CLUSTAL W --- LocARNA 1.4.8 - Local Alignment of RNA DroAna_CAF1_left GATTC-CAAAC--TCGGTACTC----AAT-CTTCTCG-CCA----T--TGGTCTGGAAAGAAATGAAAAAATG-TTAAAAACTA---CTCTGCA-AAGAAGAAA-ACGA--GGTGCTTCG DroEre_CAF1_left AAAGCAGGGAT--TCTACAGGT----AGTTTCAAAAATGTATTCGAACTTCAGTTTTCAAAATGGTGGACTTG-TTTGTGTTCT---GTTTGTTGTGGGAT-----AGA--TAAATAGAT DroGri_CAF1_left ATTCCACACAC--GATACTCGATCTTCTCGCCATTTG-TCTGTGT-----GTG--T-GTGGATAAATAAATC--AAGGATTAGA---CAAGTGGAATGTATA-A-TTTT--GAGGAAGAG DroMel_CAF1_left GAAATACAGAG--TTGTTTGGA----TTGTTCAGGTA-GCT-TCAA--ATCACTTTTCAAGATGGTGGACTTG-TTTGGGTTCT---GTTTGTTTTGGGATAGA-AGGG--TAGATAGAT DroMoj_CAF1_left TCCACACGCGA--TACTCAATC--TTTTCGCCGCCAG-TCTGCAAA-ATAAAGATTAGATAAAT-ATTAGAAA-TCGGCCAACTTTTGGGATCAACTTCCT------------GCTGGAG DroPer_CAF1_left CACACG-GTAC--TCAATCTTC----T-CGCCACCGG-TCTGTGAA--GGAAGCAAGAAAATTGTGTGAAACG-CTGGACATAG---ATGGATATTTGTAT-----CTATTGGGTGCTAA DroPse_CAF1_left CACACG-GTAC--TCAATCTTC----T-CGCCACCGG-TCTGTGAA--GGAAACAAGAAAATTGTGTGAAACG-CTGGACATAG---ATGAATATTTGTAT-----CTATTGGGTGCCAA DroSec_CAF1_left GAAATACAGAG--TAGTTGGGA----TTGTTCAGGTA-GCT-TCAA--ATCACTTTTCAAAATGGTGGACTTG-TTTGGGTTCT---GTTTGTTTTGGGATATA-AAGA--TAGATAGAT DroSim_CAF1_left AA-ATACAGAG--TAGTTGGGA----TTGTTCAGGTA-GCTCACAA--ATCACTTTTCAAAATGGTGGACTTG-TTTGGGTTCT---GTTTGTTTTGGGATATA-AAGA--TAGATAAAT DroVir_CAF1_left TCCACACACGG--TACTCAATC--TTCTCGCCGCCAG-TCTGTGGGTAGGGATTAGAGAAAAATGTCAGATTA-AGCCAATTCC---CAGTGA-TATGCTG-----TGG-----CTGCAG DroYak_CAF1_left AGGGCTGGGAT--TTTTCAGGT----AGCTTCAAAAATGCATTTGAATTTCATATTTCAAAATGGTGGACTTG-TTTGGGTTCT---GTTTGTTTTGGGAT-----AGA--TAAGTAGAT DroWil_CAF1_left TT-CCACACACGGTACTCAATC--TTTTCGCCATTGG-TCTGAGGA-----------AGAAGTAGAGAAAACATTTAGTTTAGA---TTAAACTTCTAAAAAGGCCTCA--AAGCAAAGG DroAna_CAF1_left GGTTAGG-AGCTCAGTTGTGCATT-AGTCTAAGCACGCCCTG-GA-GC-ACCC---GCAGCTGCTTC-ACGTGCACCTGAAGTGCACA-CAGCCAC-AGGTGGCCGCCAAGAGTGCTCAT DroEre_CAF1_left AGGAATTCGCCTCAGTTGTGCATT-ATTCTAAGCAGACCTTG-GA-GC--CCC---GCGACTGCATT-ACGTGCACCTGGAGTGCACA-CAGCCAC-AGGTGGCCGCCAAGGATGCTCAT DroGri_CAF1_left GAGGAGTTGCCTCAGTAGTGCTATAGTTCTAAGCATCACATG-GACGCCACCC---ACAGCCGTTTA-ACATGCACCTGGAGTGCACA-GAGCGG--AGCAG-ACACCAAGGATGCTCAT DroMel_CAF1_left AGGAATTCGCCTCAGTTGTGCATT-ATTCTAAGCAGCCCTTG-GA-GC--TCC---GCGACTGCTTC-ACGTGCACCTGAAGTGCACA-CAGCCAC-AGGTGACCGCCAAGGATGCTCAT DroMoj_CAF1_left TGGTAGCTGTCTCAGTAGTGCTATAGTTCTAAGCAACACGTG-GA-CG--CTGCCCGCAGCTGCTTC-ACGTGCACCTGGAGTGCACA-CAGGCGG-TCAGACG--CCGCGCGTGCTCAT DroPer_CAF1_left GAGATTTTGCCTCAGTTGTGCATT-GTTCTAAGCGA-CCCAA-GC-GC-ACCT---GAAGCTGCTTC-CCGTGTACCTGAAGTGCACA-CAGCTAC-CGGTGAACGCAAGGGCCGCTCAT DroPse_CAF1_left GAGATTTTGCCTCAGTTGTGCATT-GTTCTAAGCGA-CCCAA-GC-GC-ACCT---GAAGCTGCTTC-ACGTGTACCTGAAGTGCACA-CAGCTAC-CGGTGAACGCAAGGGCCGCTCAT DroSec_CAF1_left GGGAATTCGCCTCAGTTGTGCATT-ATTCTAAGCAGCCCTTG-GA-GC--CCC---GCGACTGCTTC-ACGTGCACCTGGAGTGCACA-CAGCCAC-AGGTGGCCGCCAAGGATGCTCAT DroSim_CAF1_left GGGAATTCGCCTCAGTTGTGCATT-ATTCTAAGCAGCCCTTG-GA-GC--CCC---GCGACTGCTTC-ACGTGCACCTGGAGTGCACA-CAGCCAC-AGGTGGCCGCCAAGGATGCTCAT DroVir_CAF1_left GATCAGCTGTCTCAGTAGTGCTATAGTTCTAAGCGTCTCGTG-GACGCCACCC---GCAGCTGCTTA-ACGCGCACCTGGAGTGCGCA-CAGGC---GGGCAGACGTCACGCACGCTCAT DroYak_CAF1_left AGGAATGCGCCTCAGTTGTGCATT-ATTCTAAGCAGACCTTG-GA-GC--CCC---GCGACTGCTTC-ACGTGCACCTGGAGTGCACA-CAGCCAC-AGGTGGCTGCCAAGGCTGCTCAT DroWil_CAF1_left ACGAATCTCTCTCAGTTGTGTTTA-GATTTACGCAAAACAAAATG-CC-ATCA---GCAACTGCTTCAATGTGCACCCAAAGTCCACAGCAGCTGCCAGATGAAACACATGTTTGCTCAT DroAna_CAF1_left GGCCACATGATGCCATGTTCTGTACCCCTGC--ACAACCTCATCATCGACAGTCAAGAAATC-----G-TTAATAAA---GTGTAAG-GGA-AACAAACCTCAACAGAGATGCGTTTCTC DroEre_CAF1_left GGCCACATGATGCCATGTTCTGTACCCCTGC--ACAACCTCATCATAAGCTAGGAACAAGTA---TGGTAAGTGAAT---AGAGAGGTGAGAAACAAACCTCAACGGAGATGCGCTTCTC DroGri_CAF1_left GGCCACATTTTGCCATGTTCCGTACCCCTGC--ACAACATCATCATGGACAAAGAAGATTCT---C-T-AAAGGTAC---A-ATAACAGAA-TACACACCTCAACTGAGATGCGCTTCTC DroMel_CAF1_left GGCCACATGATGCCATGTTCTGTACCCCTGC--ACAACCTCATCATAAGCTAGGAATAGGGA---AGGTAAGTGAAT---AAAGATGAGAACAACAAACCTCAACGGAGATGCGCTTCTC DroMoj_CAF1_left GGCCACATAATGCCATGTTCTGTACCCCTGC--ACAACATCATCATAGACAGAATGAAATAT-----CTGCTAGAAT---ATCTCTTTGTT-TACCTACCTCAACGGAAATTCGCTTCTC DroPer_CAF1_left GACCACATAATGCCATGTTCTGTACCCCTGC--ACAACATCATCATCAGCAGAACTCTAGTC-----T-ACAGGAAG---TGTGATGCGAA-AACTAACCTCGACAGAAATGCGCTTCTC DroPse_CAF1_left GACCACATAATGCCATGTTCTGTACCCCTGC--ACAACATCATCATCAGCAGAACTCTAGTC-----T-ACAGGAAG---TGTGATGCGAA-AACTAACCTCGACAGAAATGCGCTTCTC DroSec_CAF1_left GGCCACATGATGCCATGTTCTGTACCCCTGC--ACAACCTCATCATAAGCTAGGAATAGGAA---AGGTAAGTGAAT---AAAGAGGAGAACAACAAACCTCAACTGAGATGCGCTTCTC DroSim_CAF1_left GGCCACATGATGCCATGTTCTGTACCCCTGC--ACAACCTCATCATAAGCTAGGAATAGGGA---AGG-AAGTGAAT---AAAGAGGAGAACAACAAACCTCAACAGAGATGCGCTTCTC DroVir_CAF1_left GGCCACATTTTGCCATGTTCTGTACCCCTGC--ACAACATCATCATGGACAGCACAATATGACAGCGAAACGTGAAAACAAAAGTCTTGGTTTACACACCTCTACGGAAATGCGCTTCTC DroYak_CAF1_left GGCCACATGATGCCATGTTCTGTACCCCTGC--ACAACCTCATCATAAGCTAGGAATGAAAT---GGTAAAGTGCGT---AAGGAGTTGAAAAACAAACCTCAACGGAGATGCGCTTCTC DroWil_CAF1_left GGCCACATACTGCCATGTTCTGTACCCCTGCGCACAGCTTCATCATTGGCTAAGAGAGATCG---GTGTGGGGGAAG---A---------A-CCTTTACCTCGACAGAGATGCGTTTCTC DroAna_CAF1_left GCCGTAGACTTCCGATCCGGGGACGAAG------TTCC DroEre_CAF1_left GCCGTAGACCTCGGATCCGGGTACAAA----------- DroGri_CAF1_left GCCGTACACCTCCGAGCCGGGCACAAAG------T-TG DroMel_CAF1_left GCCGTAGACTTCGGATCCAGGTACAAA----------- DroMoj_CAF1_left GCCGTAGACTTCGGAGCCGGGCACAAAG--------TT DroPer_CAF1_left TCCGTAGACTTCGGATCCAGGCACAAAG------T-TG DroPse_CAF1_left TCCGTAGACTTCGGATCCAGGCACAAAG------T-TG DroSec_CAF1_left GCCGTAGACTTCGGAGCCGGGTACAAA----------- DroSim_CAF1_left GCCGTAGACTTCGGAGCCGGGTACAAA----------G DroVir_CAF1_left GCCGTACACTTCCGAGCCGGG----------------- DroYak_CAF1_left GCCGTAGACCTCGGATCCGGGCACAAA----------- DroWil_CAF1_left GCCATAGACCTCAGAGCCGGGCACAAAATTTCTGG-TC