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


DroAna_CAF1_left   CCATTATGATTTGTTCCTTTTGACTT---TATTTTCGACATTATTTGATTT--ACCAAAAACCGACCCAACGAGTGCCCCCAGAAACCAAACCCCTTCACGACCT-AACCACCCAGCAAA
DroEre_CAF1_left   TTCTCAGTATGATTTCTCCGCATTATTTTCCTTCTTGTTTGCCAA--CATCTTTTCAACCAAAAACCGAACCAA--AGAAATCCAGAAGATCCTTTAAAA-ACCA-AACCACCTAGCAAA
DroGri_CAF1_left   GTTGCTTCATTTTGTTTGTTATTTTG---CCAAAGATATATAAAAACCATA--AGAGCTGATGATCCCAACCTGTACCTAAACAAGAACAAAAACAAAAAACAAA-AACCAGCAAGCAAA
DroMel_CAF1_left   TTTTTAATATGATTTCTCCGTATTATTTTTCTTCTTGTTTGCCAT--CATCGTTTCAACCAAAAACCGAACCAA--TGATATCCAGAAGATCCTTTAAAT-ACCA-AACCACCTAGCAAA
DroSec_CAF1_left   TTTTTAATATGATTTCTCCGCATTATTTTTCTTCTTGTTTGCCAA--CATCTTTTTAACCAAAAACCGAACCAA--TGATATCCAGAAGATCCTTTAAAA-ACCA-AACCACCTAGCAAA
DroSim_CAF1_left   TTTTTAATATGATTTCTCCGCATTATTTTTCTTCTTGTTTGCCAA--CATCTTTTCAACCAAAAACCGAACCAA--TGATATCCAGAAGATCCTTTAAAA-ACCA-AACCACCTAGCAAA
DroYak_CAF1_left   TTTTTAATATGATTTCTCCGCATTATTTTCCTTCTTGTTTGCCAA--CATCATTTCAACCCAAAACCGAACCAA--AGAAATCCAGATGATCCTTAAAAA-ACCAAAACCTCCTAGCAAA
DroWil_CAF1_left   ATTATGAGTTTCGATCTACATTAAATTTTCGTTT-GCCAAACCAA--AAAAAAAACAATATTAGGAACCACCAA--AACCACCTCAACTTGAACCTTAAA-ACCTCAATT-AAATGCAAA

DroAna_CAF1_left   AAGGACTACACC-AAGGACCTTTTTCTCTCTGGCAAATTGAGGTAGTAGGTTGTATAGTAGCAACTAAGA-ATCGTACTATACAATGTGCTAGCTTTCTTTGCTTGACAATAAGCCGCAT
DroEre_CAF1_left   AAGGACTACACC-AAGGACCTTTTTCTCTCTGGCAAATTGAGGTAGTAGGTTGTATAGTAGTAATTACAC-ATCATACTATACAATGTGCTAGCTTTCTTTGCTTGACTACAAGCCGCAT
DroGri_CAF1_left   AAGGACTACACC-AAGGACCTTTTTCTCTCTGGCAAATTGAGGTAGTAGGTTGTATAGTAGTATCTATCT-ACCATACTATACAGCTTGCTAGCTTTCTTTGCTTGACTATAAGCAGCAT
DroMel_CAF1_left   AAGGACTACACC-AAGGACCTTTTTCTCTCTGGCAAATTGAGGTAGTAGGTTGTATAGTAGTAATTACAC-ATCATACTATACAATGTGCTAGCTTTCTTTGCTTGACTACAAGCCGCAT
DroSec_CAF1_left   AAGGACTACACC-AAGGACCTTTTTCTCTCTGGCAAATTGAGGTAGTAGGTTGTATAGTAGTAATTACAC-ATCATACTATACAATGTGCTAGCTTTCTTTGCTTGACTACAAGCCGCAT
DroSim_CAF1_left   AAGGACTACACC-AAGGACCTTTTTCTCTCTGGCAAATTGAGGTAGTAGGTTGTATAGTAGTAATTACAC-ATCATACTATACAATGTGCTAGCTTTCTTTGCTTGACTACAAGCCGCAT
DroYak_CAF1_left   AAGGACTACACC-AAGGACCTTTTTCTCTCTGGCAAATTGAGGTAGTAGGTTGTATAGTAGTAATTACAC-ATCATACTATACAATGTGCTAGCTTTCTTTGCTTGACTACAAGCCGCAT
DroWil_CAF1_left   AAGGACTACTTAAAAGGACCTTTTTCTCTCTGGCAAATTGAGGTAGTAGGTTGTATAGTAGTAATTATTCAATCATACTATACAATGTGCTAGCTTTCTTTGCTTGACTATAAGCCACAG

DroAna_CAF1_left   TTGATTTGAAAATCCC-CCCCCAATGGAGTTCTATGTGGAATCGAAGC-CATAAGTGGTGGTGATGTGATA-AAAT-TTAATTTATGCAAAGAATTATTATTATTG-AGAAGTAGTGCTG
DroEre_CAF1_left   TTGATTAAAGAATCCCAATCGAA-CTGCACCACTTGCTCCACCCAATC-C-CA-GCCATA---CAAAAGTT-GGTG-GTG-CAACAAATTTTGATTGTGGGCAACAAA-AAAGT-GCTCT
DroGri_CAF1_left   AGAACGAAACCCTC-T-CACACACTGAAAAAAAAAACACCACTGAATC-T-CAAATC-----CCAGCCATA-CAAT-GTG-TGTGCGTGTGTGTGTATGTGTTGCT-TGTGCGT-GTGTG
DroMel_CAF1_left   TTGATAAAAGAATCCCAATCGAA-CTGCACCACTTAATAAACCCAATCCC-CA-GCCATA---CAAAAGTT-GGTG-GTG-CAACAAATTTTGATTGTGGACAACAAAGAAAGT-GTTCT
DroSec_CAF1_left   TTGATTAAAGAACCCCAATCGAA-CTGCACCACTTACTAAACCCAATCCC-CA-GCCATA---CAAAAGTT-GCTG-GTG-CAACAAATTTTGATTGTGGGCAACAAAGAAAGT-GTTCC
DroSim_CAF1_left   TTGATTAAAGAACCCCAATCGAA-CTGCACCACTTACTAAACCCAATCCC-CA-GCCATA---CAAAAGTT-GGTG-GTG-CAACAAATTTTGATTGTGGGCATCAAAGAAAGT-GTTCC
DroYak_CAF1_left   TTGATTAAAGAATCCCAATCGAA-CCGCACCACTTACTCCACTTAATC-C-CA-GCCATA---CAAAAGTT-GGTG-GTG-CAACAAATTTTGATTGTGGGCAACAAA-AAAGT-GTTCC
DroWil_CAF1_left   ATATGATCTAAATAGACAGTTGA-CACCAGCCATATATACATTTA--T-C-AA-TTGTGA---AAAGTGCATATGATACA-GTTCAAATAA-TATTATTGGTATTAGTGACA-T-GTGCA

DroAna_CAF1_left   TTGAG--AA
DroEre_CAF1_left   GAGCCGGAC
DroGri_CAF1_left   TAAAA--GT
DroMel_CAF1_left   GAGCC--AA
DroSec_CAF1_left   GAGCC--AG
DroSim_CAF1_left   GAGCC--AG
DroYak_CAF1_left   GAGCCGGAC
DroWil_CAF1_left   --AAT--GT