CLUSTAL W --- LocARNA 1.4.8 - Local Alignment of RNA


DroEre_CAF1_left   AGCCC---CGCA-GCCA--GCAGCCACAAAAT-GCAG-TA-GCAACAC--CAACACGAG-CCAGGAGAAAGGGACAGAACGTAGCGGCTGCAAGTATACAGCTC---TTAGCG-GCTCCG
DroGri_CAF1_left   TGAC---TGTTCTATTTTGGTTTGCT--GCTT-GCTT-GA-TTAGATA--AATTTTGTT-TGGCTTCGTTGAGCATTCGTTGCTCGCGTGCCTCTAGACGACAT---TTAGCG-TTCAAG
DroMel_CAF1_left   GCGA---CAGCA-AACATCAGCAACA--AAAT-GCAG-TA-GCAACAG--CAACACGAG-CCAGGAAAAAGGGACAGAACGTAGCGGCGGCAACTAAATGACTT---TTAGCG-ACGCAC
DroMoj_CAF1_left   GGCAAAAGTTCT-ATTTATATTGTGT--GCTAGCTAGTGATTAGATAA--GCTTCATAA-TGTATGCTATAACCTATTGCTGAGCA------ACTAATTTACGT---TTTGCG-CCTCGA
DroPer_CAF1_left   CGAT---TAGAT-AAGCCCCAAAGCA--GCAA-CAAC-TA-GAGACAG--ACAGGCTAT-GGGGCGGTGGACACCTCAACGGAGCACGCGTGACTACACGCCAC---TTAGCG-CCATTG
DroPse_CAF1_left   CGAT---TAGAT-AAGCCCCAAAGCA--GCAA-CAAC-TA-GAGACAG--ACAGGCTAT-GGGGCTGTAGACACCTCCACGGAGCACGCGTGACTACACGCCAC---TTAGCG-CCATTG
DroSec_CAF1_left   TACG---ACAGC-AACAGCAGCTACA--AAAT-GCAG-TA-GCAACAG--CAACACGAG-CCAGGAAAAAAGGACAGAACGTAGCGGCGGCAACTAAACAACTT---TTAACG-ACACGT
DroVir_CAF1_left   TATA---ATGT--GCT--GGCGATTAGATAAG-CTTC-TC------TG--TTTGTTTTG-CCTAACTAGGGCTGCGCTGCT--GGGCGTGCGCCTTAGTCAAAG---TTAGCG-GCGTTT
DroWil_CAF1_left   TTTT---AATAT-GCGGGCGATTAGA--TAAG-GTTC-GC-GGCATTTGGCAAGGGCAGGCCCCAACATATTCCTATGTCTGTGTGTGGATATGACTGTTCCCAGGGCCTTCGACTGCCT
DroYak_CAF1_left   AAAT---ACGAC-AGCAGCAACCACA--AAAT-GCAG-TA-GCAACAA--GAACACGAG-CCAGGAACGAGGGACAGAACGTAGCGGCTGCAACTATACAGCTC---TTAGCG-CCACCC
DroAna_CAF1_left   GCTT---GCGAT-TAGATAAGCCCCA--AAGA-GCCA-GA-GAATCG---CCA---GAG-T-TGTGGAAAGGGACGGAACGTAGCAAGCGTGTGTAATCGGAAC---ATGGTT-TCGAAC

DroEre_CAF1_left   CCAGCACAACGCCGAAATAGCTCAGTTGGGAGAGCGTTAGACTGAAGATCTAAAGGTCCCCGGTTCAATCCCGGGTTTCGGCAACGCGCTA-TT---TTTTTTTTAATT-TTTACGAATT
DroGri_CAF1_left   CAATAAGAGTGCCGAAATAGCTCAGTTGGGAGAGCGTTAGACTGAAGATCTAAATGTCCCCGGTTCAATCCCGGGTTTCGGCAATAAGT-GGAT---TTCTTT-TTCCT-ATTTTTTTCT
DroMel_CAF1_left   TCCACACGTCGCCGAAATAGCTCAGTTGGGAGAGCGTTAGACTGAAGATCTAAAGGTCCCCGGTTCAATCCCGGGTTTCGGCAATTCACAT-TT---TTGCT----CGT-GAATTCTTTT
DroMoj_CAF1_left   CCAACATAGCGCCGAAATAGCTCAGTTGGGAGAGCGTTAGACTGAAGATCTAAAGGTCCCCGGTTCAATCCCGGGTTTCGGCAAG-CAAAACTT----TTTTGTTTTTT-AAATCTATTT
DroPer_CAF1_left   CCATCACAGCGCCGAAATAGCTCAGTTGGGAGAGCGTTAGACTGAAGATCTAAAGGTCCCCGGTTCAATCCCGGGTTTCGGCAAGCAAAAA-TC---CTTTTT-ACTTC-TCTTTTTTTT
DroPse_CAF1_left   CCATCATAGCGCCGAAATAGCTCAGTTGGGAGAGCGTTAGACTGAAGATCTAAAGGTCCCCGGTTCAATCCCGGGTTTCGGCAAGCAAAAA-TC---TTTTTT-ACTTC-TCTTTTTTTA
DroSec_CAF1_left   CTAACACGTCGCCGAAATAGCTCAGTTGGGAGAGCGTTAGACTGAAGATCTAAAGGTCCCCGGTTCAATCCCGGGTTTCGGCAACAAGAAA-CT---TTTTT-----ATTTTTTATTATT
DroVir_CAF1_left   TGTGCATGCCGCCGAAATAGCTCAGTTGGGAGAGCGTTAGACTGAAGATCTAAAGGTCCCCGGTTCAATCCCGGGTTTCGGCAAGCAATAT-TT---TTTTGT-TTTCA-ATTTTTTTTT
DroWil_CAF1_left   ACGACACAGCGCCGAAATAGCTCAGTTGGGAGAGCGTTAGACTGAAGATCTAAAGGTCCCCGGTTCAATCCCGGGTTTCGGCAAGCGTTCA-TT---TTTTTT-TTGTT-ACTTATTTTT
DroYak_CAF1_left   CTAACGTAGCGCCGAAATAGCTCAGTTGGGAGAGCGTTAGACTGAAGATCTAAAGGTCCCCGGTTCAATCCCGGGTTTCGGCAAAGCAACT-TTTTTATTTT----TTA-AATACTTATT
DroAna_CAF1_left   CACTCA-TATGCCGAAATAGCTCAGTTGGGAGAGCGTTAGACTGAAGATCTAAAGGTCCCCGGTTCAATCCCGGGTTTCGGCATTTACTTT-TT---GCTTATTTTTAC-TTTAGTTTTG

DroEre_CAF1_left   ACTTTTTA-TTTTTAAG-AA---CTTAATTTATATT-GATAACGCT-----CTTCCATTAT-TTTCTACAAA----CAAAAGGCTTT
DroGri_CAF1_left   GTGATAA--TAACACAT-TT---TTTGTTTGGCAAAATATGATCTG-----TTAATGATTTTTAAATAGCTG----AAGCATTTGAC
DroMel_CAF1_left   TTACTTTT-AAGAATTT-ACCTCGACTATTAAATATTTT-GAATGCA----GCTCAAGAAC-AAGAAGCATT----TAAATTTTTAA
DroMoj_CAF1_left   TAGAATGT-TATAATTG-TT---TTTGAATGGATAATAATTAGGTG-----GTAATATAAA-TAAACTATAT----GAGCATTGAAA
DroPer_CAF1_left   TAGTTTTA-CAGTAAGA-AA---TCTTTTAAAAGGACTTACCTCAA-----TTATTTTAAA-TACACTTGAG----TTTAACTTTTA
DroPse_CAF1_left   AACGTACTTACCTCAAT-TA---ATT-TAAATACACTTGAGTTGAA-----CTTTTAATTT-TAATCTAATT----TTGGTGATTAT
DroSec_CAF1_left   --TTTAT--TATTACAGCAT-ACATTTTCAATTTATATT-TATTTGT----TTTTTTTGTC-AAGAATATAT-TTTTTTTGAAGAGT
DroVir_CAF1_left   AAATTGTT-TAAATGTT-TG---TTCTAGCATAAAT-----TGATGAAATATTTATGTTTT-----ATATTAAATTCAAGCTGATAT
DroWil_CAF1_left   AATATTTG-TGAATATT-TC---TTTTTATGGAATTGCTTTTTCAT-----TGTACTCACA-TAGATTCTTT----AATTTATTTTG
DroYak_CAF1_left   TTATCTTA-TATATATT-TG---AAATTTTGGATTATTA-TTTCAAA----GCAAGT-AAA-GTTTATTGAA---TATATATTTCAG
DroAna_CAF1_left   TTTAATTA-ATTAAGAA-GA---CATTGCGGCTGAGCAAACAAATC-----TTTA-AAAGT-AAAAAGATTT----CTTAATGATTT