CLUSTAL W --- LocARNA 1.4.8 - Local Alignment of RNA DroEre_CAF1_left CT-CTAATTGC--AGC-TT-----AGCACT-GACAAGTC--AAACA-CACCGA-AAAAGTGCCAGATAAGTAGACACTTCAAGTGCAGTGTAAC--CAAGTGAACTG-TGACA-A--CC- DroMel_CAF1_left CT-CTAATTGC--AGC-TT-----AGCACT-GACAAGTC--AAACA-CACCGA-AAAAGTGACAGATAAGTAGACACTTCAAGTGCAGTGTAAT--CAATTGAACTG-TGACC-A--TC- DroMoj_CAF1_left CA-GCTTAAAA--TTG-AC-----AACTCA-AACAG-CG--AGTG---GGCGG-AAGTGAGCGACGCTTTGCCTCGCCGGTTGGGTAAGTAGACATGTGACCAAGTG-A-AAC-A--GA- DroPer_CAF1_left AT-TGAGCCAT--GGC-CA-----ATAATC-TGTGGGCA--ACATA-ATCCGT-TTATGGCTCTAATTGCAGCTTAAGTCAAACAACCAGGAAC--CAGG-AAGT-GCAGTGC-G--AA- DroPse_CAF1_left TC-ATCATTGA--GCC-ATGGCCAATAATC-TGTGGGCAAAACATA-ATCCGT-TTATGGCTCTAATTGCAGCTTAAGTC-------GAACAAC--CAGG-AAGT-GCAGTGC-G--AA- DroSec_CAF1_left ACTCTAATTGC--AGC-TT-----AGCACT-GACAAGTC--AAACA-CACCGA-AAAAGTGCCAGATAAGTAGACACTTCAAGTGCAGTGTAAC--CAAGTGAACTG-TGACC-A---C- DroSim_CAF1_left CT-CTAATTGC--AGC-TT-----AGCACT-GACAAGTC--AAACA-CACCGA-AAAAGTGCCAGATAAGTAGACACTTCAAGTGCAGTGTAAC--CAAGTGAACTG-TGACC-A--TC- DroWil_CAF1_left CA-A--ACAGA--AGT-CT-----CAAATA-GACAC-TG--ATAG---AGAGA-GAGAGATTTTGGTAAGTAGACGTATAAAATGTGCATTGTCTTGTTGTAAAGTG-A-AGTGA--AAC DroYak_CAF1_left CT-CTAATTGC--AGC-TT-----AGCACT-GACAAGTC--AAACA-CACCGA-AAAACTGCCAGATAAGTAGACACTTCAAGTGCAGTGTAAC--CAAGTGAACTG-TGACA-A--CA- DroGri_CAF1_left AC-TGACAAGT--CAA-AC-----AA-----CTAAGTGG--GAGAAGCTTAAGCATTACCATTGGGTAAGTAGACATGTGAGCTGCATTGTGCA--CAAGTGAAACT-CAAAT-CTCAA- DroVir_CAF1_left GC-TTCAAATTGTCAACTC-----AA-ACAGTTAAGTGC--GAGCAGCTTCGA-CTTATCGCTGGGTAAGTAGACATGTGA---GCATTGTTA-----AGTGAAACA-AATAT-CTTAA- DroEre_CAF1_left GAATA----AAAAAACCGAAGTCTTTTTACCATCAGCGAGGTATAGAGTTCCTACGTTCCTAT--TC---AG----TCGTAGGAACTTAATACCGTGCTCTTGGAGGACTGTCGACCATC DroMel_CAF1_left GAACG-A--AAAAAACCGAAGTCTTTTTACCATCAGCGAGGTATAGAGTTCCTACGTTCCTATATTC---AG----TCGTAGGAACTTAATACCGTGCTCTTGGAGGACTGTCGACCAGC DroMoj_CAF1_left GATTGTA--AAGATAACGAAGTCTATATACCATCAGCGAGGTATAGAGTTCCTACGTGCAAAT--TG---CAATAGTCGTAGGAACTTAATACCGTGCTCTTGGAGGGCTGTCGACCAAC DroPer_CAF1_left AAGT--A--TCTAAAGCGAAGCCTCTTTACCATCAGCGAGGTATAGAGTTCCTACGTGCCGTA--TCCAAAG----TCGTAGGAACTTAATACCGTGCTCTTGGAGGGCTGTCCATCAAC DroPse_CAF1_left AAGT--A--TCTAAAGCGAAGCCTCTTTACCATCAGCGAGGTATAGAGTTCCTACGTGCCGTA--TCCAAAG----TCGTAGGAACTTAATACCGTGCTCTTGGAGGGCTGTCCATCAAC DroSec_CAF1_left GAACG-A---AAAAACCGAAGTCTTTTTACCATCAGCGAGGTATAGAGTTCCTACGTTCCTAT--TC---AG----TCGTAGGAACTTAATACCGTGCTCTTGGAGGACTGTCGACCATC DroSim_CAF1_left GACCG-A---AAAAACCGAAGTCTTTTTACCATCAGCGAGGTATAGAGTTCCTACGTTCCTAT--TC---AG----TCGTAGGAACTTAATACCGTGCTCTTGGAGGACTGTCGACCATC DroWil_CAF1_left AAATTTG--AAATAAACGAAGCCTATTTACCATAAGCGAGGTATAGAGTTCCTACGTGCAAAT--TG---CAATAATCGTAGGAACTTAATACCGTGCTCTTGGAGGGCTGTCGAACAAC DroYak_CAF1_left GAAAG-AACAAAAAACCGAAGTCTTTTTACCATCAGCGAGGTATAGAGTTCCTACGTTCCTAT--TC---AG----TCGTAGGAACTTAATACCGTGCTCTTGGAGGACTGTCGACCATC DroGri_CAF1_left AACCG-A--AAGATAACGAAGTCTATTTACCATTAGCGAGGTATAGAGTTCCTACGTGCAAAT--TG---CAATAATCGTAGGAACTTAATACCGTGCTCTTGGAGGGCTGTCGACCAGC DroVir_CAF1_left GATTT-A--AAGATACCGAAGTCTATATACCATCAGCGAGGTATAGAGTTCCTACGTGCAAAT--TG---CAATAATCGTAGGAACTTAATACCGTGCTCTTGGAGGGCTGTCGACCAGC DroEre_CAF1_left ATAAAGTTGAA--AG--ACATATCGAATTTGAAGTGATAAGGTGAA-TG--TTTTA-ATTCGTTA-AATTACCAACTCATAAA------ATCTTGCTTGAACTTTAACTTGACATAAAAT DroMel_CAF1_left ATATAGTTAAA--AG--ACAACTTGAAATTGAAGTAATAAAGTGAA-TT--ATTTA-ATATAAATATA-TAAATATATTCAGTT-T-GAAGTTTACCTAGACATAATATGTATAAGAAAG DroMoj_CAF1_left AAAACGAATAA--AG--TGAACAAGTTAA---ATATATCTATAAATATCCTTAATT-ATTAATTATAA-AAATA-------AAG-A-TTT---CAGATATTTAAATTAT-CAT--TATA- DroPer_CAF1_left GAACGTGAAAC--AG--TGT-ATCTTTAA---AGAGTGTATCTTAA-GT--GTA-G-ATGTG--G-CC-GGG--ATGCGTCTT----ACAACCCCACGAAACAATCGCAGGGCAGAT--- DroPse_CAF1_left GAACGTGAAAC--AG--TGT-ATCTTTAA---AGAGTGTATCTTAA-GT--GCA-G-ATGTG--G-CC-GGG--ATGCGTCTT----ACAACCCCACGAAACAGTCGCCGAGCAGAT--- DroSec_CAF1_left ATATAGTTGAA--AG--ACACATTGAAAATTAAGTGAATGATTTAA------------TATAAATATA---------TCCAGTG-T-GAAGTTTACCTAGACATAAAATGTGAAAACATG DroSim_CAF1_left ATATAGTTGAA--AG--ACAGATTGAAAATTACGTGATAAAGTGAA-TG--ATTTA-ATATAAATATA-TAAATATACACAGTG-T-GAAGTTTACCTAGGCATAAAATGTGAATGAAAG DroWil_CAF1_left AAAATGAAATA--AA--GTGATTAAATAC---ATAATTCTAATTCTTACTTAAGCT-GGAGCTCACTG-CAGCA-------AAC-A-AAA---GCTCTTCTAAGAACTA-GTC--TTTA- DroYak_CAF1_left ATAAAGTTAAA--AG--ACATATCGAAATTGCAGTGATAAAGTGAA-TG--TTTGA-ATTCGTAG-AATTCTTAGCTCATAAAA-T-ATATCTAGTGTGAACATTACCTTGACATAAAAT DroGri_CAF1_left ATTGATCAAAA--CA--ATTAAGTGACTA-----AGTGAAGCAAAA-CG--TTA-CAAATGT--G-CT-GCA--AAGTGATATAT-TATTATGCAAT--TTATGTGATAACTTTAAGTTT DroVir_CAF1_left AAGAAAAGAAAAAAACTATAAAGTGACAA-----AGTGAAACAAAA-TG--TTT-GGATATA--T-TT-TTA--AAGTGAAATATTTGATTTGAATG--TAAAGCTCCTTAAATATTGTC DroEre_CAF1_left GCGGGAGAAGA-AATATCCTATA--------ATCTTTAAAT DroMel_CAF1_left ATAA-ACCAGA-G---TTAGATC--------GTCTATAGAA DroMoj_CAF1_left -TGT-A-TAATAA---AACTTGA---------AGAGTG-GA DroPer_CAF1_left -CGA-A-TTCCTC---CCCTAGA---------GGAACCCTT DroPse_CAF1_left -CGA-A-TTCCTA---CCCTAGA---------GGAACCCTT DroSec_CAF1_left ACAA-ACCAGA-A---TTAGATCGTCTGTTAAATCTTGTAA DroSim_CAF1_left ATAA-ACCAGA-G---TTAGGTC--------GTCTGTTTAG DroWil_CAF1_left -GTA-G-ATTTCT---ATCAATA---------AATTGAGAG DroYak_CAF1_left GTGT-AAAAGA-T---AATGATA--------ATAATAATAA DroGri_CAF1_left ACAA-TATCGA-C---TTAAGCT--------GGTAAATAAA DroVir_CAF1_left AATA-AATCGT-G---TCCTTCT--------AGCA-AATTC