CLUSTAL W --- LocARNA 1.4.8 - Local Alignment of RNA DroAna_CAF1_left TAAAAATAGTTCGAGTACTTGATTTCAGTTGC-GGTTATCGG---GGGTTCTGCTGATAAGAACCGGGCGGTTTCATTTGTT-TCATTGGAAGTTTAGTTTTGTTCGAGGCGAGACTCGA DroEre_CAF1_left TCCTATCAAAT-GGGTTCAATA-----AGC-T-TCAGTTCTT---AAAGATTCTTGATA---AGAAGTTAGAGTGGGTTTGA-CAACAAATAGTAGTTTTC---ACAATAAACTTTTTCG DroMel_CAF1_left GTTTTTATATT-ACCTTTAATT-----AGC-T-TCAGTTCAT---AGAGATTCTTGATA---AGAAGTTGGATAGGGTTTGA-CCAGAAATAGTACTTTTC---ACATCAAAATTTTTCG DroMoj_CAF1_left TTACGGCATTT-TATTGACATA-----ATT-A-TTGTTCGAT---TATTCACAATAAAC---ACAATCAAGCTCTCA-TGGAGTTGAG-AAGTCTCATTGG---GCCGGCGGCTGGGAAG DroPer_CAF1_left TTCAA----TA-GTTGCTAATA-----AGT-T-TCATTATATGGATGGATTCTTTGATA---AGAAC-TAAAAACTGTATTA-TTGGAAATTGGGTCTTGA---GCAGAGCTTCTCACAA DroPse_CAF1_left ACACTTCAATA-GTTGCTAATA-----AGT-T-TCTCTATATAG----GTTCTTTGATA---AGAAC-TGAAAACTGTATTA-TTGGAAATTGGGTCTTGA---GCAGAGCTTCTCACAA DroSec_CAF1_left TCCTATCAAAG-GGGTTCAATT-----AGC-T-TCAGTTCAT---AGAGGTTCTTGATA---AGAAGTTGGAAAGGTTTTGG-CCAGAAATAGTACTTTTC---ACAATTAAGCTTTTCG DroVir_CAF1_left ACATAATTATC-GTTTGTTTAT-----TG--G-TCATAGAAT---TGGTTGAAAAGAAT---AAAGAGAGCGTTGTCAAAGA-GTTCAGAAGCCTCATTGC---GCCGCCGGCAGGCAAC DroWil_CAF1_left AAACA-CAATT-TTAATGATGT-----TTG-TCAAACAACAA---CAACAACAAGAGGT---AGAAC-ACTTCCGGAAACTC-TGACGAAGGTCGTTTTGG---TCCCAGCT-TGAAAAC DroYak_CAF1_left TCATATCAAAT-GGGTTCATTT-----AGC-T-TCAGTTCTC---AGAGGTTATTGATA---AGAAGTTAGAATGTGTTTGC-TCACAAATACTACTTTTC---ACAATAAACTTTTTCG DroSim_CAF1_left TCCTATCAAAG-GGGTTCAATT-----AGC-T-TCAGTTCAT---AGAGATTCTTGATA---AGAAATTGGAAAGGTTTTGT-CCAGAAATAGTACTTTTC---ACAACTAAGTTTTTCN DroAna_CAF1_left GAGACGAGGTGGCCGAGAGGTTAAGGCGTTGGACTGCTAATCCAATGTGCTCTGCACGCGTGGGTTCGAATCCCATCCTCGTCGAACCCTATTTTTTA--ATTTATTTT-T----ATTAT DroEre_CAF1_left AAGACGAGGTGGCCGAGAGGTTAAGGCGTTGGACTGCTAATCCAATGTGCTCTGCACGCGTGGGTTCGAATCCCATCCTCGTCGGAGGATACCCTTTTTGAAAATATGT-AC-A-TACAT DroMel_CAF1_left AAGACGAGGTGGCCGAGAGGTTAAGGCGTTGGACTGCTAATCCAATGTGCTCTGCACGCGTGGGTTCGAATCCCATCCTCGTCGGAAAATATCCTTTTTAAATAAAATT-TT-G-CTTAT DroMoj_CAF1_left AAGACGAGGTGGCCGAGTGGTTAAGGCGTTGGACTGCTAATCCAATGTGCTCTGCACGCGTGGGTTCGAATCCCATCCTCGTCGCACTTGGTTTTTGG--TCAAATTCTTTT-A-ATTTG DroPer_CAF1_left GAGACGAGGTGGCCGAGAGGTTAAGGCGTTGGACTGCTAATCCAATGTGCTCTGCACGCGTGGGTTCGAATCCCATCCTCGTCGAGTTGCAATTTTTGCAAGTAGGATA-GT-T-CCTAT DroPse_CAF1_left GAGACGAGGTGGCCGAGAGGTTAAGGCGTTGGACTGCTAATCCAATGTGCTCTGCACGCGTGGGTTCGAATCCCATCCTCGTCGAGTTGCAATTTTTGCAAGTAGGTTT-GTTT-CCTAT DroSec_CAF1_left AAGACGAGGTGGCCGAGAGGTTAAGGCGTTGGACTGCTAATCCAATGTGCTCTGCACGCGTGGGTTCGAATCCCATCCTCGTCGAAATATCCTTTAT-AAATATATTTT-TG-C-CTTTT DroVir_CAF1_left ATGACGAGGTGGCCGAGTGGTTAAGGCGTTGGACTGCTAATCCAATGTGCTCTGCACGCGTGGGTTCGAATCCCATCCTCGTCGCAATGGCTTTTTTT-GTCAAATTTA-TA-TGTTGGT DroWil_CAF1_left ATGACGAGGTGGCCGAGTGGTTAAGGCGTTGGACTGCTAATCCAATGTGCTCTGCACGCGTGGGTTCGAATCCCATCCTCGTCGAGAACTTTCTCTGA-TATTTTGTTT-GT-T-TTGTT DroYak_CAF1_left AAGACGAGGTGGCCGAGAGGTTAAGGCGTTGGACTGCTAATCCAATGTGCTCTGCACGCGTGGGTTCGAATCCCATCCTCGTCGTTAAATATCCTTTTTATTTAT-TTT-TT-T-TATTC DroSim_CAF1_left NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-NN---NNNNN DroAna_CAF1_left TAGTTTTTATTAATT-AAGGATTAGATTAATT---TTAA-GCAT--GTT-----TAAGAGAAATT----TTTGTTTCCTACGGTTACA--A--GTGGTATTTGTATTTG DroEre_CAF1_left ATTGAATATTATCTT-TAT--T-ACTCTGTTT---TGAA-TTTTAATTT---TTTATTTCCTCCT----ATC-AAAAGTAT-ATTGAT--TTTTACG--CTGGAAAGAT DroMel_CAF1_left TGCTTTTATTCTTTT-CAG--T-TT-TATTTAT--TTATTTTATTATTG---CTTTCGTTTAAAC----AAA-AGTATATT--GATTT--TAACCCT--AGAAAAGATT DroMoj_CAF1_left CATTCAGTTAGAC-T-TAT--A-TTATTGCAC---CTAT--TCTAATTTATTAGTAACGCAACGC----TTA-CT----CT-AATTAA--TTATTTA--TTTCAATGTT DroPer_CAF1_left AAATGTTATTCTTTT-TTG--T-ACACAGTAA---CCTA-TTAA----A---TAAGTGTCATAGG----ACT-TGTATTAT-CTTGTTGGGAGATCA--AATAACTGAT DroPse_CAF1_left AAATGTGATTCTTTT-TTG--T-ACACAGGAA---CCTA-TTAA----A---TAAGTGCCATAGG----ACT-TGTATTAT-CTTGTTGGGAGATCA--AATAACTG-A DroSec_CAF1_left TGCTCTTATCTGAGT-TCT--A-ATGATGTTT---TCAA-GTCTAAAAT---TTC-AGTAAAAGC-----TA-AGTACATG--TGATT--CTAACCTAAACTGAGAATG DroVir_CAF1_left AT-TTTTAATGCTTTACTA--T-TAGATTAATTTTATTG----CTATTT---AATATT-ATCAAT-----AA-AAGACATT--TCCGC--TTTTCTT--TTCAACTACC DroWil_CAF1_left AG-CTTTAACCGTTA-TTT--G-TTAAAGATC---AATA-TTTAAATTT---TAA-A----TATTATCGAAC-CCATCAAA-CAAAAA--AGCCAAG--CTTCAAGATG DroYak_CAF1_left TTTTACAGTTTTATA-TTT--T-GCTTTTAAC---CTAA-CAAAA-GTA---TATTGAGTTTATC----ACT-AA---AAG-ANNNNN--NNNNNAA--AAAAATTAAC DroSim_CAF1_left NNNNNNNNNNNNNNN-NNN-NN-NNNNNNNNN---NNNN--NNNNNNNN---NNN-NNNNNNNNN----NNN-NNNNNNNN-NNNNNN--NNNNNNN--NNNNNNNNNN