CLUSTAL W --- LocARNA 1.4.8 - Local Alignment of RNA DroAna_CAF1_left A-GT-ATGC--AGT-GTATC-TTTCGC-TGTTTTTGGAGG----TGA-TAATTCAT--TCTATTTC------GGATTTTTTTCAAGTCTTCCGCTTG---GCAG-----CTACCTA-GAG DroEre_CAF1_left G-TGAGCGA---TG-TATCT-GCTTGT-GGATGGAGGGGG-AG-GGG-GAGAATAG--GT--TCTT------GTACGTTTCTTCTTCTTCTTGCTTG---ACAA-----TCG---T-TGG DroGri_CAF1_left G-GCGTCAC--AGC-TGCC-TGTGATCTAAC-GAAATGCC-AATGCG-A--GCAGCGTGT--TCAC------A--GTTGC--TAGAAATAAAGTCTGAG-AAGA-----TCC---A-TTG DroMoj_CAF1_left T-AATATGT--TGT-TGTTGGTATAATACAA-CATTATTA-TTATTT-TATTGTGA--GG--AATT------AGCTTACG--CTTCCAACTATAA-GATGTCAT-----TTG---A-CTA DroPer_CAF1_left A-TGGTTGC--TAT-GGGGT-GGGATC-ACTTTTTTCGGA-CT-TGT-GTGTTCTA--AG--ATTC------TTCTTCAATGCCGATCACCGATCGG---A-TC-----GCT---A-CGT DroPse_CAF1_left A-TGGTTGC--TAT-GGGGT-GGGATC-ACCTTTTTCCGA-CT-TGT-GTGTTCTA--AG--ATTC------TTCTTCAATGCCGATCGCTGATCGG---A-TC-----GCT---A-CGT DroSec_CAF1_left G-CG-ATG-----A-AT-CA-GGGCGT-TGATATTATAGG-----GTGGGGAATAG--GT--TCTT------GTTCATTTCTCGAGCGTCTTGCTTG---AAGA-----CCG---T-TGT DroSim_CAF1_left AACG-CTG-----T-AT-CA-GTGCGT-TGATATTATAGG-----GA-GGGAATAG--GT--TCTT------GTTCATTTCTCGAGCGTCTTGCTTG---ACGA-----CCG---T-TGT DroWil_CAF1_left A-TATACAACACGT-TTTTGTGTAATGCCTA-CAAACAGA-ATTACG-TAAATCTT--TT--CAAC------TACAAGTG--ATCACAAAAACAC-----AAAA-----TAG---A-TGA DroYak_CAF1_left T-CAGCGTG---CT-GGCGT-TCGAGGGTTG-AAATAGGT-TC------TACTTCT--TT--TCTTGTACGATTCTTTAGTT-------CTTGCTTG---ACAACACAACAG---ATGGC DroMel_CAF1_left G-AC-AGGC--GAAAGATGT-ATTAGT-GCGTTGATATTATAG-GGT-GGGAATAG--GT--TCTG------GTTAATTTCTTGAGTGTCTTA----------C-----AAC---T-GTT DroAna_CAF1_left CGATCAG--AAAGAAC-AAATAATTCAA-TAAA-GTAAC-AAAATAAGCAAAAAATTATCCACTTGGCAGCGGTGGGATTCGAACCCACGCCTCCGAGGAGACTGGTGCCTTAAACCAGC DroEre_CAF1_left CGAAG-A---TCGGA---AGAAT---AA-AAAT-TTTGG-CAATTAAGGGATAAAAAAAAAACTTGGCAGCGGTGGGATTCGAACCCACGCCTCCGAGGAGACTGGTGCCTTAAACCAGC DroGri_CAF1_left CTTGT-TAATATTGA---GAGAA--TAT-TTTA-AAATA-AATTGAAAAATAAAAAAAATCACTTGGCAGCGGTGGGATTCGAACCCACGCCTCCGAGGAGACTGGTGCCTTAAACCAGC DroMoj_CAF1_left AAGAT-ATAAGAGTA---AATAT--TTT--TTT-ATAAT-AAATTAAAAAATTAATTTTTCACTTGGCAGCGGTGGGATTCGAACCCACGCCTCCGAGGAGACTGGTGCCTTAAACCAGC DroPer_CAF1_left AGCTG-T---TGAAA---AAGAT---AG-AAAATCT-GGAAAATTTACAAAAAATCAATTCACTTGGCAGCGGTGGGATTCGAACCCACGCCTCCGAGGAGACTGGTGCCTTAAACCAGC DroPse_CAF1_left AGCTG-T---TGAAA---AAGAT---AG-AAAATCT-GGAAAATTTACAAAAAATCAATTCACTTGGCAGCGGTGGGATTCGAACCCACGCCTCCGAGGAGACTGGTGCCTTAAACCAGC DroSec_CAF1_left TGTTG-G--CACTGATCGAAAAA---AT-ACAA-AATAC-AATACTAAGAAAAAA-TAAAAAATTGGCAGCGGTGGGATTCGAACCCACGCCTCCGAGGAGACTGGTGCCTTAAACCAGC DroSim_CAF1_left TGTTG-G--CACTGATCGGAAAA---AT-ACAA-A-------------GAAGAAA-AAAAAACTTGGCAGCGGTGGGATTCGAACCCACGCCTCCGAGGAGACTGGTGCCTTAAACCAGC DroWil_CAF1_left AAAAC-ACAAATAAA---AAGAA--AAC-CTAA-AGGGA-ATTACACAAAAAATTATTTCCACTTGGCAGCGGTGGGATTCGAACCCACGCCTCCGAGGAGACTGGTGCCTTAAACCAGC DroYak_CAF1_left AAAGA--T--CGGAA---AAAAT---AC-AAAA-TAAGGCTATTATGGGGATGAAAAAAAAACTTGGCAGCGGTGGGATTCGAACCCACGCCTCCGAGGAGACTGGTGCCTTAAACCAGC DroMel_CAF1_left GTTGG-A---ACTGAT--CGGAA--AAATATAA--A-AG-AA---ATTGTAAATAAAAAAAACTTGGCAGCGGTGGGATTCGAACCCACGCCTCCGAGGAGACTGGTGCCTTAAACCAGC DroAna_CAF1_left GCCTTAGACCGCTCGGCCACGCTACCATGTGTCTGACGTT-CGTCAAAGTGCTTCT-ACAAGTCCGCA---CAGAACAAGTTTGA---AA--TTCTCGATT-CT---GTCCAGTT---TC DroEre_CAF1_left GCCTTAGACCGCTCGGCCACGCTACCTCGATGGG-GCGCATGTCCAA-TGCTCATG-AATAGACGCTA--GATAG-C-ATCT-GAGACGTTCTAA-CA-AGA-CTGGCACATAAG--A-- DroGri_CAF1_left GCCTTAGACCGCTCGGCCACGCTACCACGTCTAC-AG-CTGTGCCCAACAGCGTAA-AACTGTAAAAA--ACGTT-TCCATTGATTA-TCA-GCAGAATAG--AAT-AAATTGTG--TAT DroMoj_CAF1_left GCCTTAGACCGCTCGGCCACGCTACCATTTGTTG-CTCTTGTGTCAAAGTCTATAT-ATGAGAGAATA--ACAAA-A-AGAGAACGC-ACA-TAATGCCATG-CGC-TCGCGCAC--T-G DroPer_CAF1_left GCCTTAGACCGCTCGGCCACGCTACCATTTCCTA-AATAGCCGCCAAATGGCTGTT-AACAGAAACAG--AGTTT-T-GTTCGGTTCTGAC-TGT-TG-GGT-TTAATTAAAACC--T-- DroPse_CAF1_left GCCTTAGACCGCTCGGCCACGCTACCATATTCTG-CTGCGTTGTCAAATGC-GTGTTAAG-AACTTGC--GGCGC-T-GGTTCGTCGCGTAGATG----TGA-GTTCTT-GCTTAGAA-- DroSec_CAF1_left GCCTTAGACCGCTCGGCCACGCTACCTCGTTCTG-GCTTA-TGTCAAACGCTCGTG-AACAGACGAGCT-ACAGAGACGTTCTAA---GACGAGCGCACATAAGAA-GTATCTGT---GC DroSim_CAF1_left GCCTTAGACCGCTCGGCCACGCTACCTTGTTGTA-GTTCA-TGTCAAACGCTCATG-AAGAGACGAGCA-ACAGAGACGTTCTAA---GACGAGCACACATAAGAA-GTATCTGT---GT DroWil_CAF1_left GCCTTAGACCGCTCGGCCACGCTACCATGTCTGT-CGACCGAGACAAATGACACAA-AAATGGAAACA--CCTCT-A-TTTGCTTGT--CT-GTT-TAATAT-GAA-CCTTCATT--T-T DroYak_CAF1_left GCCTTAGACCGCTCGGCCACGCTACCTTGTTGTG-GCGCA-TGTCCAACACTCATG-AAGAGACGATGCTAGACA-G-CAACTGAGCCGTTCTAA-GA-CGACTG-ACACTAAG---A-- DroMel_CAF1_left GCCTTAGACCGCTCGGCCACGCTACCGTGTTGTA-GTCTA-TGTCAAACGCACATC-AAGAGACAAAA--CGAGA-A-TGTAATAGCTGATTTGTTTTCAAACGTC-TGGCC-----G-- DroAna_CAF1_left ----CCTCACAA-TATACTGTTGTTCT-CGG--GC---T DroEre_CAF1_left AG-TAAATATA--TATGCCAGTGGAACTATTT-TTATGG DroGri_CAF1_left TT--GATGTAA--TTGTGC-TTA-AACGTTTTGCACGAT DroMoj_CAF1_left TAAAATTTCCA--TTGCTT-GGT-TTTGTTGT-GCTCGC DroPer_CAF1_left TG-GCGTGAGA--CTTTATATCTCAAT-GTTC-CCTATG DroPse_CAF1_left ACAGATACTTT--TGTATCTCTGTTGT-GCAA-CTATTT DroSec_CAF1_left ----ATGCTTGT--GGAACTACTTTTA-TGGA-CGCAAC DroSim_CAF1_left ----CTGCTTGTGTGGAACTACTTTTA-TGGA-CG--CA DroWil_CAF1_left GATATTTCACT--ATTTTTATGAGTGGGCACC-CCACCC DroYak_CAF1_left -AG-TATCGTAT-CTCCTT-GTGGAAC-TATT-TTTATG DroMel_CAF1_left AAAATTATACT--TTGAAATTGTGCTA-TTCC-AGCATT