CLUSTAL W --- LocARNA 1.4.8 - Local Alignment of RNA DroAna_CAF1_left TGCAATCGTCG-GGTCAACAACGCCGC-GACTCCCAGACTCCCGGAG--TCCAGTGTC-G-GAAATA---TATCTTTA-ATTGC--AGCACTA-GAACATTACGG-AG----GATGGTGA DroEre_CAF1_left ACAAATTATAATATATATCTTCACATC-TGGATTTGGTCTCATCTTT--ATCTGCATC-TGGATCCG---CGACGACG-T-ATA--ATTTTCA-GCACTTT-TGG-AT----TAAGGCGA DroGri_CAF1_left CGTCGGGTCAACAACGGTCCCGAGCGC-AGTTATCGAGCGATGAGCA--TACTGTGTTACACTG------TGTTTACA-C-CGGGGGGACACT-CCAAAGG-ACA-CT----CTTGTAGA DroMel_CAF1_left ACAAATTAGAATATACATCTTTACATC-TGGATATGGTTTCATCTTT--ATCTGCATT-TGGATCCG---CGACGACG-C-ATA--ATTTTCA-GCACTTT-TGA-AT----AATGGCGA DroMoj_CAF1_left GCAACTCAGTTGCGGCCGTGCAATCGT-CGGGTCAACAACGTCGGTA--GCTGCCCTT-GCAGACGG---CGATTCGA-G-ATT--TTACACT-TTTCAGG-AGC-GA----ATTGTTGA DroPer_CAF1_left TCTAGAACTGACAACTT-TGAATCGAG-AGCCGGGGGCTGCAACCAC--ATCTGCGGA-TCCTTTCGACTGCATTCGT-----A--ATTTTCTTTCAGCGG-TTA-TG----TAGGATGA DroPse_CAF1_left TCTAGAACTGACAACTT-TGAATCGAG-AGCCGGGGGCTGCAACCAC--ATCTGCGGA-TCCTTTCGACTGCACTCGT-----A--ATTTTCTTTCAGCGG-TTA-TG----TAGGATGA DroSec_CAF1_left ACAAATTAAAATATAAATCTTCACATC-TGTATTTGGTTTCATCTTT--ATCTGCATC-TAGATCCG---CGACACGG-C-ATA--ATTTTCA-GCACTTT-TGG-AT----AATGGCGA DroSim_CAF1_left ACAAATGAAAATATAAATCTTCACATC-TGTATTTGGTTTCATCTTT--ATCTGCATC-TAGATCCG---CGACACGG-C-ATA--ATTTTCA-GCACTTT-TGG-AT----AATGGCGA DroVir_CAF1_left CAACAACGGTAGCTGC--CTGCAGCAC-GAATATT--ATTTGGTTATTTGGTTTTGAA-GAGC-GTG---CGATGAAAAC-TGA--GG-TGTTTATAGCGG-AGCACT---TATTGTAGA DroYak_CAF1_left ACAAATTATAATACAAATTTTCACATC-TGGATATGGTTTCATCTTT--ATCCACATC-TCGATCCG---CGACGACG-C-GTA--ATTTTCA-GCACTTT-TGG-AC----TAAGGCGA DroWil_CAF1_left CAAGAAGGCCGCGAGCCATTTCAACGCACTAAAATAAATACGACAAC--GACCACGAC-GAATACAT---ACGAAACG-G-TC-------ACC-GGGTACC-GGT-CACTTTCCAGATGA DroAna_CAF1_left TTTTGTGCAACTTCGTATACGTATACTGAATGTATCCTGAGTGTATCCTATCCGGTATACCTTCAGTATACGTAACACGAGGTAACACCTTCAACGCGGGACGTGAAAACTTAAT----- DroEre_CAF1_left TTCTGTGCGACCTCGTAAACGTATACTGAATGTATCCTGAGTGTATCCTATCCGGTATACCTTCAGTATACGTAACACGAGAAAGCACGAGCAACGTGGGATGTGAAACACTTTTTAA-G DroGri_CAF1_left ACCTGTGCAACTTCGTATACGTATACTGAATGTATCCTGAGTGTATCCTATCCGGTATACCTTCAGTATACGTAACACGAGGAAACACCAGCAACGCGGGATGTGTTTTGTATATATA-T DroMel_CAF1_left TTCTGTGCGACCTCGTAAACGTATACTGAATGTATCCTGAGTGTATCCTATCCGGTATACCTTCAGTATACGTAACACGAGAGAGCACTAACAACGTGGGATGTGAAACACTTTTTAA-G DroMoj_CAF1_left GCCTGTGCAACTTCGTATACGTATACTGAATGTATCCTGAGTGTATCCTATCCGGTATACCTTCAGTATACGTAACACGAGGAAACACCAGCAACGCGGGATGTGTGAAAACTTCAA--T DroPer_CAF1_left ACCTGTGCGACTTCGTATACGTATACTGAATGTATCCTGAGTGTATCCTATCCGGTATACCTTCAGTATACGTAACACGAGGAAACACCAGCAACGCGGGATATGTCGAACTGAATTT-A DroPse_CAF1_left ACCTGTGCGACTTCGTATACGTATACTGAATGTATCCTGAGTGTATCCTATCCGGTATACCTTCAGTATACGTAACACGAGGAAACACCAGCAACGCGGGATACGTCGAACTGAAACC-G DroSec_CAF1_left TTCTGTGCGACCTCGTAAACGTATACTGAATGTATCCTGAGTGTATCCTATCCGGTATACCTTCAGTATACGTAACACGAGATAGCACGAGCAACGTGGGATGTGAAACACTTTTTAA-T DroSim_CAF1_left TTCTGTGCGACCTCGTAAACGTATACTGAATGTATCCTGAGTGTATCCTATCCGGTATACCTTCAGTATACGTAACACGAGATAGCACGAGCAACGTGGGATGTGAAACACTT-TTAA-T DroVir_CAF1_left GCCTGTGCAACTTCGTATACGTATACTGAATGTATCCTGAGTGTATCCTATCCGGTATACCTTCAGTATACGTAACACGAGGAAACACCAGCGACGCGGGATGTGTGATATATTTAG--A DroYak_CAF1_left TTCTGTGCGACCTCGTAAACGTATACTGAATGTATCCTGAGTGTATCCTATCCGGTATACCTTCAGTATACGTAACACGAGAAAGCACGAGCAACGTGGGATGTGAAACACTTTTTAA-T DroWil_CAF1_left ATCTGTGCAACTTCGTATACGTATACTGAATGTATCCTGAGTGTATGCTATCCGGTATACCTTCAGTATACGTAACACGATGAAACACCAACAACGCGGGATGTGTGAAACACTTTTTAT DroAna_CAF1_left A--------------TTCTGAAATAT-T---TAAAACACTAAGCACTT--TTATAATAGAATTAAATACAATTTAAACA-CTTTTCACTGA----ATATT--TTTTA-AGTTATCA-CTT DroEre_CAF1_left A--------------CTCTACAATAC-A---CGTAGCACTTT--G-TT--ACTTGGTATTACACTTTTTTAAACT-GCT-CGACTTAGAAA---TACACA--ATTTA-AACATAAA-TAT DroGri_CAF1_left A--------------AATTTCGATAA-A---TAATACACTGA----AA--ACACTTTGTCACACTTGAGCAATCT-GTT-GCACTTGTTGCCATTCCACAGCACATG-ATATTGTT-AAT DroMel_CAF1_left A--------------CACCTTAATAC-A---CGTAGCACTTT--G-TT--ATATGGTCTTACACTTTTTTAAATA-TCT-CGACTTATAAA---TATATA--ATTTA-AATATAAA-TAC DroMoj_CAF1_left A--------------ACCATTTAATC-G---TAAAGCGAATT--T-CT--TATCATTCACGTGAACTACTTATTT-CAT-TAGTTATATTA---CTTATA-CACATA-CTTTGACA-ATT DroPer_CAF1_left AACGTGTAAACCGAGCACTGTGATTTAT---TCTAGCACTTTG---TA--ACACTTTGTCTTAGCCGTTTTCTCA-----CTTTTCACCTT----GT--------------AATCG-AAA DroPse_CAF1_left -------------AGCACTGTGATTTAT---TCTTGCACTTTG---TA--ACACTTTGTCTTAGCCGTTTTCTCA-----CTTTTCACCTT----GTAAT--CCAAAAATAAAATAGTTC DroSec_CAF1_left A--------------CATCTTAATAC-A---CGTAGCACTTT--G-TT--ATATAGTTTTACACTTTTTTAAAAA-TCT-CTACTAAGAAA---TACATA--ATTTA-AATATAAA-TAC DroSim_CAF1_left A--------------CACTTTAATAC-A---CGTAGCACTTT--G-TT--ATATGGTTTTACACTTTTTTAAATA-TCT-CTACTAAGAAA---TACATA--ATTTA-AATATAAA-TAC DroVir_CAF1_left T--------------TGCATTAAAAT-AAAACAC--CAAAAC--A-CTTTGTAA--ATACTGGAAAAACTGTTGA-ATT-TATATAATAAA---TGTATT--ACATA-TTTTATAT-CCG DroYak_CAF1_left A--------------CTGCTTAATAC-A---CGTAGCACTGT--G-TT--ATTTGGTATCACACTTTCTTATAAATACA-CAATTTAAACA---TATAT----ATTT-CAATAAATGCCC DroWil_CAF1_left T--------------CTTTTGTGTTT-T---AGTTTAGATAA--T-AAA-ATT--AATCAATTTATTTATATACA-CTTCCTACAAGAAAC---TGCAAT--AAACCTATAACAAT-GTA DroAna_CAF1_left T-GTAA DroEre_CAF1_left T-TCAA DroGri_CAF1_left T-AAAT DroMel_CAF1_left T-TTAA DroMoj_CAF1_left A-CACG DroPer_CAF1_left T-AAAA DroPse_CAF1_left A-CAAA DroSec_CAF1_left T-TCAA DroSim_CAF1_left TTCAAT DroVir_CAF1_left A-TTTA DroYak_CAF1_left G-CTAT DroWil_CAF1_left T-ACAA