CLUSTAL W --- LocARNA 1.4.8 - Local Alignment of RNA DroAna_CAF1_left CCATTTT-A-TTTTATGGAATT-CCACGGCGGTAA-G-CCCTCTAAC-TTTGTTGTCC-GACGGATTAGCACCCGGCTTTTTTGGACTCTCCACTGATGGATGG--ACAA-CC--TGATG DroEre_CAF1_left TGATTCC-TGATTCCTCCAGTT-TGTTTTCTATTC-A-CGCTTTAAA-GTAAACAACTTGATT--GTGTGATGCAAAGCTCCACTATG---ACTCGATTCACTGGGGATT-GC-TTGACG DroMel_CAF1_left AGTTTGT-T-TTCTATTCACGC-TTTAGTGCACTT-A-TTTACTCGA-TTGTATGATC-CAAA--GCTCCTCTTTGACTCGCCGAATTCC-TGTCGATTCAATGGGTATTGGT-TTGATG DroMoj_CAF1_left ATTCACG-C-CTGTCTGCATTG-TCACGAATATAT-T-CATTTAC-AGTTTATTTATT-GATA--GAATCTGC-AGCGCACTGGGTTGAT-CGTTGTCGTTGTCGCATGT-ATTTAGTTG DroPer_CAF1_left CTCGCAG-A-ACAATACAATAG-ACCATTATATGT-G-CAGTTCTCTGGC-CGCAAGG-GACT--TGACTTTC-CTCCCCGCAGGATTAG-TCGTGTACGAGCTTTCGCG-TG-CTGATG DroPse_CAF1_left CTCGCAG-A-ACAATACAATAG-ACCATTATATGT-G-CAGTTCTCTGGC-CGCAAGG-GACT--TGACTTTC-CTCCCCGCAGGATTAG-TCGTGTACGAGCTTTCGCG-TG-CTGATG DroSec_CAF1_left AGTTTGT-T-TTCTATTCACGC-TTTAGTGCACTT-A-TTCACTCGA-TTGTGTGATC-CAAA--GCTCCACTTTGACTCGCCGAATTCC-TGTCGATTCAATGGAGATT-GC-TTGATG DroSim_CAF1_left AGTTTGT-T-TTCTATTCACGC-TTTAGTGCACTT-A-TTCACTCGA-TTGTGTGATC-CAAA--GCTCCACTTTGACTCGCCGAATTCC-TGTCGATTCAATGGGGATT-GC-TTGATG DroWil_CAF1_left TTTTCCA-T-TATGTAA-GCTT-ATTAAAATGCCA-TGCACTTTTAA-GCACTTTTCC--GAT--TTTTTACGCACACACACACACACAC-TTTTTTCACCCATTTTCCG-CC-CTGTTG DroYak_CAF1_left TTGCAGA-T-TCCTCCAGTTTT-TTTTCTATTCAC-G-CTTTAGTGC-ACTTTAGTGC-ATTA--ACTCTTCTGTGACTCGCCGAATTCT-TGCACATTCAATGGGGATT-GC-TTGATG DroGri_CAF1_left AGCTCTC-A-AGCAATGACTTGGCGATTCTCTTCGCA-TAGTTGGTC--GCCAGTTAG-TCAA--TATAGCACGATTTATTTATATGAAT--TTGTTGCTGGCTTCAACA-CT-TTGATG DroVir_CAF1_left AGTTTCTTA-TGCTAAAACTCG-ATGACGACTTTT-A-GATACTTCA-ATGAATACAT-TATT--TAACATACTTAATTATGCTTAATTT--AAATAGTTGCTGCACTTA-GT-TAGTTG DroAna_CAF1_left AATTGGTGATACGAGCCCTTATCAGTTCTCCGTCCAGTTGTCTCATTATGCACACGGGGCGCGAGAATGATAAGGGTACGAATGCACCGGCCGGACT-----C-----GCCG-----GCA DroEre_CAF1_left AATTGGTGATACGAGCCCTTATCAGTTCTCCGTCCAGTTGTCTTTAAATGCACACGGGGCGAGAGAATGATAAGGGTACGAATGCACCGGCCAACCCT-------CGGGTCA-----GCC DroMel_CAF1_left AATTGGTGATACGAGCCCTTATCAGTTCTCCGTCCAGTTGTCTTTAAGTGCACACGGGGCGAGAGAATGATAAGGGTACGAATGCACCGGCCAACCCT-------CGGGTCA-----GCC DroMoj_CAF1_left ACTTGGTGATACGAGCCCTTATCAGTTCTCCGTCCAGTTGTATAGATATGCACACGGGGCGCGAGAATGATAAGGGTACGAATGCACCGGCCAATGCCCA-ACGGCAGATTG-----GCC DroPer_CAF1_left AGTTGGTGATACGAGCCCTTATCAGTTCTCCGTCCAGTTGTCTTTTAATGCACACGGGGCGCGAGAATGATAAGGGTACGAATGCACCGGTCGACCCGGAGTCCCCGGGCCG-----ACC DroPse_CAF1_left AGTTGGTGATACGAGCCCTTATCAGTTCTCCGTCCAGTTGTCTTTTAATGCACACGGGGCGCGAGAATGATAAGGGTACGAATGCACCGGTCGACCCGGAGTCCCCGGGCCG-----ACC DroSec_CAF1_left AATTGGTGATACGAGCCCTTATCAGTTCTCCGTCCAGTTGTCTTTAAATGCACACGGGGCGAGAGAATGATAAGGGTACGAATGCACCGGCCAACCCT-------CGGGTCA-----GCC DroSim_CAF1_left AATTGGTGATACGAGCCCTTATCAGTTCTCCGTCCAGTTGTCTTTAAATGCACACGGGGCGAGAGAATGATAAGGGTACGAATGCACCGGCCAACCCT-------CGGGTCA-----GCC DroWil_CAF1_left AGTTGGTGATACGAGCCCTTATCAGTTCTCCGTCCAGTTGTCTAGATATGCACACGGGGCGCGAGAATGATAAGGGTACGAATGCACCGGTCAGCTT---------TAACTG-----ACT DroYak_CAF1_left AATTGGTGATACGAGCCCTTATCAGTTCTCCGTCCAGTTGTCTTC-AATGCACACGGGGCGAGAGAATGATAAGGGTACGAATGCACCGGCCAACACT-------CGGGTCA-----GCC DroGri_CAF1_left AGTTGGTGATACGAGCCCTTATCAGTTCTCCGTCCAGTTGTATAGTTATCCACACGGGGCGAGAGAATGATAAGGGTACGAATGCACCGGCCAAAACC-------ATATGCAGGCTGGCC DroVir_CAF1_left ACTTGGTGATACGAGCCCTTATCAGTTCTCCGTCCAGTTGTCTAGATATGCACACGGGGCGCGAGAATGATAAGGGTACGAATGCACCGGCCAAAGCCC------AAATTTAGGCTGGCC DroAna_CAF1_left CTGGGTTGGGTT-GC-CA----CTTTTCAGACAC------T-TTTCACTCGATACT--CACCCCATGACCTC---TT-TT-GTTTTTTTCTGGGAGCCAGA---CAGTCCATCAATCACT DroEre_CAF1_left CAG-----TTTA-TCCACTGATTTGCACACTTCT------GTTTTGCAAGGATACT--TA-CCCA-CGTATC---GA-TT-ACGCGCATCAATCAATCATT---CAATCAATCGGCAGCT DroMel_CAF1_left CAG-----TTAA-TCCACTGATTTGCACACTTTTCTTTATA-CATACGAGGATACT--TACCCCA-CGTTTC---GA-TT-ACGCGCATCAATCAA----T---CAATCATTCAATCATT DroMoj_CAF1_left ATTT----ATAC-AC-ACACACCCACACACATGC------A-CACG-CACATGTGC--TGCAACT-GATACT---CA-CCATTATTTGGCTTTTAGCTGCC----AATCAATCATAT-CG DroPer_CAF1_left CCG-----CACG-CC-GCT-TGCCACACTTTTCC------A-CTTGCCACTTTATG--CTTGCAA-TGTACT---CA-CCAATACTCAACCAATCGATGGT---GTCTCCCCCAGCTGTC DroPse_CAF1_left CCG-----CACG-CC-GCT-TGCCACACTTTTCC------A-CTTGCCACTTTATG--CTTGCAA-TGTACT---CA-CCAATACTCAACCAATCGATGGT---GTCTCCCCCAGCTGTC DroSec_CAF1_left CAA-----TTAA-TCCACTGATTTGCACACTTTT------T-TATGCAAGGATACT--TACCCCA-CGTATC---GA-TT-ACGCGCCTCAATCAATCAAT---CATTCAATCATTCGCG DroSim_CAF1_left CAG-----TTAA-TCCACTGATTTGCACACTTTT------T-TATACAAGGATACT--TAGCCCA-CGTATC---GA-TT-ACGCGCCTCAATCAATCAAT---CAATCATTCAATCATT DroWil_CAF1_left CTT-----CGCG-TCTAG--ATCCACTTACC--C------C-AAATCCATATATGA--TTTTTAA-CTGGC----CA-TCAATCACTCACTTGCAACAAAT---G-----ACTATAAAAT DroYak_CAF1_left CAG-----TTAACTACTCGTATATCCACTGATTT------G-CACACTTTTTTACA--AGG-ATA-CTTACC---CA-CG-TATCGATTACGCGCATCAAT---CAATCACGCAATCAAT DroGri_CAF1_left ATT-----TATA-ATCCC--AGACACACACACAA------A-----CTAACAGCTGCTGCTGC----AGTTGCTATTGAT-ACCCACCATTATTTGGCTTTCAGCTGTCAATCAATCATT DroVir_CAF1_left ATT-----TATA-CACAC--ACACACACGAACGT------A---G-CACACACACACACAGGC----GTGGCTGTGTTGT-TGCTGATACTCACCATTATTTGGC-TTTTAGCTGTCAAT DroAna_CAF1_left C--ATGG DroEre_CAF1_left G-TGAAA DroMel_CAF1_left C---GCG DroMoj_CAF1_left CAGCTGC DroPer_CAF1_left CATCAAT DroPse_CAF1_left CATCAAT DroSec_CAF1_left C-AGCTG DroSim_CAF1_left C-GCGCA DroWil_CAF1_left TTGT-TT DroYak_CAF1_left C-GGCAG DroGri_CAF1_left T--AGGT DroVir_CAF1_left C--AATC