CLUSTAL W --- LocARNA 1.4.8 - Local Alignment of RNA DroEre_CAF1_left AATTGA---AA-CAGCAAACTC--CGTT---GGCCAAAG-AC-TGT-GCGATGCGTTTTTAAA-CTAACTCGTTCC--GGAGCAAT-AAA---A--AAGA-CAGAT---AAAA-TA-TTT DroMel_CAF1_left CCAA-A---GA-CAGCCGTTGC--GGATTT-GGTCGGTC-AA-TTT-GAGGAAAGCAATGATT-TTTTAAGCCACC--AATTGAAC-TAA---A--AATA-AAAAA---GAGT-TA-CAA DroAna_CAF1_left TTTG-CTGTAACATTGA-AATA--GGATATTTACTGGCC-AA-ATA-CAGCAGTGC-CAGGAT-TTGTCTACTTCATGGAAAAAAG-AAA---AACTAAA-ATATTTCTATAA--AAAAT DroGri_CAF1_left ACTT-C---GAGCAGCT-TTAAATTTATGA--GTCAACT-AATTGCCCTGGCACTG-AGGAAA-CAATTCAGAAAG---AGCACTA-AAA---A----TA-GAGAA---ACAA-AA-AAA DroMoj_CAF1_left A-----ATAGA--GCGA-CTCT--CAACGAGCTGCGCTC-AA-TTT-ATGATTAAA-TAAATT-CGTTTGGCACAACTAAAAATAT-TAA---AACATTT-TTTTA---AAAA-TAATGA DroPer_CAF1_left ACTA-T----A-T--AA-TTGC--G--CAG-G-AGAAAA-TC-TT--TGGTGAGAG-TGAGAA-ATAACATCAGGG---TAAACAG-AAA---G-CAAAA-AAAAA---AAAA-AA-ACT DroPse_CAF1_left AACT-A---TA-T--AA-TTGC--G--CAG-G-AGAAAT-TC-TT--TGGTGAGAG-TGAGAA-ATAACATCAGGG---TAAACAG-AAA---G-CAAAA--AAAA---AAAA-AA-ACT DroSec_CAF1_left GTTT-G---CG-GATTT-TGTC--GGTCAA-T-TGGAGG-AA-AGCAATGATTTTT-AAACTA-CCAATTGGAGTA---AAAATAA-AAA---AGAGATA-CGAAT---AAAATAT-TTG DroSim_CAF1_left GTTT-G---CG-GATTT-TGTC--GGTCAA-T-TGGAGG-AA-AGCAATGATTTTT-AAACTA-CCAATTGGAGTA---AAAATAA-AAA---AGCGATA-CGAAT---AAAATAT-TTG DroVir_CAF1_left CCTG-C---GCTGCGAA-CTGC--TCCCAATTTACGACC-AC-A----CTAATTGT-CTTGGC-ACAGCGGAAACTG---TTTTAG-AAACGCAACAGAC-AATTA---ATAA-AAAA-G DroWil_CAF1_left CAAT-A---TT-TATAT-TTAA--G--CAA-G-ACAAATTAC-TT--TCACTAAGC-CAATAA-AAAAGTGTTAAA---CAATTAA-TAA---GATATGTTTATTG---TTAA-GA-GTG DroYak_CAF1_left TTGG-T---GG-TCAAT-TGGC--TGAAAG-CGATGATT-TT-TTAAACTAACTCG-TTCCGGAGCATTTGCG-CT--AAAAA-TGAAAA---A--GATA-CAGAT---AAAATA--TTC DroEre_CAF1_left AGAAA-AAA-AGCGGT-CCCCTAAGGTTCTACCGAGATTTGAACTCGGATCGCTGGATTCAGAGTCCAAAGTGCTAACCATTACACCATAGAACCAGGTGA-AGGTCCCACCAAA-ATTT DroMel_CAF1_left ATAAA-AAAGCGAGTT-CCTCAAAGGTTCTACCGAGATTTGAACTCGGATCGCTGGATTCAGAGTCCAAAGTGCTAACCATTACACCATAGAACCAGGTGA-AAGTCCAACGAAA-ATTG DroAna_CAF1_left ATTAAATTT-AAAATATATTTTCAGGTTCTACCGAGATTTGAACTCGGATCGCTGGATTCAGAGTCCAGAGTGCTAACCATTACACCATAGAACCGGATGAGTCCTTTAGGGATA-AATC DroGri_CAF1_left ATAAA-AAA-AGAA-A-ATCACTAGGTTCTACCGAGATTTGAACTCGGATCGCTGGATTCAGAGTCCAAAGTGCTAACCATTACACCATAGAACCGGTTGG-CT-ACTTACAAAT-TATT DroMoj_CAF1_left AAA-A---A-AGAATCTTCGACTAGGTTCTACCGAGATTTGAACTCGGATCGCTGGATTCAGAGTCCAAAGTGCTAACCATTACACCATAGAACCGGTT-GAATGTGGCT-GCGA-AATT DroPer_CAF1_left AAAAA-GTT-TGCATC-GACATCAGGTTCTACCGAGATTTGAACTCGGATCGCTGGATTCAGAGTCCAAAGTGCTAACCATTACACCATAGAACCAGTTGA-CTGGCGCCCAGAA-AATG DroPse_CAF1_left AAAAA-GTT-TGCATC-GACATCAGGTTCTACCGAGATTTGAACTCGGATCGCTGGATTCAGAGTCCAAAGTGCTAACCATTACACCATAGAACCAGTTGA-CTGGCGCCCAGAA-AATG DroSec_CAF1_left CAAAA-AAA-GTGATT-TCCCACAGGTTCTACCGAGACTTGAACTCGGATCGCTGGATTCAGAGTCCAAAGTGCTAACCATTACACCATAGAACCAGGTGA-AAGTTCAACGAAA-ATTT DroSim_CAF1_left CAAAA-AAA-GTAATT-TTCCACAGGTTCTACCGAGACTTGAACTCGGATCGCTGGATTCAGAGTCCAAAGTGCTAACCATTACACCATAGAACCAGGTGA-AAGTTCAACGAAA-ATTT DroVir_CAF1_left AAAAAAAGA-AATTTC--ACTCAAGGTTCTACCGAGATTTGAACTCGGATCGCTGGATTCAGAGTCCAAAGTGCTAACCATTACACCATAGAACCGGTTGA-TGAAGGCA-GCCT-AATT DroWil_CAF1_left AAGCA-AAA-AAATTC-CACCTTAGGTTCTACCGAGATTTGAACTCGGATCGCTGGATTCAGAGTCCAAAGTGCTAACCATTACACCATAGAACCAGTTGT-CAGCACGGCGAACGAATA DroYak_CAF1_left AGAAA-AAA-AGAGTT-TCCCGAAGGTTCTACCGAGATTTGAACTCGGATCGCTGGATTCAGAGTCCAAAGTGCTAACCATTACACCATAGAACCAGGTGA-AAGTCCCACGAAA-ATTT DroEre_CAF1_left GCACTACTGAAATCAGTGATCTT--GAAAGAGCTTTTATGCT--ATAAAATCTATCTATCTAT--CTT-TAAATCTATAAGAAA--A-CCAAAT-ATTACTTTGTCACGCATAAGAAATC DroMel_CAF1_left GCACACTTGAAATCGGTGATCTT--ACAAGAGAATGAAAGAG-CTTTTATACCGCTAAATCTA--TAG-AAATTTAGTCTTATA--A-TAGATA-GTTATAGTTATATA-AGGTAAAAGC DroAna_CAF1_left GCAGGTTTTAAATAGC-GGGGTTTGTGAATATGTGGAAATTA--AAACAAGAATATTAATAT----AC-TTAATTATTTAAATTCATACATATA-TAATAAAG-ATA-CATAATACACAT DroGri_CAF1_left GAGGGTCTTCAAGCGC-TCGGCA--ACAAAGTACAAAGAAAG--TGTTGGCAAC-TTTTGCTGCTGTT-GCGTTTTGATTTATT--TTTAGATT-TTTATTTTTACA-TTAAGAAAGTAG DroMoj_CAF1_left GAAGATGTTGTATCTC-TCAC--ACACACCTCGTGTTTGGCA--GTTCATTATAATTGTGAG----AAATCAGTTTGACTGAATGTGTGTGAAA-GCAGCGGCTATT-TATAGATTTGAT DroPer_CAF1_left GCCCAAAAGACAGCTTGTC-GGT--GTGTGTGTGCGTGAGAA--AGCCAAAGAGAAAGGCATG--CTC-GTTCGGGCTAAAAAT--AGAACGATTAACA-ATAAATATGTATCTACATAT DroPse_CAF1_left GCCCAAAAGACAGCTTGTC-GGT--GTGTGTGTGCGTGAGAA--AGCCAAAGAGAAAGGCATG--CTC-GTTCGGGCTAAAAAT--AGAACGATTAACA-ATTGTTAATAATATTTATAA DroSec_CAF1_left GCACACTTGAAATTAGTGATCTT--ACAAGAGAATCAAAGAA--TTTTATACTAAAAAATATA--TAG-AAATTTAGTTTTATA--ATAATAT--AATATATAATAATATAATTTATAAT DroSim_CAF1_left GCACACTTGAAATTAGTGATCTT--ACAAGAGAATGAAAGAA--TTTTATACTACAAAATATA--TAG-AAATTTAGTTTTATA--ATATATA--GTTATAGTTATTTAATGTAGAAGTA DroVir_CAF1_left GGGGTAGTTATATCTC-TTGGCT--ACATAGTATACGAAATT--CATTGTGTGAGAAATTTTT--GGC-TGAGGCATGCTGATA--AAATTGTC-TATTTTTAGATTTTATAAGGTATTT DroWil_CAF1_left ACATTCTGGAAATTAAGGCCCAA--AGAGAAGACACCACAAATAAGAGAAAGTT--AAATA-T--AAC-TTAAGAGAAAATATA--ATTGGCAAGAAGA-AAGAAAAATTATAATGAAAT DroYak_CAF1_left GCACTCCTGAACGCGGTGATCTT--AAAAGGGAATGAAAGAG-CTTTTATACCATAAAATCTA--CAG-GAATTCAGTGTTATT--ATAAAAT--AAAA-CCAAATATAATGCTGTCATG DroEre_CAF1_left TA DroMel_CAF1_left AA DroAna_CAF1_left AA DroGri_CAF1_left GT DroMoj_CAF1_left AA DroPer_CAF1_left GT DroPse_CAF1_left AT DroSec_CAF1_left AA DroSim_CAF1_left AT DroVir_CAF1_left CT DroWil_CAF1_left AA DroYak_CAF1_left AA