CLUSTAL W --- LocARNA 1.4.8 - Local Alignment of RNA DroAna_CAF1_left GTT--GCT-ATAAA-AGTTGGCTCAGGTAAGGGTTGCTTTCTCGAAC-GCTGTCGTATC-G---AACA--TGTTC--GCCTGCTTGTGCGCAGAA--GTAGCAAGTTAGCCGGCGGGTTT DroEre_CAF1_left AAT--GCC-C-AGT-GGAGGGTTAAATTCTTGAATGCT-GCTATCGA-ACATGTTC-GG-TTGCAGGC--GCAAC--AGCAACATTTGCGTTAAA--ACACTAGTTTAGTCACTGAGTGC DroGri_CAF1_left ATT--ACATC-ATT-GAAGTGTGAAATAAATCTGCACA-AGAATAAA-CAACCACT-TT-TCGCATGC--T-GAA--TGCAGCGCATTCGTTAAA--GTTGATGTTTAATCAGCGTGCG- DroMel_CAF1_left TAT--GCC-C-AGC-GGAGGGTTAAATTCTTGAATGCT-ACTATCAA-ACATGTTG-GG-TTGCAACC--ACAAC--AGCAACTCTAGCGGTAAA--ATGCTATTCTAGTCACAAAAAGC DroMoj_CAF1_left ATT--ACA-T-CATTAAAGTGTTAAATGACTAGCCAAA-A---TTGAAATTAA-TCCAGACAAAAGCA--TTAAA--CGCAGCATATTCGCTTAA--GTTGCGGTTTTACCAGCGAGCGA DroSim_CAF1_left TTT--GCC-C-AGC-GGAGGGTTAAATTCTTGGATGCT-GCTATCGA-ACATGTTT-GG-TTGCAACC--GCAAT--AACCACTCTTGCGCTAAG--TTGTTACTTTAGTCATAATATGG DroVir_CAF1_left TTT--GCA-G-CAT-TACATCATTAAAATGTACAATCA-AATAGCAA-AAGGT--C-GA-ACATTACCACACAAC--AGCTTTGAATTGGCTGAA--TTAAATGTTTATCGAGCGAGCGT DroYak_CAF1_left TAT--GCC-C-AGT-GGAGGGTTAAATTCTTGAATGCT-GCTATCGA-ACATGTTC-GA-TTGCAGCC--GCAAC--AGTGACTTTTACGTTAAA--ACGCTATCTTAGTCTGTGGCAGC DroPer_CAF1_left ACA--GTG-C-AAT-TAACTTTTCAACAGTGAAACCCG-A-TTGCCC-ATTCAAGG-GT-TAAAGCA---CTTATTCCCCCATCTCTGAA-CTAGTGCTAGAAGTTAAGTCACA-CGTCA DroPse_CAF1_left TAACTTTT-C-AAC-TGTGAAACCCGATTGCCCATTCA-A-GGGTTA-AAGTATTT-AT-TCTCGAA---GCGAC--CCCCACCTCTGAA-CTAGTGCTAGAAGTTAAGTCACA-CGTCA DroAna_CAF1_left CAACATGGGGATATAGCTCAGTGGTAGAGCATTCGACTGCAGATCGAGAGGTCCCCGGTTCAAACCCGGGTGTCCCCTTGTTT--TTTGCTTATTTTT-ATTATATTTTATTTTA-CTT- DroEre_CAF1_left CAACGTGGGGATATAGCTCAGTGGTAGAGCATTCGACTGCAGATCGAGAGGTCCCCGGTTCAAACCCGGGTGTCCCCTTGTTTTTTTTGCTTATTTT--CTTATTTCTCACGCACTTAT- DroGri_CAF1_left TTCGCAGGGGATATAGCTCAGTGGTAGAGCATTCGACTGCAGATCGAGAGGTCCCCGGTTCAAACCCGGGTGTCCCCTAGGTA--AACCTTTTTATTAATTTTTTTTTCATTATTTTAA- DroMel_CAF1_left CAACGTGGGGATATAGCTCAGTGGTAGAGCATTCGACTGCAGATCGAGAGGTCCCCGGTTCAAACCCGGGTGTCCCCTTGTTT--TTTGCAATT-TT--CTTATTATTCACACACTTATT DroMoj_CAF1_left CCGCATGGGGATATAGCTCAGTGGTAGAGCATTCGACTGCAGATCGAGAGGTCCCCGGTTCAAACCCGGGTGTCCCCTGGTTT--TTTATTTTATTTA-TTTTTTTTAATTTTA-AGAA- DroSim_CAF1_left CAACGTGGGGATATAGCTCAGTGGTAGAGCATTCGACTGCAGATCGAGAGGTCCCCGGTTCAAACCCGGGTGTCCCCTTGTTT--TTTGCTGATTTT--CTTATTTCTCATACACTTGT- DroVir_CAF1_left CCGCATGGGGATATAGCTCAGTGGTAGAGCATTCGACTGCAGATCGAGAGGTCCCCGGTTCAAACCCGGGTGTCCCCTGATTT--TTTTATATTATT--TTCAATAACCATTC--ACTG- DroYak_CAF1_left CAACGTGGGGATATAGCTCAGTGGTAGAGCATTCGACTGCAGATCGAGAGGTCCCCGGTTCAAACCCGGGTGTCCCCTTGTTTT-TTTGCAAATTTT--GTTATTTCTTACGCACTTTT- DroPer_CAF1_left GAATGTGGGGATATAGCTCAGTGGTAGAGCATTCGACTGCAGATCGAGAGGTCCCCGGTTCAAACCCGGGTGTCCCCTGATTT--TTTTTG--TTTTT-TTCTTTTTCAAAGCACTTTT- DroPse_CAF1_left GAATGTGGGGATATAGCTCAGTGGTAGAGCATTCGACTGCAGATCGAGAGGTCCCCGGTTCAAACCCGGGTGTCCCCTGATTT--TTTTTTTGTTTTT-TTCTTTTTCAAAGCACTTTT- DroAna_CAF1_left TTCTTAATTAT--AAAAGTT---ATA-TACCT-T-ATATCTAAGTA-GCT-----TTTAGCTACGATTTTTG--TGTCTTCTTCTTCATA-AAAAACAATT DroEre_CAF1_left AGTATTCTTTT--CTATACA---GTTT-TTTA-A-TGATCTTTTGA-ACA-----AAAATATAACTTTGATA--TTT--TGTACGACATTGATGCGTGTTT DroGri_CAF1_left A-AAAATATTT--CGA-----CTATTTCTGTT-GATAGCTTTGCTT-TTAGTCGCATTTTAATAAGTGTATC--AGT--TAAAATACTGCTTTCGTAAGCA DroMel_CAF1_left GT-TATGTTTTCTACATATT---GTGT-ATTA-TATTTCCTTTTGG-CTT-----AAAATGTAACTCTAAGA--TTG--TTGAAATAATT-TTAG--TGCG DroMoj_CAF1_left ATCATATATTG--ATCGTAT---TTTG-CTTT-TGACAGCTATCGT-TAT-----TAAACAGTAGGCT--TATCAAC--AAAATAAAATAATCGTTTCAAC DroSim_CAF1_left GTTGTTTCATA--GGAAACTATATAGA-TAGT-TTATATAGTTTTT-AAA-----ATTACCTTTTGGCTAAA--AAT--ATAACTATTT----GACTTGAA DroVir_CAF1_left ATTT-TTGTTT--ATTAGGA-GGAGC--TTTTTGCATC--AATTAA-ATA-----GTATATTTAATCAATTT--CAG--CAATAATTAG---CTGCACATT DroYak_CAF1_left AGTAGTGCTTT--CTATACA---ATTTTTAAA-A-TGATCTTTTGG-ACA-----AAAATATAACCAGACGT--GTT--GTTATGAAGAC-GTTTTCCTCT DroPer_CAF1_left AATTGTTTTTG--CATGAAA---ATAATA-TC-T-TCTTCTAGGTATGAC-----ACAATAAAATAAGATGA--TTG--GTCC--ACTGCCCTCCCCCCCA DroPse_CAF1_left GATTGTTTTTG--CATGAAA---ATAATA-TT-T-TCTTCTAGGTATGAC-----ACAATAAAATAAGATGA--TTG--GTCC--ACTGCCCTCCCCCCCA