CLUSTAL W --- LocARNA 1.4.8 - Local Alignment of RNA DroAna_CAF1_left GTCCTCGTCATCTGAACTGAGTATCTGTT--G-AAGATTTAAGAATACATTATATACTAGAATG--T-ATG---------GGGAAGGATTTAGCTTTTGT---TTTGAGAG--TTTGAGG DroEre_CAF1_left T-CCTCGTCATCAGAGCTAAGAACCTGTG--C-AAAAGAT---CAC-CAAAAAATATTACAATA--T-TTG-------TTTGAAATCAATGCCCTTATAAACAATAAAAGT--GCTCGGG DroGri_CAF1_left ATCCTCCTCATCGGAGTCAACAATCTGTGTGC-AATTCAAA-TGTA-TTAA---GAACAATTTCTAC-TTG-------GCGATAT-TTTG-TAAATTAAAA--ATGGTTAA--TGGTTTT DroMel_CAF1_left T-CCTCATCATCAGAACTGAGAACCTGTG--C-AAAAGAAGATCAT-CAAGAATTATTAGAATA--T-TCG-------TTCGAAATCAATGCCCATATAA---AAAAGTGT--TCTTAGG DroMoj_CAF1_left C-T--CTTCATCCGAGTCAAGGATCTGATGGCAAAAATAAAATGAA-TAAATAGCAATTCT-AT--AATTC-------TGCTTTTGTAAA-TCTAGTCAA---AGCTTTTA--TATATTT DroPer_CAF1_left C---TCATCATCCGAACTGATTACCTGCA--G-TATTCATAGAAAT-ATAAACATTTGTGTTAA--A-CTG-------ATGAAAACTAGAGCCATCTCTA---GTGGGGGCCATTTTCGT DroPse_CAF1_left C---TCATCATCCGAACTGATTACCTGCA--G-TATTCATAGAAAT-ATAAACATTTGTGTTAA--A-CTG-------ATGAAAACTAGAGACATCTCTA---GTGGGGGCCATTTTCGT DroSec_CAF1_left T-CCTCATCATCAGAACTGAGCACCTATG--C-AAAAGAAGATCAT-CAAAAATTATTAGAATA--T-TCG-------TTCGAAATTAATGCCTATATAA---AGAAGTGT--TCTTAGG DroSim_CAF1_left T-CCTCATCATCAGAACTGAGCACCTATG--C-AAAAGAAGATCAT-CAAAAATTATTAGAATA--T-TCG-------TTCGAAATTAATGCCTATATAA---AGAAGTAT--TCTTATT DroYak_CAF1_left GTCCTCATCATCGGAGCTGAGAACCTGTG--C-AAAAGAAGTTCA--CAAAATTTATTAGAATA--T-TCG-------TTCGAAATTAATGACCATTTAA---AGAAGTGT--TCTTGGG DroVir_CAF1_left A-GGCTGTATCCTCCTCATCGGAGTCAAG--T-ATC----TGTTGT-GCAAGAAAGTGTATCA---A-TAAATTGCCTGGCGATGCATTGGACTT-TGAA---CG-TTAGT--GTGCTTG DroAna_CAF1_left CACTCAGCA-AGGTTTGTAGTCAT-TTT-GAGGACAGCAAAGTGGAGCCAGCCAACGCCTGTCACGCGACTAACTGCGCCGGCGACGGCCTCCGCCCCA--CCTGCTCATCCGAATCAGA DroEre_CAF1_left CACTCAGTT-GAGGTTGAAGTCAT-TTT-G-GGACAGCGAAGAGGAGCCAGCGACTGCCCGTCACGCGACTAACTGCGCCGGCGGTGGCTTTTGCCCCA--CCCGCTTGTCCGAATCAGA DroGri_CAF1_left TGCTCAGCTAAATTCTTTAGTCATTTTG-T-GGCCAGCAGAGACTCATTCGCCTTTACCTGACACGCGACTAACTGCGTGGGTGAAGATCCCAGTGTAC--TCCGCTTGACCACATCAGA DroMel_CAF1_left CACTCAGTT-GAGGTTGTAGTCAT-TTT-G-GGACAGCGAAGTGAAGCCAGCGACTGCTCGTCACGCGACTAACTGCGCCGGCGGTGGCTTTTGCCCCA--CTCGCTTGTCCGAATCAGA DroMoj_CAF1_left TACTCAGCTAAATGTTGAAGTCAT-TTTAT-GAGCAGCAGAGACACGTTCGCCTGCACACAAACCGCGACTAACTGCGTCGGTGCAGGACAAGACGTGA--ACCGTCTGCCCAACTCAGA DroPer_CAF1_left TACTCAGCT-GAGATTGTAGTCAC-TTT-G-GGACAGCCGAGTGGAGCCAGCCTCCGCCTGTCACGCGACTAACTGCGTCGGCGGAGCCTTTTGCTCCA--TCTGCTTGTCCGAATCAGA DroPse_CAF1_left TACTCAGCT-GAGATTGTAGTCAC-TTT-G-GGATAGCCGAGTGGAGCCAGCCTCCGCCTGTCACGCGACTAACTGCGTCGGCGGAGCCTTTTGCTCCA--TCTGCTTGTCCGAATCAGA DroSec_CAF1_left CACTCAGTT-GAGGTTGTAGTCAT-TTT-G-GAACAGCAAAGTGGGGCCAGCGACTGCCCGTCACGCGACTAACTGCGCCGGCTGTGGCTTTTGCCCCA--CTCGCTTGTCCGAATCAGA DroSim_CAF1_left CACTCAGTT-GAGGTTGTAGTCAT-TTT-G-GGACAGCGAAGTGGGGCCAGCGACTGCCCGTCACGCGACTAACTGCGCCGGCGGTGGCTTTTGCCCCA--CTCGCTTGTCCGAATCAGA DroYak_CAF1_left CACTCAGTT-GAGGTTGAAGTCAT-TTT-G-GGACAGCGAAGAGGAGCCAGCTACTGCCCGTCACGCGACTAACTGCGCCGGCAGTGGCTTTTGCCCAA--CCCGCTTGTCCGAATCAGA DroVir_CAF1_left TACTCAGATAAATGTTGAAGTCAT-TTTAT-GGGCAGCAGAGGCACGCCCGCCTTCACCTGGCACGCGACTAACTGCGTGGGGAAGGGCTA---CGTGCACACCGCATGCCCAACTCAGA DroAna_CAF1_left CCTTTTACTAAGACATCATAGTTGGCCC-CCAAAACA--AAGCCAGACATGCGGC-TGGG-ATCAATA--AAACTGAAGTTCAATTAAAAGTTACAAG-GTTG-GAAACAA DroEre_CAF1_left CCTTTTACTAAAACATCATAGTTAAGCCAATACGAGC--AACATAGTGA---TTT-TTGGATGCATAT--TAAAGT-TTCACGGTGTTGATAAGTTTGGTTTGAAATCATT DroGri_CAF1_left CCTTTTACTCAAACATCATAGTAGTTAGGCAA-AGGA--TTCATTTGATTCATTT-GCCATTGATTGA--TGACTT-ACTAGTTCATTTGGTTGCAGA-GATC-GATTGTC DroMel_CAF1_left CCTTTTACTAAGACATCATAGTTAAGCCAATACGAGC--AACACAGTGAGGCTACATTTG-TGTAATAT-TAGA-T-TTTTG-GGGTAATAGTAATGG-TTTA-AAAACTA DroMoj_CAF1_left CCTTTTACTAAAACATCATTGTGGACAA-AGTGAAGG--AA---AAGGGAGCGAT-CTTATTCTAGTAGCTGACTT-ACTAATTCGCTGGGCTGAATCATTCG-ATTGTCC DroPer_CAF1_left CCTTTTACTGGGACATCATTGTTAAACCGAAG--AGA--ATGAAAGTAATGGGAA-GCTAAATAAACA--CAACTC-ACCACTTCGCTGGAGTGCGGCGGCCG-ATTCTCA DroPse_CAF1_left CCTTTTACTGGGACATCATTGTTAAACCGAAG--AGA--ATGAAAGTAATGGGAA-GCTAAATAAACA--CAACTC-ACCACTTCGCTGGAGTGCGGCGGCCG-ATTCTCA DroSec_CAF1_left CCTTTTACTAAGACATCATAGTTAAGTCAATACGAGC--AACACAGTGAAGCATT-TTGGTTTAAAAA--CTAAAA-TCCAC-ATTCCATACTGCTTC-ACAG-TGTTCCT DroSim_CAF1_left CCTTTTACTAAGACATCATAGTTAAGTTAATACGAGC--AACACAATGAAGCATT-TTGGTTTAAAAA--CTAAAA-TCCAC-AATCCATACTGCTTC-ACGG-TGTTGCT DroYak_CAF1_left CCTTTTACTAAGACATCATAGTTAAGCCAATACGAGC--AACACAGTGAAGCTAG-CTTATAGTCATA--TTTGCT-TTTTA-GGAGAATATTGAAAG-TTTA-TAAACTA DroVir_CAF1_left CCTTTTACTAAAACATCATGGTGGTCAA-AGAATCACACATTTGACTTATGTTAG-ACAACTTACT-A--AATCCGTTGGTT-GCAGCG-TTCGATTG-TCCA-TCTTGCT