CLUSTAL W --- LocARNA 1.4.8 - Local Alignment of RNA DroAna_CAF1_left AATTAATTTTGTTTT--T-T-AAACAAAAAATTGTG-GTGAGAAACAAGGATGATAGTAATCCCGCGGATTTAAGAGACCGTTATGGGCACCGAAGGCG-AATTCCCACCATAT--T-CT DroEre_CAF1_left TTTCAATTCATTTCA--TTTCCCCCAAAAAGGTGTG-GAGGGAAACAAGGATGATAGTTATCTCGCGGATTT-AT-AACCGACTCGAGCACCGAAGGCT-AATCCCCACCATTCCTCACT DroGri_CAF1_left AAAATATGTCCGACA--A-A-AAATTGAAATTTGTG-GAGGGAAACAAGGATGATAGTTTTCCCACGGATTTGAT-AACCGTTATGGGCACCGAAGGCGTAATTCCCACCAAAT--T-GT DroMel_CAF1_left GTACTCGTATTTCAT--TTCACAAAAAAAAGGTGTG-GAGGGAAACAAGGATGATAGTTATCTCGCGGATTT-AT-AACCGATTCGAGCACCGAAGGCT-AATCCCCACCATTCCTTACT DroMoj_CAF1_left ACAATGAATTGAGAA--A-A-AAAATTTTA-GTTGTGGAGGGAAACAAGGATGATAGTTTTCCCACGGATTTGAT-AACCGTTATGGGCACCGAAGGCGTAATTCCCACCAA-A--T-TT DroPer_CAF1_left TGAGTTTCGTAAATA--A-ATGTTCAAAATATTGTG-GAGGGAAACAAGGATGATAGTTTTCCCACGGATTTGAC-AACCGTTACGGGCACCGAAGGCG-AATTCCCACCTGTTCAA-TC DroPse_CAF1_left TGAGTTTCGTAAATA--A-ATGTTCAAAATATTGTG-GAGGGAAACAAGGATGATAGTTTTCCCACGGATTTGAC-AACCGTTACGGGCACCGAAGGCG-AATTCCCACCTGTTCAA-TC DroSec_CAF1_left GTTTTCTCGTATTTC--ATTTCACAAAAAAGGTGTG-GAGGGAAACAAGGATGATAGTTATCTCGCGGATTT-AT-AACCGATTCGAGCACCGAAGGCT-AATCCCCACCATTCCTCACT DroSim_CAF1_left GTTTTCTCGTATTTC--ATTTCACAAAAAAGGTGTG-GAGGGAAACAAGGATGATAGTTATCTCGCGGATTT-AT-AACCGATTCGAGCACCGAAGGCT-AATCCCCACCATTCCTCACT DroVir_CAF1_left TATATTCGGATAAAG--T-A-AAAAAGTAAATTGTG-GAGGGAAACAAGGATGATCGTTTTCCCACGGATTTGAT-AACCGTTATGGGCACCGAAGGCGTAATTCCCACCAAA---T-TT DroYak_CAF1_left TCATTTCATTTCATTTTATTTCTCAAAAAAGGTGTG-GAGGGAAACAAGGATG--ATAAAACTCGCGGATTTAAA-ACCGGATTCGAGCACCGAAGGAC-AATC-CCACCATTCCTCACT DroAna_CAF1_left GATCTGCCTCCTCTCGCATAATCGGCATTAATTACAATTAAATTAATCCGGCCAAAGAGAGGGGCTTTTTGA-GTT--TTTAA---ACGATAGA---------------T-TGC-GC--G DroEre_CAF1_left CTGCCTTCTCCTCATGCATAAACGGAATTAACTACAGTCTCATTAATCCGGCCAAATAGAGGGGCATTTCTA-CTT--TCAATAG-ATT--CTA----------------AACT-CTGG- DroGri_CAF1_left AATCTGCCTACTCTCGCATAATCGGCATTAATTATATTATCATTAATCCGGCCAAAGAGAGTGGCTCTTATA-AAA--G-------TGTATACC---------------T-ACC-TT--G DroMel_CAF1_left CTGCCTTCTCCTCATGCATAATCGGAATTAACTACAAACACATTAATCCGGCCAAATAGAGGGGCATTTCCTACTT--TC-TATATTTCAGATTTACACATTCTACAAAGTACGGAGTAG DroMoj_CAF1_left AATCTGCCTACTCTGACATAAACGGTATTAATTATAATCAAATTAATCCGGCCAAAGAGAGTGGCTCTATAA-TTA--TGCAC---GT---ACG---------------A-TAC-GCGCA DroPer_CAF1_left AATCTACCTCCTCTTGCATTTACGGCATTAATTATTGTAAAATTAACCCGGCCAAAGAGAGGGGCACCGCTC-TCA--GCGAT---TC---ATT---------------TCAAA-AACGC DroPse_CAF1_left AATCTACCTCCTCTTGCATTTACGGCATTAATTATTGTAAAATTAACCCGGCCAAAGAGAGGGGCACCGCTC-TCA--GCGAT---TC---ATT---------------TCAAA-AACGC DroSec_CAF1_left CTGCCTTCTCCTCATGCATAATCGGAATTAACTACAAATACATTAATCCGGCCAAATAGAGGGGCATT-TCTATAT--TT-TAGATTG---ATT---------------CTACG-AGTAG DroSim_CAF1_left CTGCCTTCTCCTCATGCATAATCGGAATTAACTACAAATACATTAATCCGGCCAAATAGAGGGGCATTTTCTATAT--TT-TAGATTG---ATT---------------CTACG-AAGTA DroVir_CAF1_left AATCTGCCTACTCTTGCATAATCGGCATTAATTATAATTAAATTAATCCGGCCAAAGAGAGCGGCTCGCTAT-CAA-AAATTC---GT---ACT---------------T-AAT-AAAT- DroYak_CAF1_left CTGCCTTCTCCTCATGCATAATCGGAATTAACTACAAACTCATTAATCCGGCCAAATAGAGGGGCACATTTT-CTACTTTTCT---AT---ACT---------------C-AAT-AAAAA DroAna_CAF1_left TTTTGAAC-CGCCA--ATT----------TCAGGTGAATGAAATTATATACTCGC-CGCTC-TACGCTGAGCACCACGAAAACGCCCATTCA-ACATGC--G-C-CAGA--ACTA--CAT DroEre_CAF1_left ACT-CG-----ATG--TC-----------GTG--CTCTCGCCTGGAAGGGCGCGA-CTCTC-AACGCAGAACGC--CATCGACGCACTTACAAATGCGC--CGT-CTGAATTTCA--CTT DroGri_CAF1_left AAGAATAA-CAGGA--ACA----------CAAACATTTTTATTATTTTAAATAGA-TTTCC-CGAGCGAGGATT--CG--AACTCTCGACCG-CGAGAA--C-C-CGTC--AAAT--AGA DroMel_CAF1_left ATT-CG-----ATG--AC-----------GTG--CTCTCGCCTGTAAAGGCGCGA-CTCTC-AACGCAGAGTGC--TATGGACGCACTTGCAAACGCGC--TGT-C-------TA--AAT DroMoj_CAF1_left CGG-TAAA--GATG--ATA----------AGAT-G---CGAAGAAAAAGACACAA-TCACT-TCCGAAAGTGAGA-TTTGAACCTGCGGT----AACTC--G-C-ACGA--CTAT--GCA DroPer_CAF1_left AAT-GA------AATATTT----------GAGTCTTTGTCTCCGGGCGGTCTCGA-ACCTATGTCATC---AAAAGAGTCTGCGAGACT-CA-ACGCGC--AGCACCAA--ACAGGT--C DroPse_CAF1_left AAT-GA------AA--TTT----------GAGTCTTTGTCTCCGGGCGGTCTCGA-ACCTATGTCATC---AAAAGAGTCTGCGAGACT-CA-ACGCGC--AGCACCAA--ACAGGTCAC DroSec_CAF1_left ATT-CG-----ATG--ACC----------GTG--CTCTCGCCTGAAAAGGAGCGA-CTCTC-AACGCAGAGTGC--CATGGACGCTCTTTCATACGCGC--TGT-CTAAATTTCA--CTT DroSim_CAF1_left AAT-CG-----ATG--AC-----------GTG--CTCTTCGCTGGAAAAGCGCGA-CTCTC-AACGCAAA-TGC--CATGGACGCTCTTNNNNNNNNNNNNNNN-NNNNNNNNNN--NNN DroVir_CAF1_left CTATGT------CA--ACA----------CCACCGCGATGAGATTTGAACCCGCGAACGCAGCCCGAA---AATTTAATAAACGGAACGTCA-GCGAGC--G-A-CGCCA-CGAG--CGC DroYak_CAF1_left CTC-TGTACTCGAT--ATACTCGATGGTCGTG--TGCTCGCCAG-GAATGCGC---GACTC-AACGCAGAACGC--CATGGACGCACTTCCAGACACGC------TGTC--TGAA--TTT