CLUSTAL W --- LocARNA 1.4.8 - Local Alignment of RNA DroAna_CAF1_left AT-------CAAGTCTGATAAAAAGATTTAGG-CTCAA-TCGTTTCTGAAAACTATTA-AAACTATT---ATTAAAAAAAATATCAA-AAACTTATAGTTGTTAGATTC--A-GAGTTTC DroEre_CAF1_left GA---ATGTTC-----CAGTCCATAAAACTA--TTATG-TATATTTTGT--ATATATT-TTATGCTTATAAATCTGCAAAAAAAGATGACTATTTAAACTTCACAACTA--T-TGTGTTC DroGri_CAF1_left TG---AACAGA-----AAATATGTA--TTTC---TAAA-G--GGAACTGAAAAACTAA-TGATTGGT---ATATTTTAATC--CGTAGATACTCCAAGTTTCTAAGCAT--TTCAGGTAT DroMel_CAF1_left CC---AATCGA-----TAAATGTTTTAATAT--CCCTT-CAGATATTTTATGATTATA-TATCTGCAA--AAAAAAGAGATTACGATGGAGCTTAAAACTCCACTACTG--T-TCTGTTC DroMoj_CAF1_left GAAACAATTGT-----GAATGGAACGACTT----GTTG-CTGATTTG--CTGTATTCC-TTCGAGTACCAATAAAAAA-AAAAAGTTTTTATAAACATTGA-ATGACTT-CA-TTATAAT DroPer_CAF1_left CTG-CTAGACA-----TAAATTAACTGGAA----AAAA-GGGTTATT--ATCCATTGT-AATCAGCCAATATACATAC-AAATCTGTAATAAAAGAATTAT-CCAACATTTG-CAATCTC DroPse_CAF1_left ACTGCTAGACA-----TAAATTAACTGGAA-----AAA-GGGTTATT--ATCCATTGT-GATCAGCCAATATACATAC-AAATCTGTAATAAAAGAATTAT-CCAACATTTG-CAATCTC DroSec_CAF1_left TC--CAATCGA-----TAAATGTTTTAATAT--CCCTT-CAGATATTTTATGATTATA-TATCTGCGA--AA-AAGGAGATTACAATGGAGCTTAAAACTCCACTACTG--T-TTTGTTC DroSim_CAF1_left A-----ATCGA-----TAAATGTTTTAATAT--CCCTT-CAGATATTTTATGATTTTA-TATCTGCAAAAAAAAAAGAGATTACGATGGAGCTTAAAACTCCACTACTG--T-TTTGTTC DroYak_CAF1_left GTTTCATGTGA-----TAAAACTATTACGTACACCTGTCGCATAT-TTTATGCTATTAAATCTGC-AAA-AAAATTGAGATTAC------GATTTAAACTTTACTATTG--T-TCGGTTC DroVir_CAF1_left AAAGTTAAATA-----CAAT--AA--AAACG--AGCAA-TATCAAAC--GATCCTCTT-GATGA--GA--TGTTCCGAGTA-ACGAAATCTCCAAAAAAGT-AAAGTAT--TGAAACATT DroAna_CAF1_left GATCTTGTTGACTGTTCCATTGAACAACTGACTAGATGCAGCATAGCGCTCTCAAAATTCGTTTTCCAACGTCAGCTATGCCGACATCTTGCCAATTTAACAACAGATTCTT--GGCTAT DroEre_CAF1_left GATCTCGCTGACTGTTCCATTGAACAACTGACTAGATGCAGCATAGCGCTCTTTAAAAGCGCTTTTCAACGTCAGCTATGCCGACATCTTGCCAATTTACCAACGGAGGTGCTATACG-A DroGri_CAF1_left GGATATGTTGAGTGTTCCATTGAATAACTGACTAGATGCAGCATAGCGCTA-TAAGATGCGCTTTCAAACGTCAGCTATGCCGACATCTTGCCAATTCACCAACAGATGAGAATCGCG-A DroMel_CAF1_left GATCTCGCTGACTGTTCCATTGAACAACTGACTAGATGCAGCATAGCGCTCTTCAAAATCGCTTTTCAACGTCAGCTATGCCGACATCTTGCCAATTTACCAACGGAGTTGATATACG-A DroMoj_CAF1_left G--ACTGTTGACTGTTCCATTGAATAACTGACTAGATGCAGCATAGCGCTATGC-AATGCGCTTTGAAACGTCAGCTATGCCGACATCTTGCCAATTCAACAATAGATGCGATAAAC--- DroPer_CAF1_left GA-TCTGTTGACTGTTCCATTGAATAACTGACTAGATGCAGCATAGCGTTCTCAAAGATCGCTTTTCAACTTCAGCTATGCCGACATCTTGCCAATTTACCAACAGATGCGGTACGA--- DroPse_CAF1_left GA-TCTGTTGACTGTTCCATTGAATAACTGACTAGATGCAGCATAGCGTTCTCAAAGATCGCTTTTCAACTTCAGCTATGCCGACATCTTGCCAATTTACCAACAGATGCGGTACGA--- DroSec_CAF1_left GATCTCGCTGACTGTTCCATTGAACAACTGACTAGATGCAGCATAGCGCTCTTCAAAATCGCTTTTCAACGTCAGCTATGCCGACATCTTGCCAATTTACCAACGGAGGTGCTATACG-A DroSim_CAF1_left GATCTCGCTGACTGTTCCATTGAACAACTGACTAGATGCAGCATAGCGCTCTTCAAAATCGCTTTTCAACGTCAGCTATGCCGACATCTTGCCAATTTACCAACGGAGGTGCTATACG-A DroYak_CAF1_left GATCTCGCTGAGTGTTCCATTGAACAACTGACTAGATGCAGCATAGCGATCTTCAAAATCGCTTTTCAACGTCAGCTATGCCGACATCTTGCCAATTTACCAACAGAGGTGCTATACG-A DroVir_CAF1_left G-TTTTGTTGATTGTTCCATTGAATAACTGACTAGATGCAGCATAGCGCTATAAAAATGCGCTTTCAAACGTCAGCTATGCCGACATCTTGCCAATTGAACAACAGATGCGAGGCGA--- DroAna_CAF1_left ATGATCGCTCCAATCTGCTAC-CGAACCGCGTTCGCACAAAAAATTCACGGAAA-TATTCTCACAGGC--CAGAAAGCA-AGC-GACT-TC--T-ATT----GCTCGATTGTCAATGGCT DroEre_CAF1_left TCGATCCGACATGGCTCAAAACCAAACCGATTTGGACC--ACAATTCACCGAAA-CATTCTCACTGGG--CACAAT-TG-GTC-GTCT-AT--TACTC----GCTTGTT-GTCAATGGCT DroGri_CAF1_left GAGATAACGAG--AAACGTTTGTAGT-TGAACCACAAA--TTCCAGAAAAAACA-CACTTTTAACAAG--TTCAAC--------AATA-TA--TTTGTTATTGTAATTTAG-CA-TGATA DroMel_CAF1_left TCGATCCGACATGGACGAAACCCCAACCGTTTTGGTTC--ACAATTCACCGAAA-CATTCTCACTGGT--CACAAA-TG-CTC-GTCT-AT--TACTC----GCTTGTTATCCAATGGCT DroMoj_CAF1_left CGAAATATTTATAAATATAGATGATA-TATA---------------TATTTGAAACACAA-ATTAA-A--CAACTT--CAAACAATTC-GTTGTTGTA----ATTTCGCATGAACGAAGC DroPer_CAF1_left TCCGAGACGCGCGACGACGATTCACA-TAAA---------------CATTCTCA-CAGGG-CACAAGT--GATTCG--G-TTC-GGCC-AAGACGATA----TGTGTATGTTATTTGGCT DroPse_CAF1_left TCCGAGACGCGCGACGACGATTCACA-TAAA---------------CATTCTCA-CAGGG-CACAAGT--GATTCG--A-TAT-GTGT-ATGTCATTT----GGCTCGGACAACCGGCCA DroSec_CAF1_left TCGATCGTAGATGGCCGAAACACCAACCGATTTGGTTC--ACAATTCACCGAAA-CATTCTCACTGGG--CACAAA-TG-CTC-GTCT-AT--TACTC----GCTTGTTATCCAATGGCT DroSim_CAF1_left TCGATCGTAGATGGCCGAAACCCCAACCGATTTGGTTC--ACAATTCACAGAAA-CATTCTCACTGGG--CACAAA-TG-CTC-GTCT-AT--TACTC----GCTTGTTATCCAATGGCT DroYak_CAF1_left TCGAGCCGACATGGCTCAAACCCAAACCGATTTGGCCG--ACAATTCACCGAAA-CATTCTCACTGGGCGCACAAA-TG-GTC-GTCTTAT--TACTC----GCTTGTT-GTCAATGGCT DroVir_CAF1_left CGGGATAAACAA----C-----------GCGACAAA-A--ATGTTGCTAGCAAA-TTTTGTTAT-T-G--TAATTT-CG-CAT-GAAC-GA--AACTT----ATTTTTATCAATGA--AT DroAna_CAF1_left TTTATCAATGA-AACG---CT----TGT DroEre_CAF1_left TTTATCAATGA-AACG---CTT-GTTGT DroGri_CAF1_left GAAACTTTTTT-TTAT---CAA-T-GAA DroMel_CAF1_left TTTATCAATGA-AAGG---CTT-G-TTG DroMoj_CAF1_left G-TATTATTATTTTTTTTTTTT-A-TCA DroPer_CAF1_left C-GGACAGCCG-GCCA---CAAGA-CAG DroPse_CAF1_left CAAGACATCAG-CATT---TAT-C-AAT DroSec_CAF1_left TTTATCAATGA-AACG---CTT-G-TTG DroSim_CAF1_left TTTATCAATGA-AACG---CTT-G-TTG DroYak_CAF1_left TTTATCAATGA-AACG---CTT----GT DroVir_CAF1_left TTCTTGTTTTC-TTAT---TTC-T-CTT