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


DroAna_CAF1_left   --ACCAGCA-ATTACAAAATAATTGAATTCCTCAGAGTTGTGGTCCGCCTTTCTATTAATATATTTTTATTAGAAAATGTG-ATAAGGTTCATGAGCACTTTTGGACTGG-CATGGAATC
DroYak_CAF1_left   --AGCGAGTGGAGAACGAGCATCTGAAA----TTGGTTACTTTTTCTATATTAATCTTTTTATTTGTTAGATAAGTAGTGCATTAACCAACATGAATTTCCATTTTGACACGCAAGAATC
DroMel_CAF1_left   CAAGCGAGTGGAGAACGGGCTTTTAAAA----TTGCTTAGTTTCTCTATACAAAAGTTCTCATTTCTCAGATAAAAAGTGTGCTTATGTCTATGAGTAGAATTTGA--CAAATTGAAATC
DroSec_CAF1_left   CAAGCGAGTGGAGAACGGGCGTCTGATA----TTGCTTAGTTTTTCTATTTAAAAGTTCTCATTTCTCAGATAAAAAGTGGGCTTATGTGTATGAGTATAATTTGA--CAATCATAAGTC

DroAna_CAF1_left   AACATCCTCGATAGTATAGTGGTTAGTATCCCCGCCTGTCACGCGGGAGACCGGGGTTCAATTCCCCGTCGGGGAGA--TGGATGATTTTTTTACTTTATTTTATTTTTATTATTAAATA
DroYak_CAF1_left   AGCGTCCTCGATAGTATAGTGGTTAGTATCCCCGCCTGTCACGCGGGAGACCGGGGTTCAATTCCCCGTCGGGGAGAGATGTATTAATATTTTTTTGTCAACCAAATTTGTTTTTTAATA
DroMel_CAF1_left   AACATCCTCGATAGTATAGTGGTTAGTATCCCCGCCTGTCACGCGGGAGACCGGGGTTCAATTCCCCGTCGGGGAGA--TGTGTA-TTAAACTTTTTTTT---------TTTAATAGGAA
DroSec_CAF1_left   AACATCCTCGATAGTATAGTGGTTAGTATCCCCGCCTGTCACGCGGGAGACCGGGGTTCAATTCCCCGTCGGGGAGA--TGTTATTCTTTTTTTGTTACTAT-TTTTTTTTTAATAGGCA

DroAna_CAF1_left   GTTACTGATATGTAATTGTATTTTTTAAACCCTTTCCCATGGGTATTACGAAATTT-GAAA------------AATAGTC
DroYak_CAF1_left   TACATATTTTGTTGTTACATCATTAATAATTTATTAGTTAAAAATATACCAAAGCT-TAAACAG---------TAAAATA
DroMel_CAF1_left   ATTATTTAGCAGTGGAATATAACCATAGTTGTATCTGCAAAATGATTAAACAACTTAAAT-TAAAGGGCTGGGCAAAACC
DroSec_CAF1_left   ATTATTTACTTGTGGAATAAAACCATAGTTGTATCTGCAAAATGATTAACCAACTTAAAT-TAACGG----------GTT