CLUSTAL W --- LocARNA 1.4.8 - Local Alignment of RNA DroAna_CAF1_left AGGAACAT-AGTT-ACGAAATGGTTTT-ATTAA-A-TAGAA-------TAAA--ACTT-C-AA-TAAAT-GTAA----C-C-AAA------A-TTA--TTT-AATT-TAAGAGTA-AAT- DroEre_CAF1_left ATATCTAC-AAGT-CACC---A-GCTT-A-AGACT-T-TTA------A-CGAG-ATCA-T-TT-GAATA-ATAT-AA-G-TTTTC------A-TA---ATT-TCTCTATCTCTATATAT- DroGri_CAF1_left TCGCGAAT-AATT-GCCTTACG-AATA-AT-TAAA-TA-TA--A---ATTAT--ATTAAAGAA-GTTTT-TCGT-TAAAAT-AATTTGTAAATTTA--TTAGAAATCGAAA-CTT-AAGA DroMel_CAF1_left ATAAATAA-GCAG-CGT---TA-AATT-T-AAATC-T-ATATCGTTGAATAAGAGAAG-T-TTTTA-TA-ACTATAG-A-A-AAT------A-TATAGACATTTTT-AAAAAATT-AAAA DroPer_CAF1_left GAACTTGT-TTTC-GTCCCCTTGAGAT-TCGCT-A-TATGG------A-AGA--TCGA-C-TG-TATTT-GCGA-AA-A-G-ATT------T-TA---TCGTAGCT-GAGGTATT-AGGT DroPse_CAF1_left GAACTTGT-TTTC-GTCCCCTTGAGAT-TCGCT-A-TATGG------A-AGT--TCGA-C-TG-TATTT-GCGA-AA-A-G-ATT------T-TA---TCGTAGCT-GAGGTATT-AGGT DroSec_CAF1_left ATTGTTTG-AATA-CGAGAAGT-TTTT-A-T-ATCAT-T-T------ATGTAT-ACAA-T-AT-ATATA-ATAT-AA-T-A-TAT------A-TAT--ATA-AAAT-ATATACAT-ATT- DroSim_CAF1_left TAAAAATA-TAAG-CAGCGTTA-AACT-T-AAATC-T-GTA------T-TGTT-TGTA-T-AC-GAGAA-GTTT-TT-A-T-ATC------A-TTT--ATA-AAAT-ATATACAT-ATT- DroVir_CAF1_left ATATTTTG-TATC-CTATATTTGTTCT-AGATA-G-CACTA-------TAGAG-ACAA-C-TT-TGATG-ATAA-AT-GCT-TTT------A-TAT--GGA-AATT-AAAA-TAA-TAAA DroWil_CAF1_left GCATGTGA-TTTC-ACAAAATGGGGTA-AA-TTAT-TT-GA------TTTAT--TTTA-T-TT-ATTGGTATTT-AT-ACA-AAAAAGAAAG-AAT--AGA-AATT-GGGG-TGA-AAAA DroYak_CAF1_left TATGCAAACCTCAGCAGATTAA-AATT-T-ACAAT-C-ATA------T-GGTT-TAAA-T-AGGAGAAATTTTT-AT-C-A-TTT------CACA---ATA-TTTCTAAAT-TTT-TTT- DroMoj_CAF1_left ACAAAGGT-ACTA-AACTGGATATGACTTCGAT-T-TAGGT------C-TGA--TGAC-G-TT-T-TTTCAATC-AA-G-T-AAA------A-TAT--GTT-TATATTAAT-TTT-ATG- DroAna_CAF1_left --AAAA-TA-AAAA---GTAAAC--AT--AAAAAAACCCGACTCCGTGACAATGTTTGG-TTTCAACATTGCCGTGACCAGGATTCGAACCTGGGTTACCACGGCCACAACGTGGGGTCC DroEre_CAF1_left -TTTAT-AT-ACTT---AAATA-T-AA--AAAAAATCCCGTTTCCGTGACAATGTTTAT--TTCAACATTGCCGTGACCAGGATTCGAACCTGGGTTACCACGGCCACAACGTGGGGTCC DroGri_CAF1_left A--AAA-AA-TATT---ACATATA-CA--TCTACAACCTGACTTCGTGACAATGCTCGC-CGAGAACAATGCCGTGACCAGGATTCGAACCTGGGTTACCACGGCCACAACGTGGGGTCC DroMel_CAF1_left AGAAAC-CCCTTTT---AAAAAAT-TAAAAAGAAACCCCATCTCCGTGACAATGTTTAT--TTCAACATTGCCGTGACCAGGATTCGAACCTGGGTTACCACGGCCACAACGTGGGGTCC DroPer_CAF1_left G--AAT-AA-AAGA---GAAATAA-AA--AAGAAAACCCAACTCCGTGACAATGCATAT-TTGCAGCATTGCCGTGACCAGGATTCGAACCTGGGTTACCACGGCCACAACGTGGGGTCC DroPse_CAF1_left G--AAT-AA-AAGA---GAAATAA-AA--AAGAAAACCCAACTCCGTGACAATGCATATTTTGCAGCATTGCCGTGACCAGGATTCGAACCTGGGTTACCACGGCCACAACGTGGGGTCC DroSec_CAF1_left --TAAG-CA-AATT---TAAAAAT-A---AAAAAACCCCATTTCCGTGACAATGTTTAT--TTCAACATTGCCGTGACCAGGATTCGAACCTGGGTTACCACGGCCACAACGTGGGGTCC DroSim_CAF1_left --TAAG-CA-AATT---TAAAAAT-AA--AAAAAACCCCATTTCCGTGACAATGTTTAT--TTCAACATTGCCGTGACCAGGATTCGAACCTGGGTTACCACGGCCACAACGTGGGGTCC DroVir_CAF1_left T--TTA-TT-TACG---TACCAAA-AA--AGTACAACCAGGCTCCGTGACAATGCATT---TATAGCACTGCCGTGACCAGGATTCGAACCTGGGTTACCACGGCCACAACGTGGGGTCC DroWil_CAF1_left A--TTA-AA-GTTGTAAAAACTTA-AA--AAAAAAACCCAATTCCGTGACAATGCATAT--CGCAGCATTGCCGTGACCAGGATTCGAACCTGGGTTACCACGGCCACAACGTGGGGTCC DroYak_CAF1_left --ATAG-TT-AAAT---ATAAAAATAA--CAAAAAACCCGTCTCCGTGACAATGTTTGT--TTCAACATTGCCGTGACCAGGATTCGAACCTGGGTTACCACGGCCACAACGTGGGGTCC DroMoj_CAF1_left --TTCTATT-AAAG---AATAAAAAAT--CTAGAAATCCAGACCCATGACAATGCAATC--CGATGCATTGCCGTGACCAGTATTCGAACCTTGGTTACC-----CAC-------GGTTC DroAna_CAF1_left TAACCACTAGACGATCACGGCTACGTCGGGTTGTTGATTCAGGCCGGCGAGAAACCAAACTTATGCTACAGCTTAAA-CGAAAA--TTAAAAAATATT--T-CT-AAAAAGTGTTTA-AA DroEre_CAF1_left TAACCACTAGACGATCACGGCTACAACAGGGTGTAGGGCATGACCAGCCAGATTCCAAATCTAAGGCACAGTGTTGC-AGAACG--ACAC--AAAACT--A-ATAAATCCTAATTAC-TG DroGri_CAF1_left TAACCACTAGACGATCACGGCTACACCAGGTTGTCGATAATTGGCGTCCAAAAAGCTGTTTTTTAAGA-AATCTTAC-AAAATAAAAGATATTGATGC--A-TATTTTTCCTTTCTC-TT DroMel_CAF1_left TAACCACTAGACGATCACGGCTACAACAGGGTGTTGGGCACGGGCAGCCAGAATCCAAATCTAAGGCACAGTGTTGC-AGAACG--ACACACAAAAGT--A-ATTAATATTAATTAC-TG DroPer_CAF1_left TAACCACTAGACGATCACGGCTACGCCGGGTTGTTGGAAGCCGACGGCCAAAACGCTGTTTTCACAAGCGTGGCATGTGGCAGG--AA-ATCAAAGTC--A-AATCACAGAAATCGA-AA DroPse_CAF1_left TAACCACTAGACGATCACGGCTACGCCGGGTTGTTGGAAGCCGACGGCCAAAACGCTGTTTTCACAAGCGTGGCATGTGGCAGG--AA-ATCAAAGTC--A-AATCACAGAAATCGA-AA DroSec_CAF1_left TAACCACTAGACGATCACGGCTACAACGGGGTGTTGGCCAATGCCAGCCAGAATCCAAATCTAAGGCACAGTGTTGC-AGAACG--ACACACAAAACT--A-AGTAATATTAATTAC-TG DroSim_CAF1_left TAACCACTAGACGATCACGGCTACAACGGGGTGTTGGGCACTGCCAGCCAGAATCCAAATCTAAGGCACAGTGTTGC-AGAACG--ACACACAAAACT--A-AGTAATATTAATTAC-TG DroVir_CAF1_left TAACCACTAGACGATCACGGCTACGCTTGGTCGCTGAGAGGCCGCGACCAAAGTACTGTTTTTTTAGGAATCTAACGTTTTTGC--TT--TTATCTTGTTC-AATAATAAAACTCTT-TA DroWil_CAF1_left TAACCACTAGACGATCACGGCTACATCGGGCTGTTGAATCGGGCCGGCCAACACGCTGTTTTCAGAGGCATGCGCAGAAAAAAT--AA--ACTACAAAAACTATGAACTTTAATTTT-TG DroYak_CAF1_left TAACCACTAGACGATCACGGCTACAACGGGGTGTTGGGAATGCCCAGCCAGAATCCAAATCTAAGGCACAGTGTTGC-AGAACG--GCAGAGAAAATT--A-ATAAATCTTAATTAC-TG DroMoj_CAF1_left TAACCACTAGACGATCAGGGCTACTTCTGGATGATCCGATTCAAGTGGCACCGGAAAAA-C-TATACCTTTTTCAGTTGCCTCA--ATTTTTACGACC--A-TTTTTTGCAAATAACAAT DroAna_CAF1_left ATCATAATTTCACATTTTAT--AAGC DroEre_CAF1_left CGAGCAATCAG-TTAAGAAAAACGAT DroGri_CAF1_left TAGGTGAACCA-AACTTAC---ACAC DroMel_CAF1_left AAAGCAATCAG-TTGATAAA--AACG DroPer_CAF1_left TATTTAATCTT-GGTTAACA--ATGA DroPse_CAF1_left TATTTAATCTT-GGTTAACA--ATGT DroSec_CAF1_left AAAGCAATCAG-TTGATGAA--AACG DroSim_CAF1_left AAAGCAATCAG-TTGATGAA--AACG DroVir_CAF1_left AA-GTCAAAAG-CGCCCAAG--AAAA DroWil_CAF1_left TA-CATTTTAA-CAT-TAAT--ATGT DroYak_CAF1_left CAAGCAATCAG-TTGATAAA--CACG DroMoj_CAF1_left AATAATAACTG-AAAATACA--ACTA