CLUSTAL W --- LocARNA 1.4.8 - Local Alignment of RNA DroAna_CAF1_left AGAACACAAATCCCTGCTGCCATCAAATGG-CTAT-GGACGCGAATA-AATAGCAACACAA-ATCATGACCCACATAGACCAAAT-GCCTGAA-GATCTATTGG----CTA-ATCG-ATG DroEre_CAF1_left TGATCTCAAGTTTCCGCTGCCTGCGATGGC-CTAG-AAAAGCAATCG-AATCCCAAGACAA-ATCATGACCCACATAGACCAATA-GCCGGCA-TATCTGCTTG----GTA-ACCA-ATG DroGri_CAF1_left TTTTTGCACGGACTGGCCACAAGCTGCCGC-TGCG-AAC---GGACAAGCCCACAAGACAA-ACCATGACCC--ATAGACCAATT-GTCCAGA-GTGCTAACCA----AAA-GTTA-ACC DroMel_CAF1_left AT--CTCAAGTTCCTGCTGCCAGCGATGGG-CTAG-AAAGGCAAACGAAATCCCAAGACAAAATCATGACCCACATAGACCAATC-GCCTGGA-GATCCTCATG----GCA-ACCA-ATG DroMoj_CAF1_left AT--CGTGGAACATGTTCGCCCGGCCCGGCCAGTG-GAC-G---GCA-ACCTTTAAGACAA-ACCATGACCCACATAGACCAAATTGCCCAGT-GCGTGAATCA----AGA-GTCGAACT DroPer_CAF1_left CAAGCCGTTGCTGT--TGGCTATCCATCGGCTACG-AAA-GTTAACAAAATCCCAAGACAA-ATCATGACCCACATAGACCAAAT-GCCTGGGAAAGCTATTCA----AAG-ACCA-ATG DroPse_CAF1_left CAAGCCGCTGCTGT--TGGCTATCCATCGGCTACG-AAA-GTTAACAAAATCCCAAGACAA-ATCATGACCCACATAGACCAAAT-GCCTGGGAAAGCAATTCA----AAG-ACCA-ATG DroSec_CAF1_left GA-TCTCAAGTTCCTGCTGCCAGCGATGGG-CTAG-AACGGCAAACG-AATCCCAAGACAAAATCATGACCCACATAGACCAATC-GCCTGGA-GATCCTCATG----GCA-ACCA-ATG DroSim_CAF1_left GA-TCTCAAGTTCCTGCTGCCAGCGATGGG-CTAG-AACGGCAAACA-ACTCCCAAGACAAAATCATGACCCACATAGACCAATC-GCCTGGA-GATCCTCGTG----GCA-ACCA-ATG DroVir_CAF1_left GG-CCACAAGCTGACCCTGCCCC-TTAGG--CTAGCCAG--CGGACA-AATCTCAAGACAA-ACCATGACCCACATAGACCAACT-GCCCAGA-GTGCTGGCCA----AAAGACTTCGTA DroYak_CAF1_left CAATCTCAAGTTCCCGCTGCTGGCGATGGT-CTAG-ACAAGCAAACG-AATCCCAAGACAA-ATCATGACCCACATAGACCAATG-GCCTGAA-GATCTGCTTG----GTG-ACCC-ATG DroWil_CAF1_left CTTAAATTT--T-TCAACTAGATCAACAGT-TATA-AAAATAAAAAC-AATCTCAAGACAA-ATCATGACCCACATAGACCAAAA-ACAATGC-GGGTTACGAAACAAAAA-TCAA-AGC DroAna_CAF1_left ACA-CT-TACT-GGCTG---CT-CGCCTTTCTCCCAA-TT-TCAAGGCGTTG---TAGATC--GTAAA-AG-CCAT-TGATTAA----CTTTT-AGA-C-TCAGGCCCTTAG--TGCTA- DroEre_CAF1_left TCC-CC-AGTT-TGCAG---CG-CGTCCTTCTCCCAA-AC-TCAGGGCGATG---CTGTCA--ACCGG-GG-GCAT-AGGCCAC----CACTT-GGA-C-TCCGGCTCCTCA--AGCC-- DroGri_CAF1_left TAC-GGCTAGC-AGCTG---CA-CGTCCATCTCCCAAAAC-TCAAGGCGTTA---CAGCTG--CTGCT-GT-GCAT-TAACTTT----TGGTCAGGT-CACTGGAC-GCCTGACAGCCAA DroMel_CAF1_left TTC-CT-AGTT-TCCAG---CG-CGTCCTTCTCCCAA-AC-TCAGGGCTATG---CTGTCA--ACAGT-GG-GCAT-TGACCTC----CATTT-GGA-CTCCG-GCTTCTAAAGAGACC- DroMoj_CAF1_left ATG-CC-TCCA-GTCAGCTGTCACATTCATCTCCCAA-AT-TCTGGATGTGACTGCTGCGCT-GGGGC-TG-TGTCTTGACTCT----TGCTT-CGCTCACTGGGCACTAGATGACCTC- DroPer_CAF1_left CTT-GG-GATC-AGCTA---AG-CGTTTTTCTCCCAA-ATTACAAGACGCCG---CGGCTG--ACCCT-ATACCAT-TGGCCTT----TGAAT-AGA-CCCTG-GCCCCCTGACAGTTG- DroPse_CAF1_left CTT-GG-GATC-AGCTA---AG-CGTTTTTCTCCCAA-ATTACAAGACGCCG---CGGCTG--AGCCT-ATACCAT-TGGCCTT----TGAAT-AGA-CCCTG-GCCCACTGACAGTTG- DroSec_CAF1_left TCC-CT-AGCT-TGCAG---CG-CGTCCTTCTCCCAA-AC-TCAGGGCGACG---CTGTCA--ACAGT-GG-GCAT-TGACCTC----CATTT-GGA-CTCCG-GCTCCTAAAGAGTCC- DroSim_CAF1_left TCC-CT-AGTT-TTCAG---CG-CGTCCTTCTCCCAA-AC-TCAGAGCGATG---CTGTCA--CCAGT-GG-GCAT-TGACCTC----CATTT-GGA-CTCCG-GCTCCTAAAGAGCCC- DroVir_CAF1_left CGC-TG-AGCACAGCTG---CA-TGTCCATCTCCCAA-AT-TCTGGACTGTG---CAGCTT--GCCCA-GC-GAGT-TGGCTTT----TGGAC-GGCGCCCTGG-ACGCTAGACAGCCA- DroYak_CAF1_left TCC-CC-AGCT-TGCAG---CG-CGTCCTTCTCCCAA-AC-TCAGGGCGATG---CTGTCA--ACAGG-AG-GCAC-AGGCCGC----CATTT-GGA-C-TCCGGCTCCTAAGAAGCC-- DroWil_CAF1_left -CTCTT-GCCA-ACTAT---AT-ATCTTATCTCCCAA-AT-CAAATGATAAT---ATAGCAGGAGCAATAG--GCG-TTGGTTTCTCTTTCGA-AACTTGCAC-GTTTCGTT--AGCTA- DroAna_CAF1_left CCACTGCCA-A-AGGA---TAG-AT------------CTTCCC-C-TGGCCAAGCTCTCTCCCACGGCCAGGTGGTATA-----AAAGTAACACG-TCAAGTGCACC-CGCCACAGGT-C DroEre_CAF1_left CCCCTGTCA-A-AGGA---TCA-TT------------CTGCCC-A-AGGCCAAGATCTCTCCCACGGCCAAGGGATAGA-----TGAGA-TAGCA-ACCAGTGCGCC-AGCCACAGGA-C DroGri_CAF1_left ATGCCGCCACTGAGGATTAACACAG------------TTGCCA-T-AGGCCAAGTTCTCTCCCACGGCCTATGAGGAGC-----TGGTT-AATCA-AC-----CACC-CGCCACAGGT-G DroMel_CAF1_left CCGTGTCAA-GAAGGA---TCA-CT------------CTACCC-A-AGGCCAAGATCTCTCCCACGGCCAAGGGTTAGA-----TGGGA-TAGCA-GCCAGTGCGCC-AGCCACAGGT-C DroMoj_CAF1_left AAGCTGTCT-G-GTGA--TAGA-CG------------CTGCCT-G-GAGCCAAGCTCTCTCCCACGGCTCCAGAGCAGC-----GGCTC-T-GCAGTTTTTAGCACC-CGCCACAGGT-G DroPer_CAF1_left TCGTTGCCC-A-AGGA--TACT--C------------TTTACCAAACGGCCAAGCTCTCTCCCACGGCCCTGGTTAGAGGACAACTGAA-CTGCT-TGAAGTGCACC-AGCCACAGGA-G DroPse_CAF1_left TCGTTGCCC-A-AGGA--TACC--A-------------------AACGGCCAAGCTCTCTCCCACGGCCCTGGTTAGAGGACAACTGAA-CTGCT-TGAAGTGCACC-AGCCACAGGA-G DroSec_CAF1_left CCGTGTCAA-AAAGGA---TCA-CT------------CTACCC-A-AGGCCAAGATCTCTCCCACGGCCAAGGGTTAGA-----TGGTA-AAGCA-GCCAGTGCGCC-AGCCACAGGA-C DroSim_CAF1_left CCGCGTCAA-AAAGGA---TCA-CT------------CTACCC-A-AGACCAAGATCTCTCCCACGGCCAAGGGTTCGA-----TGGGA-TTACA-GTCAGTGCGCC-AGCCACAGGA-C DroVir_CAF1_left ACGCCGCCA-G-AGGG---TT--AG------------CTGCCC-C-AAGCCAAGCGCTCTCCCGCGGCTTGGGTGCAGC-----TG--C-ATGCA-TATTGCGCACC-AGCCACAGGT-G DroYak_CAF1_left CCCCTGTCA-A-AGGA---TCC-TT------------CTGCCC-A-AGGCCAAGATCTCTCCCACGGCCAAGGGATAGA-----TGAGA-TAACA-GCCAGTGCGCC-AGCCACAGGA-C DroWil_CAF1_left TCATAGTCC-G-AGGA---TAA-CAACAATTTGCTCAAAACCC-T-TAGTCAAGCTCTCTCCCACGACAAAAGGGTTT----------------A-GT----GCAATGCTTCACCGTTTC DroAna_CAF1_left -ACTA--TG-AAA DroEre_CAF1_left -ACTG--TGTTCG DroGri_CAF1_left -ACA---G--ACC DroMel_CAF1_left -ACTG--G--GCT DroMoj_CAF1_left -TCGC-----TGC DroPer_CAF1_left -----------CA DroPse_CAF1_left CACAG----TGCA DroSec_CAF1_left -ACTG--G--GCT DroSim_CAF1_left -ACTG--G--GCT DroVir_CAF1_left -ACAACCCTCGCC DroYak_CAF1_left -ACTG--TGTTCG DroWil_CAF1_left -ATAG--A-TCCG