CLUSTAL W --- LocARNA 1.4.8 - Local Alignment of RNA DroAna_CAF1_left TGTGATATGATTGC-GAAATACATAAGGTCAC-AAGCCTTTTAACGACATGGTATAAGAA-AGATGAACACAATCGG------TT---------ATGA--CATCC----TGCC---GCCG DroPer_CAF1_left GA---TATGATTCA-AGAGTACATAAGGTCAC-AAACATTTTAACGACATGGTATAAGAA-AGATGCTTTCCGTCCA------CTC-------TGTGCTCCATCC----TGCC---CTGC DroPse_CAF1_left GA---TATGATTCA-AGAGTACATAAGGTCAC-AAACATTTTAACGACATGGTATAAGAA-AGATGCTTTCCGTCCA------CTC-------TGTGCTCCATCC----TGCC---CTGC DroEre_CAF1_left CG---TCAAAATGG-CTGTGATATGATTGCGA-ATACATAAGTTCACAAACATTTTAACG-ACATGGTATAA--GAA------AGA-------CGTTGTTCAATC----GCTT---TTGA DroGri_CAF1_left AC---AAGC-ATTT-TAACGACATGGTATAAG-AAAGA--AAGAAAGAAACACACAAAGG-AGAAGGAGGAG--GAA-CAGGAGGAGGCGGCGACTGCACGAACC----GGCCCCGGCGA DroMel_CAF1_left AA---A----ATGG-CTGTGATATGATTGTGA-ATACATAAGTTCACAAACATTTTAACG-ACATGGTATAA--GAA------AGA-------CGTGGTTCAGTCAGTCGGTT---ATGA DroMoj_CAF1_left CA---TACGGTCAC-AGACATTTTAACGACATGGTATAAGAAAATTGCAATTCGAATGCAAATGAAGATGGA--GAT------TGA-------GGTGGATAATCC----AGTG---ACAC DroSec_CAF1_left CG---TCAAAATGG-CTGTGATATGATTGCGA-ATACATAAGTTCACAAACATTTTAACG-ACATGGTATAA--GAA------AGA-------CGCGGTTCAGTC----GGTT---ATGA DroSim_CAF1_left CG---TCAAAATGG-CTGTGATATGATTGCGA-ATACATAAGTTCACAAACATTTTAACG-ACATGGTATAA--GAA------AGA-------CGCGGTTCAGTC----GGTT---ATGA DroVir_CAF1_left AT---ATGATATAAAATACATAAGGTCACAGG-CATTT--TA--ACG------ACATGGT-ATAAGAAAATT--GCAATGCAAAAA--CGATAATCGTCCTTGCC----AGCCCATTCTG DroWil_CAF1_left GC---TGTGA------TATGA--ATAGAGACA-CAACATAAAGTCACAAACATTTTAACG-ACATGGTATAA--GAA------AGT-------TGCAGTCAATTC----ACAT---ATTC DroYak_CAF1_left CG---TCAAAATGG-CTGTGATATGATTGCGA-ATACATAAGTTCACAAACATTTTAACG-ACATGGTATAA--GAA------AGA-------CGTGGGTCAATC----GATT---ATGA DroAna_CAF1_left CGCCCCTTTCTGAC-------GGT--TT--TCT--GA-CGATTCCCACGAAACTCATCAAAATGGCTGTGATATGAGTAGATAA--T-GGCAACATTTCACAGCC-CTTTGAGGAGTTAC DroPer_CAF1_left CCC-GATCGATGAT-------GGA--TTG-CTG--GC-CATTCCACACGAAACTCATCAAAATGGCTGTGATATGATTTGATAA--A-TGCAACATTTCACAACC-GTTTGATGGGTTAC DroPse_CAF1_left CCC-GATCGATGAT-------GGA--TTG-CTG--GC-CATTCCACACGAAACTCATCAAAATGGCTGTGATATGATTTGATAA--A-TGCAACATTTCACAACC-GTTTGATGGGTTAC DroEre_CAF1_left AA--TATGTTTTCT-------TAA-CCCG-CTTT-TTAAA-TTCGCACGAAACTCATCAAAATGGCTGTGATATGAGTAGATAA--TAGTCGACATTTCACAACC-CTTTGAGGAGTTAC DroGri_CAF1_left GG--GACAATGATC-------ACT--GTGATGAA-AGCAA-TTCGCACGAAACTCATCAAAATGGCTGTGATATGACTTGATAA--T-ACCCACATTTCACAACC-CCTTGAAGAGTTAC DroMel_CAF1_left AA--TATGTTTTTT-------GAT--CCG-CTGC-CGCGA-TTCGCACGAAACTCATCAAAATGGCTGTGATATGAGTAGATAA--TAGTCGACATTTCACAACC-CTTTGAGGAGTTAC DroMoj_CAF1_left AA--AACGGATGGG-------ACA--ATG-CTGAAAGCAA-TTCACACGAAACTCATCAAAATGGCTGTGATATGACTTGATAA--T-GGCTACATTTCACAACC-CCTTGAAGAGTTAC DroSec_CAF1_left AA--TATGTTTTTC-------GAT--CCG-CTGA-CCAGA-TTCGCACGAAACTCATCAAAATGGCTGTGATATGAGTAGATAA--TAGTCGACATTTCACAACC-CTTTGAGGAGTTAC DroSim_CAF1_left AA--TATGTTTTTC-------GAT--CCG-CTGC-CGAGA-TTCGCACGAAACTCATCAAAATGGCTGTGATATGAGTAGATAA--TAGTCGACATTTCACAACC-CTTTGAGGAGTTAC DroVir_CAF1_left CC--GACGAGGGCA-------ATG--A-A-TTTA-AGCAA-TTCGCACGAAACTCATCAAAATGGCTGTGATATGACTTGATAA--C-GGCAACATTTCACAACC-CCTTGAAGAGTTAC DroWil_CAF1_left TA--AGGATACCATCCATTTCGAATACTG-TTGCAGGAATACTCGCACGAAACTCATCAAAATGGCTGTGATATGAGTTGAATAAAATGGCAACATTTCACAACCCCCTTGAAGAGTTAC DroYak_CAF1_left AA--TATGTTTGAAATACAT-GAAATAAG-TTGC-CGAGA-TTCGCACGAAACTCATCAAAATGGCTGTGATATGAGTAGATAA--TAGGCGACATTTCACAACC-CTTTGAGGAGTTAC DroAna_CAF1_left GTAAGAACTCGA-TGGATCGTCCTTTTTTGAGGGGATTCTTGT---------AGC--AC--ACTTGTTGGCGTAGCATTATCCTTTAACTCG-CGTCGCGGATTTGGA--TTAT-CGT-- DroPer_CAF1_left GTAAGTATGGGG-ATGACGGTTTTTT--TTTTGTCCAAATAGTACG-AG--CCGA--AC--ACTTGTTGGG------CAC--ATGGG--------GCTGGGGGCTGGG--GCTG-CACAT DroPse_CAF1_left GTAAGTATGGGG-CTGACGGTTTTTTTTTTTTGTCCAAAAAGTACG-AG--CCGA--AC--ACTTGTTGGG------CCC--ATGGGGCTGG-GGGCTGGGGGCTGGG--TCTG-CACAT DroEre_CAF1_left GTAAGAATTGTG-TCTT-GGATCACGA-ACACTTGTTGGC-TTAGC-AT--CCAA--TCG-TTATCCCCAA-------TC--GTTATCGCACACGTAGACATTCGCAT--CGAG-CGGGG DroGri_CAF1_left GCAAGAATTGGG-TGGGCTTGGTTCGC-TCACAGTCTGCA-GATGT-AT--GCAA--GAATAAAATAATGA------GAT--ACAAACACTT-GTTGGCTTTGTTGTA--ATAT-TGTTG DroMel_CAF1_left GTAAGAATTATG-GCTT-GGATCACAA-ACACTTGTTGGT-TTAGC-AT--CCAA--TCG-TTATGCCCAA------TTC--GCGAACTGGC-TTTCTGCATTCGCAT--CGAG-CGGGG DroMoj_CAF1_left GCAAGAATTGAATGGGC-GGAGATCGT-TAAGTGTCCCAT-ATAATGAGATGCAA--AC--ACTTGTTGGT------TGT--GTTTGTTGTA-GTCCTGTTTACCGGT--G----CGGCG DroSec_CAF1_left GTAAGAACTATG-GCTT-GGATCACGA-ACACTTGTTGGC-TTAGC-AT--CCAA--TCG-TTATACCCAA------TTC--GCGAACTGCC-TTTCTGCATTCGCAT--CCAG-CGGGG DroSim_CAF1_left GTAAGAACTATG-GCTT-GGATCACGA-ACACTTGTTGGT-TTAGC-ATATCCAA--TCG-TTATACCCAA------TTC--GCGAACTGCC-TTTCTGCATTCGCAT--CCAG-CGGGG DroVir_CAF1_left GCAAGAATTGAG-TGGG-TTGGTCTTT-ACGTATCGAAGC-GACGT-TA--TCTA--TC--ACCGTAATAA------GAT--GCAAACACTT-GTTGGGTTTGTTGTAGTCCTGTTTATG DroWil_CAF1_left GTAAGAAATTCC-ATCT-TTTGCCGGA-ACGGATTCCAAA-AAAAC-AC--TTGTTGGCT-CCACTCACTT------GCA--GAGTGCAATA-ACTCCAACCACGGAC--CC-C-CTCTC DroYak_CAF1_left GTAAGAATTATG-GCTT-GGATCACGA-ACACTTGTTGGC-TTAGC-AT--CCAA--TCG-TTATCCCCAA------TTC--GCGAACTGGC-TTTCTACGTTCGCAT--CGAG-CGGGG DroAna_CAF1_left ---------ATTT--TTTATCGTAGAA DroPer_CAF1_left AGGCGGGGTACAT--ACGAGTATGTAC DroPse_CAF1_left AGGCGGGGTACAT-----------ACG DroEre_CAF1_left ---------TCCC--AGGTCACAGGTC DroGri_CAF1_left ---------GCGA--AGTAATACTCTT DroMel_CAF1_left ---------TCAT--AGGTCACGCCAC DroMoj_CAF1_left ---------ACTCAACACCTATAAATT DroSec_CAF1_left ---------TCAT--AGGTCACGGGTC DroSim_CAF1_left ---------TCAT--AGGTCAC--GGG DroVir_CAF1_left ---------GCGT--TATTTGTTACTT DroWil_CAF1_left ---------CACC--ACTGCGTTCTCG DroYak_CAF1_left ---------TCGA-GCGTTCAC-AGGT