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


DroEre_CAF1_left   CTTAAATTC-------ATCATAAAAACGG-TAAAACAAA--GTGCAAG-TATCAGTTTTCATAATAAATATGTAAAA----TTAAAGAAATACATA-ATTATA-ATG---CAAAAAAGAT
DroMel_CAF1_left   AAAGTGAAA---------AAAAAATATTAAAATACTATA--TTACAAA-TAATA-AATTTGCAAAA-TTGTA-ACAAATAATAAATTATA----TA-AAGTAC-CTCAACAAAAAGTTGG
DroMoj_CAF1_left   AATTGTATAC------AAACCTGCAGAGA-ACG-CTATA--AATTCTCCGAATA-ATTTGATAACT-TTTAT-AATT--TAAAATTTAAA----AA-AATATA-TATGATATACAAAAAG
DroPer_CAF1_left   CATTAGGTATGCAAAGATCAGAAAATCAG-GAT-CGGGT--TATCAAT-ACATA-TAAGATAAAAT-AATA--------TAACTCAATATT---TC-AGTCTA-GTATTGC-AAAAAAAG
DroPse_CAF1_left   TGAATAAA------TGTACAGGAAATCAG-GAT-CGGGA--TATCAAT-ACATA-TAAGATAAAAT-AATAT-AATA--TAACGTATCATT---TC-AGTCAA-GTATTGCAAAAAAAAG
DroVir_CAF1_left   CAAACATCCA------TCCATTCAGAGCT-CAC-TGAAA-GTATTTAT-GCAAA-A-AGATTTTAT-ATTTT--GCG--GAACTTTGAAAA---ATTAGCTTA-CATTAAAAACTAAAAA
DroWil_CAF1_left   ATTTATTTGA------AACGTTTAAGCGC-ATTCACAAT--TATTTGCATTAAT-AGTGGATGACT-ATATC-CATTATATTTTTATATA----TA-AAATAA-TCT---AAAAAAAAAG
DroYak_CAF1_left   ATAATAAACA------GCCGATGTAAATC-AGC-TTTTA--CAATAAA-AATTAAATTACTGATT--ATTAG-TATCA-ATGTTATATAT-----A-ATACACGTGTTATCAAAAATAGA
DroSim_CAF1_left   TCTAGAACTA------AGCAACGAAAAAC-CCA-ATAGATGTCGCTTT-AAACG---AAAATGCCA-TAGAT-GAATATAAAGTGATCTT----TG-TTTTT---GTGAGCAAAAATTTA

DroEre_CAF1_left   ACCTTTCCCA-TACCGGGAATCGAACCCGGGCC-TTCTGGGTGAAAGCCAGATATCCTAGCCACTAGACCATATGGGATACACCA-TCTTTTAG-T-CAAAACACCAA-TACAATACA-T
DroMel_CAF1_left   TTGCTTCCCA-TACCGGGAATCGAACCCGGGCC-TTCTGGGTGAAAGCCAGATATCCTAGCCACTAGACCATATGGGACACATAC-CTATTTAG-T-CAAT-CTCCTA-TAT--TAGTTT
DroMoj_CAF1_left   TAACTTCCCA-TACCGGGAATCGAACCCGGGCC-TTCTGGGTGAAAGCCAGATATCCTAGCCACTAGACCATATGGGACCGGTGG-TGGTGCTGTC-AAATAACATAT-TTG--AGTATT
DroPer_CAF1_left   TTACTTCCCA-TACCGGGAATCGAACCCGGGCC-TTCTGGGTGAAAGCCAGATATCCTAGCCACTAGACCATATGGGATATACTTGTCTTTGGT-C-CAAAACTGCAT-TTT--GTTAGA
DroPse_CAF1_left   GTACTTCCCA-TACCGGGAATCGAACCCGGGCC-TTCTGGGTGAAAGCCAGATATCCTAGCCACTAGACCATATGGGATATAGTCATCATTGGT-C-CAAAACTGCAT-TTT--CTTAGA
DroVir_CAF1_left   GTACTTCCCA-TACCGGGAATCGAACCCGGGCC-TTCTGGGTGAAAGCCAGATATCCTAGCCACTAGACCATATGTGATTGAACA-ACAAATTG-C-CAAATTAACTA-TTT--TCATAC
DroWil_CAF1_left   ATACTTCCCA-TACCGGGAATCGAACCCGGGCC-TTCTGGGTGAAAGCCAGATATCCTAGCCACTAGACCATATGGGATATATTT-GTTCTGGG-CACAAT-TTGCCAGTTT--GATAGC
DroYak_CAF1_left   TTCCTTCCCA-TACCGGGAATCGAACCCGGGCC-TTCTGGGTGAAAGCCAGATATCCTAGCCACTAGACCATATGGGATATCCAA-GATTCTGG-T-CAAA-ACACAA-TATT-GGTT-T
DroSim_CAF1_left   ATATTTCCCAATACCGGGAATCGAACCCGGGCCCTCCTGGGTGAAAGCCAGATATCCTAGCCACTAGACCATATGGGACACAAAC-AGAAACGT-GTCAAA--ACGCG-CTT--TTTGAT

DroEre_CAF1_left   CAATA-CCA--AGAT-CTCTGTCTTC--ACTAA--AAAATATGAAGCGCCTTCTGAAGAA------ATTTTGTTCCCAA-AAA--A-ATAAAGTTACGGCTAACGA
DroMel_CAF1_left   CAGTC-CCA--AAGT-TTCTGCTAAC--AGTTA--TAA---CTATT-AACACCTTCTGGAAAATTTGTCCTAAAAATAG-TGC--G-TGACGACAAAAATAAGACA
DroMoj_CAF1_left   AACAA-ATGCTTGCGACTCACAATTTTGAAGGCCATAA---CTAAA-ACCAATAGAAATT---CATTTAACTATTGTGTCACA--TGAAAT-AATATACATTTGTA
DroPer_CAF1_left   AATGC-CTGCGAATT-TGTTATTTTT--AACCA--TGT---TCCGC-CAAATGTGATTGCGCAAAAGGC--AG-ATTAA-ACC--AGTTTT-AAAATACTATGTTT
DroPse_CAF1_left   AATGC-CTACGAATT-TGTTATTTTT--AACCA--TGT---CCCGG-CAAATGTGATTGTGCAAAAGGC--AG-ATTAA-ACC--AGTTTT-AAAATACAATTTAA
DroVir_CAF1_left   CCAGCTTTTCATGAA-AGTCGATTTG--GGGA----------------TTTC-ATTAATCAGTAAACTT--AA-AAATA-CCTACAAAATA-TTCTGGTTCAAATG
DroWil_CAF1_left   AAGAC-AGA--TGCG-GGTTGAAATT--AAAAT-TGAT---CGTAG-TACAGTAAAAACTTCCATAGACGAAA-AACTT-TGC--G-ATCTCTCAATT-TTTTTGT
DroYak_CAF1_left   CAGTG-CAA--AGAT-CTCTGCCATC--ACTTT-AAAA---TGTTA-GACAACTACTGTTTCCCAAAAA-ATAAATGTC-AGT--GAAGTA-CATACATGACTAAC
DroSim_CAF1_left   CATGT-ATA--AATA-NN-----------------NNN---NNNNN-NNNNNNNNNNNNN-NNNNNNNN--NN-NNNNN-NNN--NNNNNN-NNNNNNNNNNNNNN