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


DroEre_CAF1_left   TAAATAATATAGTAAAAGT-TTTGTTAGTTTTACCAAGATGTGAAAGAAGTACCTTCATTAA-AAAGTAAGATCTGGGTACAGGTACA---CAGTATACGATACTTGCCATCTCTGATCG
DroYak_CAF1_left   TTATGTTACCAAGATTTGA-AATGTGCCTATATGTAAAAGAAGAAGTATGTACCTTTAATAA-AAAATAAGGTCTGGGTACAGGTACA---CATTATACGATACTTACCATCTCTAATCG
DroMel_CAF1_left   TGTTTATTTTAACAAGATT-C----AAAATGTGCCAAGATGTGGAAAAAGTACCCATAATAAAAAAGCCCGATTTGGGTACAGGTACAACACATTTTACGATATTTCCCATCTCTGATCG
DroSec_CAF1_left   TAATA-CATAATTAAAACATA----TAAATGTGCCAAGATGTGGAAAAAGTACCTATAATAAAAATGCCAGATTTGGGTACAGGTACAATAAATTCTACGATACTTGCCATCTCTGATCG
DroSim_CAF1_left   TGTTTATTTTAACAAGTTT-A----AAAATTTGCCAAGATGTGGAAAAAGTACTTATAATAAAAAAGCCAGATTTGGGTACAGGTACAACCAATTCTACGATACTTGCCATCTCTGATCG

DroEre_CAF1_left   CCAGTAAGCCATTGCTACTATTGCTACTTCATTTTATTTGCCATCCAATCAACGCGTTGCCATCTGTGCAACGTCGTTTATTTGTTGGCCCGGCCGAAAGAAAATGCCTTGCAATATCTA
DroYak_CAF1_left   CCAGTAAGGC------GCAATTGCTACTTCATTTTATTTGCCATCCAATCAACGCGTTGCCATCTGTGCAACGTTGTTTATTTGTTGGCCCGGCCGACAGAAAATGCCTTGCAATATCTG
DroMel_CAF1_left   CCAGTAAGCC------GCTATTGCTACTTCATTTTATTTGCCATCCAATCAACGCGTTGCCATCTGTGCAACGTCGTTTATTTGTTGGCCCGGCCGAAAGAAAATGCCTTGCAATATCTG
DroSec_CAF1_left   CCAGTAAGCC------GCTATTGCTACTTCATTTTATTTGCCATCCAATCAACGCGTTGCCATCTGTGCAACGTCGTTTATTTGTTGGCCCGGCCGAAAGAAAATGCCTTGCAATATCTG
DroSim_CAF1_left   CCAGTAAGCC------GCTATTGCTACTTCATTTTATTTGCCATCCAATCAACGCGTTGCCATCTGTGCAACGTCGTTTATTTGTTGGCCCGGCCGAAAGAAAATGCCTTGCAATATCTG

DroEre_CAF1_left   CATTTTCACATCGCTCATTTCGC---GGTGG---CTTTCGCTTTGTT----TGTTTAATTAACTTTAGGCCG-GGCCATGAAAATTTGGCCGCAAGC----------------TAAAAAT
DroYak_CAF1_left   CATTTTCGCATCGCTTATTTCGC---GGTGG---CTTTCGCTTTGTT----TGTTTAATTAACTTTAGACCGTGGCCATAAAAATTTGGCCACAAGCTGGTTGCTGGGCTAGTTAAAAAT
DroMel_CAF1_left   CATTTTCACATCGCTCATTTCGCGGCGGTGGTATCTTTTGCTTTGTTTGTTTGTTTAATTAACTTTAGGCCGTGGCTATAAAAATTTGGCCACAAGCT------------AGTTAAAAAT
DroSec_CAF1_left   CATTTTCACATCGCTCATTTCGCGGCGTTGG---CTTTTGTTTTGTT----TGTTTAATTAACTTTAGGCCGTGGCTATAAAAATTTGGCCACAAGCT------------AGTTAAAAAT
DroSim_CAF1_left   CATTTTCACATCGCTCATTTCGCGGCGATGG---CTTTTGTTTTGTT----TGTTTAATTAACTTTAGGCCGTGGCTATAAAAATTTGGCCACAAGCT------------AGCTAAAAAT

DroEre_CAF1_left   ATTGCAGCCGGGCTCAACCGGGATTTGAACCCGGGACCTCTCGCACCCAAAGCGAGAATCATACCCCTAGACCATTGAGCCACATGCCGAGCATCTGGCCACTGCAGGCTTTTGGCCGCT
DroYak_CAF1_left   ATTGGAGCCGGGCTCAACCGGGATTTGAACCCGGGACCTCTCGCACCCAAAGCGAGAATCATACCCCTAGACCATTGAGCCGCATGCCGAGCATCTGGGCACTGCACGGTTTTGGCCGCT
DroMel_CAF1_left   ATTGGAGCCGGGCTCAACCGGGATTTGAACCCGGGACCTCTCGCACCCAAAGCGAGAATCATACCCCTAGACCATTGAGCCGCATACCGAGCACCTCGGCACTGCACGATTTTGGCCGCT
DroSec_CAF1_left   ATTGGAGCCGGGCTCAACCGGGATTTGAACCCGGGACCTCTCGCACCCAAAGCGAGAATCATACCCCTAGACCATTGAGCCGCATACCGAGCACCTCGGCACTGCACGATTTTGGCCGCT
DroSim_CAF1_left   ATTGGAGCCGGGCTCAACCGGGATTTGAACCCGGGACCTCTCGCACCCAAAGCGAGAATCATACCCCTAGACCATTGAGCCGCATACCGAGCACCTCAGCACTGCACGATTTTGGCCGCT

DroEre_CAF1_left   GCTCCTCGC-----TTCTTGGCGCTTTCGCGGTGGTT-CGTT-GCTTTTGCTGACGCGGATGCTGCTGCGGTTGACGTCTTTTGGCCAACT----T
DroYak_CAF1_left   GCTCTTCGC-----CTCTTCGTGCTTTCGAGTTGGTT-CGTT-GCTTTTGATGACGTTGATGCTGCTGCGGATGACGTCTTTTCGCCAACT----T
DroMel_CAF1_left   GCTCTTCGCGGCGTTTCTTGGTGCTTTCGACCTGGCAGTC--GTTCGCTGCCATTGCTGACGTTGATGCTGCTGCGGAT-GACGT----CT----T
DroSec_CAF1_left   GCTCTTCTCG---TTTCTTGGCGCTTTCGACCTGTTT-CGTTTTTTTCCGCCTTTGCTGACGTTGATGCTGCTGCGGAT-GACGT-CT-TT----T
DroSim_CAF1_left   GCTCTTCGCG---TTTCTTGGCGCTTTCGAACTGTTT-CG--GGTTTTTGCCTTTGCTGACGTTGATGCTGCTGCGGAT-GACGT----CTTTTGG