CLUSTAL W --- LocARNA 1.4.8 - Local Alignment of RNA DroAna_CAF1_left G-GAAACC-CCTAATA-ATGG-T----CATTAA-AACGATTA-AAGAAGTCA---AGTACAATCC-AATAACGTTTAATGG---TA---ATTAAGTCATTTTTAAAACACAAAA-----T DroGri_CAF1_left ATCATTAG-TGA--TT-TTTCTT----TT-TTT-TTCAACAAAAGATCTAAGCA-ATTTAACTTAAAGTTCATTAAGTAAAAATCAAATG-A----AAAATTGAAGCTAA--T----GTT DroMel_CAF1_left TGACAAGGGACCCCAA-TGAT-G----TTCATT-A-ACACGC-TTAA-AGAACTCAAGTACGCAACA-ATAACGTTTTGAAGCAATAACAGG----A-GATTGAAAATTATATC-----T DroPer_CAF1_left CGTTCATT-GACAAGA-TTAT-A----GAAGTC-AAGTACGC-AGCGATAAC---ATTTTAGCAC--ACACTTATCAATGT---TT---TTT--TACTCAA-AAAATCAATAAA-----A DroPse_CAF1_left CGTTCATT-GACAAGA-TTAT-A----GAAGTC-AAGTACGC-AGCGATAAC---ATTTTAGCAC--ACACTTATCAATGT---TT---TTT--TACTCAA-AAAATCAATAAA-----A DroVir_CAF1_left AGCTGCGGCAGC--ACAAATTTG----GT-TTT-TGTTTACAAAGAAAATGAAA-TACGAAAAGCGTTCAAAGAAAAATTAACTTAAACCCT----G-AAGTGTAAAACA--T----TTA DroWil_CAF1_left CAC---ATTAACATGA-TTAT-A----GAAGTC-AAGTACGC-TATATATAAAAAAAAAACCCAATA-AAATAAACACAAATC---------------ATTTAAAAACAAAAATCTATGC DroYak_CAF1_left TAAAAAACAA-------AATG-ACATGGAACCCTAATAAC-G-T-------TCATTAATACGCGTAA-AGAACACAAGTACGTAGCA-ATAA----T-GTTTATATAATGAATT-----A DroEre_CAF1_left AAAACAAA--ATGACA-GGGA-A----CCCTAA-TAATGTTC-ATTAACACG---CTTAAAGAAC--TCAAGTACG-TAGC---AA---TAA--CATTCAT--AAAATATATTAA----A DroAna_CAF1_left AA----C-AATTACCAGTGAATTG-GTAGCAAAAATATTAA-TCCGCCCCCGGGTGGACTCGAACCACCAACCTTTCGGTTAAAAGCCGAACGCGCTAACCGATTGCGCCACGGAGGCCA DroGri_CAF1_left TA----AGA-AGCATAA-CATGAA-A------AAAATTATT-GTCGCCCCCGGGTGGACTCGAACCACCAACCTTTCGGTTAACAGCCGAACGCGCTAACCAATTGCGCCACGGAGGCTG DroMel_CAF1_left AA----ATG-TATAGAG-GATAAAAA------AATGTG-TTTGTCGCCCCCGGGTGGACTCGAACCACCAACCTTTCGGTTAACAGCCGAACGCGCTAACCAATTGCGCCACGGAGGCCA DroPer_CAF1_left GT----G-GGAAAATATTGGGCAA-A------AAGTTTTTG-TCCGCCCCCGGGTGGACTCGAACCACCAACCTTTCGGTTAACAGCCGAACGCGCTAACCAATTGCGCCACGGAGGCCA DroPse_CAF1_left GT----A-GGAAAATATTGGGCAA-A------AAATTTGTG-TCCGCCCCCGGGTGGACTCGAACCACCAACCTTTCGGTTAACAGCCGAACGCGCTAACCAATTGCGCCACGGAGGCCA DroVir_CAF1_left CA----ATG-AAAAA---AAAAAT-A------AAAAGTTGA-GTCGCCCCCGGGTGGACTCGAACCACCAACCTTTCGGTTAACAGCCGAACGCGCTAACCGATTGCGCCACGGAGGCCA DroWil_CAF1_left CA----AGA-AAAACCC-AATAAA-A------AAATCATTTTG-CGCCCCCGGGTGGACTCGAACCACCAACCTTTCGGTTAACAGCCGAACGCGCTAACCGATTGCGCCACGGAGGCGA DroYak_CAF1_left AA----AATTACAAAAG-TGTTAA-A------AAAGTGTTT-GTCGCCCCCGGGTGGACTCGAACCACCAACCTTTCGGTTAACAGCCGAACGCGCTAACCAATTGCGCCACGGAGGCCG DroEre_CAF1_left ATTACAACA-AAAACC--GTTAAA-A------AAAGTGCTT-ATCGCCCCCGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN DroAna_CAF1_left CGGAGACGCTCG-AGCAGCAAA-AAAATTCACA-AG--TCGGTTGTCAAAGCTGCCT--TGGTGCGAG-CTAAGTTCTAGTGCGGCC-AGCGACACGCTGGA----ACAAATCG-CCTCC DroGri_CAF1_left TTGTA-CACCAG-CTGTCTAAT-CTCACTTT---GC--TACTACACCC-AA-GTAGTTCTTATTAGAA-TTAT--GTTTCTT---AT---TG---TTAGGCTCT-GGTTTCAAG-TAAGT DroMel_CAF1_left TGTAAGGCGGAAAAAAAAT-TTTCTCAATTTCAGAA--CACAAGCAAA-AA-CAAAT-CAAAAAGGAA-AATA--AATAAAT---TC---TA---ATAAGAACTGCTAAGCATCTTAA-T DroPer_CAF1_left TGCAGGCAGCGA-AAAATCAGC-ACCAATTGTT-GT--TAAAACATCA-GA-TTAAC--AAGCATCCC-GAAA--TAAGTAT---GT-TATA---ATGCTTAAG-AAGTCTGTA-ATTTA DroPse_CAF1_left TGCAGGCAGCGA-AAAATCAGC-ACCAATTCTT-GT--TAAAACATCA-GA-TTAAC--AAGCATCTC-GAAA--TAAGTAT---GT-TATA---ATGCTTAAG-AAGTCTGTA-ATTTA DroVir_CAF1_left TGTTTGCCGGGT-GAATTTTTA-TGTACTTG---GACCTACCAAAAAA-AA-AAACACAATATGCTAA-TGTT--CAAATTT---TA---AT---AGAAATTCT-CTCACTTTG-TATGA DroWil_CAF1_left TGTCTACTCCCGAAAAATT-TGTAAATATATTTCCG--TTTACTTAAA-AG-AGATG-GCAAGTGTAT-AAAA--TTCTTAT---CT--------TGTAATTCTAAATAAAAATTATAAG DroYak_CAF1_left TGGAAACTTCGA-AAAATGTTC-TAAATTTC-AAAA--CATAAACAAA-AA-CCTG---AAAGAAATTAAAAA--G-AAGCA---TAAATAA---ATTCTAATA-AGAAGTGCT----TA DroEre_CAF1_left NNNNNNNNNNNN-NNNNNNNNN-NNNNNNNNNN-NN--NNNNNNNNNN-NN-NNNNN--NNNNNNNNN-NNNN--NNNNNNN---NN-NNNN---NNNNNNNNN-NNNNNNNNN-NNNNN DroAna_CAF1_left GTGGCGCAA-----TCGGT-TAGCGCGTTC DroGri_CAF1_left TANN--NNN---NNNNNNN-NNNNNNNNNN DroMel_CAF1_left TCAC--AAC---AGCAACGACGT-CACGTG DroPer_CAF1_left TAAG--TAG---AAGGGTC-CCCAGCCGAA DroPse_CAF1_left TAAG--TAG---AAGGGTC-GCCAGCAGAA DroVir_CAF1_left AAAT--TAA---TTAATAC-CCAAACCATC DroWil_CAF1_left ATTA--AAG---AAATAAA-TTAAATTGGT DroYak_CAF1_left GCAG--CTTAATTCGCTGT-AAACTCAACA DroEre_CAF1_left NNNN--NNN---NNNNNNN-NNNNNNNNNN