CLUSTAL W --- LocARNA 1.4.8 - Local Alignment of RNA DroEre_CAF1_left GCTCCACGCCGTCG---AAATACCGCCACTTAAA-TTTGTCTCAGCTGATAA-GTTGTCT-TTCACTC-GGGTTGTTT-ATGAACTCGTTTTGC-AGCGA--GCCAAATATAGACCTTCG DroGri_CAF1_left CTCGTGAG-TACCG---TTTTGAT-TTATTCACA-CTCTCGCTTACTGATAA-CTTAACG-AATTCGT-TTCGGATGC-TCTTGTATGCGTTTT-GGCACACTAAGTGTATCGACCTTCG DroMel_CAF1_left CCTCCACGCCGACG---AAATACCGCCACTTAAA-TTTGTCTCAGCTGATAA-GTTGTCT-TTCACTC-GGGTTGTTT-ATGAACTCGTTTTGC-AGCGA--GCCATATATAGACCTTCG DroMoj_CAF1_left TGATTTATTCAACG---TTCGCTCGCTTGCTCACTCGCTCGCTCGCTGATAA-A-CACCA-TTCGCGT-CGTTTGCTC-ATTTATGCGTTTTGGCGCA-C--GTTGCTCATCGACCTTCG DroPer_CAF1_left AAACGATCGCCTCACCGCTC-TTCTTTC-GCCGC-CTCTCTCTCACTGATAA-GTCGCCA-TTAATCC-AATTGGCTT-TTGACTTCGTTTTGC-GGC-C--TCCGAATATAGACCTTCG DroPse_CAF1_left AAACGATCGCCTCACCGCTC-TTCTTTC-GCCGC-CTCTCTCTCACTGATAA-GTCGCCA-TTAATCC-AATTGGCTT-TTGAGCTCGTTTTGC-GGC-C--TCCCAATATAGACCTTCG DroSec_CAF1_left CCTCCACGCCGTCG---AAATACCGCCACTTAAA-TTTGTCTCAGCTGATAA-GTTGTCT-TTCACTC-GGGTTGTTT-ATGAACTCGTTTTGC-AGCGA--GCCATATATATACCTTCG DroSim_CAF1_left CCTCCACGCCGTCG---AAATACCGCCACTTAAA-TTTGTCTCAGCTGATAA-GTTGTCT-TTCACTC-GGGTTGTTT-ATGAACTCGTTTTGC-AGCGA--GCCATATATAGACCTTCG DroVir_CAF1_left GAGCACA-ACAGAC---ATACGTTTTGATTTATT-CACTGCTTG-CTGATAA-CTCAACTAATTCACCACGTTCGCTC-ATGTACGCGCTTTGG-CGCAC--ACAACACATCGACCTTCG DroWil_CAF1_left TATAAAAAACCGAA---ATCGAATTATGTATTCC-ACCGGTCCG-ATAAGTT-GTCGCACATTCACTTTTTG-GCTTTTCAA-TCTGGTTTGGC-AGCGT--GCTATATATATACCTTCG DroYak_CAF1_left CCGCCGCGTCGTCG---AAATACCGCCACTTAAA-TTTGTCTCAGCTGATAA-GTTGTCT-TTCACTC-GCGTTGTTT-ATGAACTCGTTTTGC-AGCGA--GCCATATATAGACCTTCG DroAna_CAF1_left TCAAAGCT-CGTTT---TTCCCTCCCCGCAGCCA-AAAAACTAATTTCGGCTTTCATCTG-TTCGCCC-GTTCTCTTC-ATGAACTCGTTTAGC-AGCCG--TCCATATATAGACCTTCG DroEre_CAF1_left ATAGCTCAGTTGGTAGAGCGGTGGACTGTAGATTGGCAT---TA---C---GA--GTGTAGACATCCATAGGTCGCTGGTTCAAATCCGGCTCGAAGGATCGGAGCATTTTTTTTATTA- DroGri_CAF1_left ATAGCTCAGTTGGTAGAGCGGTGGACTGTAGTGAGAAAT---TG---C---AACGTTGTAGACATCCATAGGTCGCTGGTTCAAATCCGGCTCGAAGGATCTCAATTTTTTT---GTTT- DroMel_CAF1_left ATAGCTCAGTTGGTAGAGCGGTGGACTGTAGATTGGGAT---TA---C---GA--ATGTAGACATCCATAGGTCGCTGGTTCAAATCCGGCTCGAAGGATCGGAAAATTTTT---TTTT- DroMoj_CAF1_left ATAGCTCAGTTGGTAGAGCGGTGGACTGTAGAGTGAAAA---TA---CTGAAA--GTGTAGACATCCATAGGTCGCTGGTTCAAATCCGGCTCGAAGGATCTTGTAAAATTT---TTTTC DroPer_CAF1_left ATAGCTCAGTTGGTAGAGCGGTGGACTGTAGAAAGAGTT---TC---C---TA--GTGTAGACATCCATAGGTCGCTGGTTCAAATCCGGCTCGAAGGATTCCAACTTTTTT---TTTTA DroPse_CAF1_left ATAGCTCAGTTGGTAGAGCGGTGGACTGTAGAAAGAGTT---TC---C---TA--GTGTAGACATCCATAGGTCGCTGGTTCAAATCCGGCTCGAAGGATTCCAACTTTTTT---TTTT- DroSec_CAF1_left ATAGCTCAGTTGGTAGAGCGGTGGACTGTAGATTGGGAT---TA---C---GA--ATGTAGACATCCATAGGTCGCTGGTTCAAATCCGGCTCGAAGGATCGGAATATTTTT---TTTT- DroSim_CAF1_left ATAGCTCAGTTGGTAGAGCGGTGGACTGTAGATTGGGAT---TA---C---GA--ATGTAGACATCCATAGGTCGCTGGTTCAAATCCGGCTCGAAGGATCGGAAAATTTTT---TTTT- DroVir_CAF1_left ATAGCTCAGTTGGTAGAGCGGTGGACTGTAGAGTGATA----TAC--A---AA--TTGTAGACATCCATAGGTCGCTGGTTCAAATCCGGCTCGAAGGATCTCAGTTTTTTGG--TTTT- DroWil_CAF1_left ATAGCTCAGTTGGTAGAGCGGTGGACTGTAGAGCGGTAAATTTAC--A---TT--AAGTAGACATCCATAGGTCGCTGGTTCAAATCCGGCTCGAAGGATTTTTTTGTT-TGT--CTAA- DroYak_CAF1_left ATAGCTCAGTTGGTAGAGCGGTGGACTGTAGATTGGCAT---TACGAC---GA--GTGTAGACATCCATAGGTCGCTGGTTCAAATCCGGCTCGAAGGATCGGAATCTTTTT---TTTT- DroAna_CAF1_left ATAGCTCAGTTGGTAGAGCGGTGGACTGTAGAG---GA-----T---C---AA--GTGTAGAAATCCATAGGTCGCTGGTTCAAATCCGGCTCGAAGGAATTATTTTTAAAC---ATTT- DroEre_CAF1_left ---G-C--CTTTTCTTAT-TGCGAAAGGGTAAAT---TG-CAATTGT-GGAAATACATTTTTGAGGAAACATGT--TGCAGT-A-GGTAGCA-TA-TATCTTAAA DroGri_CAF1_left ---TTC--TAATTATTTTCTTTTAATTG-AGAGCATTGT-TTTTATATTAAAAGC----ATTTATTGTGGCTGGC-C-ACTA-AGTTACATTATT-TTAAAATGC DroMel_CAF1_left ---C-C--ATATACCTGA-AAAGTATTGCGAAAA-GTTT-GGATTAA-ATTGCATTTCTAAAAATGCATTTTTGT--CAGTC-A-TATTGAAGTA-GCGAGCACT DroMoj_CAF1_left TTTT-A--TTTATTTAAAAAAATTGTAATTAATA-AAAT-GAGTCAT-ATAAATATAGGAAAAAATATATTT-TA-TGCGTA-T-TTACATAA-C-AAATTGGGT DroPer_CAF1_left ATTC-A--GTTTCTTCTTTTTTGGGATTTGTTTA-GTCATATTAGAG-CAAAAAATATTAAAAAA----TTT-GT-TTAGTAAT-TGTTG-TA---GACCCTTGT DroPse_CAF1_left ---T-A--ATTCAGTTTC-TTCTTTTTTGGGTTT-TGTT-TAGGCGT-ATTACAGCAATAAATAATTAAGAA-AA-TGTATA-A-TAATATTTTT-AAACCCTTG DroSec_CAF1_left ---T-C--ATACGCCTGA-AAGGTATTGCGAAAA-GTTT-GCAATAA-ATTGCAATTCTAAAAATGCATTTTTGA-GGAGTC-A-TGTTAAAGGA-AAGAGCA-C DroSim_CAF1_left ---C----ATACACCTGA-AAAGTATTGTGAAAA-GTTT-GCAATAA-ATTGCAATTCTAAAAATGCATTTTTGA-GGAGTC-A-TATTGAAGTA-GAGAGAACT DroVir_CAF1_left ---T-C--TTTTTTTTTT-TTTA-AATCCTGTGT-TTAT-GTAATGT-GTTTATT--TAACACATTTAATTATTGCCAGTCG-A-ATTTATGAGA-TATTTAATA DroWil_CAF1_left ---A-C--AATTAATCAA-AATC-AGATCTGATA-TGTC-AAAACAT-TAACTTT--TAAAATAACATTTTTAA--TAAGCT-G-ATATAAAGCC--ATTATCTT DroYak_CAF1_left ---C-A--T-TGCAAAGA-AATGGCAGTAAATTG-CAAT-TCTGGAA-ATACAGTTTTGAGTACCTGTGACCTGT-TAATAA-A-GCCAACTTTC-CATTTTATA DroAna_CAF1_left ---T-TTTTTTTTGTATA-AGTATTTATATATTTTTTTATCATACAA-ACTTTTTTTTTCAAAGGGAATGCTTAT-TTTAAT-A-CATACTTTTAGAACCAAAAT