAATTA-CTTT-GAAGGCAC
DroGri_CAF1_left   CCCTAACTTGTGACTTTTAATACCAGTTTCACAAGTTTTGATCTCCGGTATTGGACGCAAACTTGCTGATGTTAGTA----AA-AAAAAACAAAAACAATAAAACA-AAAAGCAA--AAC
DroMel_CAF1_left   CCCTAACTTGTGACTTTTAATACCAGTTTCACAAGTTTTGATCTCCGGTATTGGACGCAAACTTGCTGATGTTAGTA----AA-AAATAAGGCAAAAACGAATTCC-CTTT-CAAGGCAC
DroSec_CAF1_left   CCCTAACTTGTGACTTTTAATACCAGTTTCACAAGTTTTGATCTCCGGTATTGGACGCAAACTTGCTGATGTTAGTA----AAAAAATAAGGCAAAGACGAATTCT-CTTG-CGAGGCAC
DroSim_CAF1_left   CCCTAACTTGTGACTTTTAATACCAGTTTCACAAGTTTTGATCTCCGGTATTGGACGCAAACTTGCTGATGTTAGTA----AA-AAATAAGGCAAAGGCGAATTCT-CTTT-CAAGGCAC
DroYak_CAF1_left   CCCTAACTTGTGACTTTTAATACCAGTTTCACAAGTTTTGATCTCCGGTATTGGACGCAAACTTGCTGATGTTAGTA----AA-AAATAAGGCAAAAAAGAAATTA-CTTT-AAAGGCAC
DroWil_CAF1_left   CCCTAACTTGTGACTTTTAATACCAGTTTCACAAGTTTTGATCTCCGGTATTGGACGCAAACTTGCTGATGTTGGCA----AA-AAGCTAAACTCATTCTTAACAATTCAT-CTATCGAT

DroAna_CAF1_left   CAGTTGGCAGT-AAGTAGAAAATTTATTCACGGG-GTCTAAAGTCTTTACCAGTTA-TGAGA---ATT-GCATTTATAAAT
DroEre_CAF1_left   GAGTATCGGAA-GTTCAGAAAAGTTATCCA-GAA-GGTAAACGCTCACACAAAACT-ATTAC---AAACTGTA-TAACCTA
DroGri_CAF1_left   AAGAAGCAAAACGGTTGGAACATTCCTTAA-GGGATGGTAAAG-CATTTTGTGTAA-TAGAT---TCC-TTATCTAATTTG
DroMel_CAF1_left   AAGTATCGGCA-ATTCAGAGAAGTTCTCCA-GAA-GGTAAAAGCTCACACAAAAAATATAAC---AAG-CTGT-ATGCCCT
DroSec_CAF1_left   AAGTAGCGGAA-GTTCAGAGAAGTTCTCCA-GAA-GGTAAAAGCTCACACAAAACT-ATTAC---AAT-CTGTACTCCCTA
DroSim_CAF1_left   AAGTATCGGAA-GTTCAGAGAAGTTCTCCA-GAA-GGTAAAAGCTTACACAAAACT-ATTAC---AAT-CTGTACTCCCTA
DroYak_CAF1_left   GACTATCGGAA-GATCAGAAAAGTTTTCCA-GAA-GGTAAAAGCTCCGAATAAACT-ATTAC---AAC-TGTATAACCTAA
DroWil_CAF1_left   TGGAAAATGTT-TCAACTAAAAGGTAAACA-CA----GTTATGTCAATAATTTGCA-TCACATTATTT-AATTTATTATAG