CLUSTAL W --- LocARNA 1.4.8 - Local Alignment of RNA DroAna_CAF1_left AGTT-T-TGAGCCC--CGGG--TCAGGGG-----TTGCG------CCTTTG-TCCC-A-TTGCG-CG----ACT---TC--TAATTA-GACGTGCAATATGTAAAAAAAAGTCCTGTAT- DroGri_CAF1_left AATG-TCAGCG--C--CAGA--TAAACGA-----CTGTG-----CCGGAAAATGTG-A-AAATG-AG----AGT---GG--GGA-TG-GTCTTATTAAGCGCGAATGTAAAAAGAAAAA- DroEre_CAF1_left TTTG-T--GTACCG-GAAAA--GCAGGCC-----ACGGG----CTCAGCAG--TCCCA-TTAGGTCC----CAG---T--CTAATTG-GGCGTGGAATATGTAAGAAACGC---AGCAT- DroMel_CAF1_left CTTT-G-TGTTCCG-GAAAA--ACAGGCC-----ACGGG----TTCAGAAG-TTCC-G-TTCTG-CG----AGG---TC--TAATTA-GGCGTGGAATATGTAAGAAACGC---AGCAT- DroMoj_CAF1_left TGTC-A-ACGCCAGATAAACGTCTGTGCCGGAAAACGGG----CGTGGACA----T-GCTTTAA-TT----AAG-CGCG--AAATATTCCGAGTGCTAATGCAAAATAGCT---TGCAA- DroPer_CAF1_left CAGT-G----CCTG-TAAGC--GGGACCG-----GAGTC----AGGGGTCT--GAC-T-CGTTT-CG----CGG---TTGTTAATTA-GGCGTGGAATATGGAAAATATAA---AGCATC DroPse_CAF1_left CAGT-G----CCTG-TAAGC--GGGACCG-----GAGTC----AGGGGTCT--GAC-T-CGTTT-CG----CGG---TTGTTAATTA-GGCGTGGAATATGGAAAATATAA---AGCATC DroSec_CAF1_left CTTT-G-TGTTCCG-GAAAA--ACAGGCC-----ACGGG----TTCAGAAG-TTCC-G-TTCTG-CG----AGG---TC--TAATTA-GGCGTGGAATATGTAAGAAACGC---AGCAT- DroSim_CAF1_left CCTTTG-TGTTCCG-GAAAA--ACAGGCC-----ACGGG----TTCAGAAG-TTCC-G-TTCTG-CG----AGG---TC--TAATTA-GGCGTGGAATATGTAA-AAACGC---AGCAT- DroVir_CAF1_left AGCG-C-ACGCGGGAAATGT--CAACGCC-----AGATA----AACGGCTG-TGCC-G-GAAAA-TG----TAC-CGGG--GAAGA-CCTAATTAAGCGCGCAATATTCGT---AGTGC- DroWil_CAF1_left GATC-A-GAATAAGCTTACT--ATTGTAT-----TTTCT----TTTAGTTA-ATTT-A-AAAAA-AT----AATACAAA--TTTTA-TTTTACAAATACAATTATAAGCAT---TAAAA- DroYak_CAF1_left CTTT-G-TGTGCCG-----G--AAAAGCA-----GACCACGGGTTCAGC-----GG-T-CCCAT-TCCGTGAGG---TC--TAATTA-GGCGTGGAATATGTTAGAAACGC---AGCAT- DroAna_CAF1_left -CCTGCTGCTTAA--CAAA--AAATGTAAGGATA-AACCCACTGACAGCGGTGGGATTCGAACCCACGCCCTTTCGGACTGGTGCCTAAAACCAGCGCCTTAGACCGCTCGGCCACGCTG DroGri_CAF1_left -CTCGCACAGCCA--CCAA--AAATAAACT-----TGTAAACTGACAGCGGTGGGATTCGAACCCACGCCCTTTCGGACTGGTGCCTAAAACCAGCGCCTTAGACCGCTCGGCCACGCTG DroEre_CAF1_left -CCTGCTGTTCAA--TTAT--CTAAAAAAAAGA-ATTCAACTTGACAGCGGTGGGATTCGAACCCACGCCCTTTCGGACTGGTGCCTAAAACCAGCGCCTTAGACCGCTCGGCCACGCTG DroMel_CAF1_left -CCTGCTGTTAAA--TGAG--GAAAAAAAAGTAATATTAACCTGACAGCGGTGGGATTCGAACCCACGCCCTTTCGGACTGGTGCCTAAAACCAGCGCCTTAGACCGCTCGGCCACGCTG DroMoj_CAF1_left -CCACCAGAAAAAAATAAAAA-TAAAAATAAATGACTTTGCTTGACAGCGGTGGGATTCGAACCCACGCCCTTTCGGACTGGTGCCTAAAACCAGCGCCTTAGACCGCTCGGCCACGCTG DroPer_CAF1_left TCCTGCTGTTGCT--CGAA--GCAAAAAATCTCTTTCGTTTCTGACAGCGGTGGGATTCGAACCCACGCCCTTTCGGACTGGTGCCTAAAACCAGCGCCTTAGACCGCTCGGCCACGCTG DroPse_CAF1_left TCCTGCTGTTGCT--CGAA--GCAAAAAATCTCTTTCGTTTCTGACAGCGGTGGGATTCGAACCCACGCCCTTTCGGACTGGTGCCTAAAACCAGCGCCTTAGACCGCTCGGCCACGCTG DroSec_CAF1_left -CCTGCTGTTAAA--TGAG--AAAAAAAAAAGAATATTAACTTGACAGCGGTGGGATTCGAACCCACGCCCTTTCGGACTGGTGCCTAAAACCAGCGCCTTAGACCGCTCGGCCACGCTG DroSim_CAF1_left -CCTGCTGTTAAA--TGAG--GAAAAAAAAAGAATATTAACCTGACAGCGGTGGGATTCGAACCCACGCCCTTTCGGACTGGTGCCTAAAACCAGCGCCTTAGACCGCTCGGCCACGCTG DroVir_CAF1_left -TTGCCACCACCAGGAAAAAAAAAATAGAAAGCATCTCAACTTGACAGCGGTGGGATTCGAACCCACGCCCTTTCGGACTGGTGCCTAAAACCAGCGCCTTAGACCGCTCGGCCACGCTG DroWil_CAF1_left -AAATCAA-ATAATT-------AAAAAAAAAAGTAACCAACTTGACAGCGGTGGGATTCGAACCCACGCCCTTTCGGACTGGTGCCTAAAACCAGCGCCTTAGACCGCTCGGCCACGCTG DroYak_CAF1_left -CCTGCTGTTAAA---TGA--GGAAAAAA-AG-AATTCAACATGACAGCGGTGGGATTCGAACCCACGCCCTTTCGGACTGGTGCCTAAAACCAGCGCCTTAGACCGCTCGGCCACGCTG DroAna_CAF1_left CCGCA---TGCCGCCTGCGAGCCAGAAGG-TTCTGATGGA-AGCAA---GCA--ATAGAATTCAGCATTATCTCTAC-A-GTTAGA------ACAATT-ATA-TTGTA-CCAATT-ACTC DroGri_CAF1_left CCGTA---TGGCGCCGTCCTATTTTCTGG-CATACAACTTAAA-CGGCTTTT--TTTCAAAATAAAACGTTCTATGAAA-TAAACT------ATCTAT-TAC-ACTTA-CGTTGT-GCGT DroEre_CAF1_left CCGCAACGAGGCGCCATCCGCCGTCTAGAAAATAAAAG-GTTCTGAACAACA--AA-GTGTTAGTTTT---TTTTTT-T-TAAAAAGAGAATAATTGT-ATTTGAGTAATTACTC-GAAG DroMel_CAF1_left CCGCAATGAGGCGCCAAGCGCCGTCTAGAAAATAAAAG-GTTCTTAAC-AAA--AA-ATGTACATTTTTTTTTCTAA-A-AATAGAA---CAATTGGT-ATTTGAGTAATTAAACCCCCG DroMoj_CAF1_left CCATA---TGGCGGCAATGTGATTTC-AAGCCCACAAC--TTTCACAT-AACCTATTTAGCAATA-AAAATGTTCTA-A-TTAGAAT---CA--AACACATT--ACCT-TTTCTA-CA-T DroPer_CAF1_left CCGC---CTGTCGCCGATCTGCCAGAGGATTGCTAACG-CCTACGACA-ACA--AA-TAGCTAGAATAT-TTTTCAA-AGAATGAGA---ACAATTTT-ATC--ATCGCATCGCT-GT-T DroPse_CAF1_left CCGC---CTGTCGCCGATCTGCCAGAGGATTGGTAACG-CCTACGACA-ACA--AA-TAGCTGGAACAT-TTTTCAA-AGAATGAGA---ACAATTTT-TTC--ATTGCATCGCT-GT-T DroSec_CAF1_left CCGCGATGAGGCGCCAAGCGCCGTCTAGAAAATAAAAG-GTTCTGAAC-AAA--AA-ATGTAGGTTTT--TTTCTAA-A-AATAGAA---CAATTGGT-ATTTGAGTAATTACTC-GCAG DroSim_CAF1_left CCGCAATGAGGCGCCAAGCGCCGTCTAGAAAATAAAAG-GTTCTGA-C-AAC--AA-ATTTACGTTTT--TTTCTAA-A-AATAGAA---CCATTGGT-ATTTGAGTAATTACTC-GCAG DroVir_CAF1_left CCATA---TGACGCCTGCCCGATTTC-AGACACACAAC--TCTAACAC-GAC--CTT-TTTTTTTGCTA--ATAGAA-T-GTTCTAA---GTAGTATCAAAC--CCAAATCTGTT-TA-T DroWil_CAF1_left CCTTG---TGTCGCCATGAGATCTAA-GGTCCCATTGG--GCTCTAGA-ATG--AAG-AATCATTCTAT--AGAATA-G-AAATTCT---CATAGGCAATTC--AAATTAACTGA-TA-A DroYak_CAF1_left CCGCAACGAGGCGCCAACCGCCGTCTAGAAAATAAAAG-GTTCTGAACGAAA--AA-ATTCTCGTTTT--TTTCTAA-A-AATAGAA---CAATT-GT-ATTTGAGTTATTACTC-GC-- DroAna_CAF1_left A--------CTAGA-ACGT DroGri_CAF1_left TCT-A-CAAAAATT-ACTT DroEre_CAF1_left TAA-T-T-GT---G-TTTG DroMel_CAF1_left TAA-T-T-----GTGTTTG DroMoj_CAF1_left ATGTATGTATGTAT-ATTT DroPer_CAF1_left GAT-G-TTTCTATT-AAAT DroPse_CAF1_left GAT-G-TTTCTATT-AAAT DroSec_CAF1_left TAA-T-T-GCGTTT-GTGA DroSim_CAF1_left TAA-T-T-GCGTTTGTGAT DroVir_CAF1_left AATTGCTTATGTTATTATC DroWil_CAF1_left GTT-ACACTAATTA-ATAG DroYak_CAF1_left AGT-AATTGTGTTT-GTGA