CLUSTAL W --- LocARNA 1.4.8 - Local Alignment of RNA DroAna_CAF1_left TGGGAAAAA---CATTTT-AAATACTA--AATTTAATTTA--A-CTTTTATAATAT--------ACAAATAAAAGA--AATATAAAATATATAAAAATGTGAATAAAAAAAGAATTAAAG DroEre_CAF1_left ACATATTTT---GATAAATAAAT--------ACATAAAC---C-ATTTATTTTCTATAGTTTAAATATATTTTTTCTTTA-ATTTTTCTGAAAATTTTCACAAAAAAAT-TATTAA---- DroMel_CAF1_left TTGAAATCC-------AT-ACATATTG--TTTACGGGTT---A-AACCATTTACTT------------TCTATAGTTTAA-ATATTTTCTTTAATTTTCAGGAAAATTT-GCAAAGAAAA DroSec_CAF1_left GGGGTTTAA---ATCCGT-ACATATTG--TTAACGGGTT---A-AGCCATTTACTG------------TCTATAGCTTAA-ATATTTTCTTTAATTTTCAGGACAATTT-GCCAAGAAAA DroSim_CAF1_left ACAAAAAAA---GATGCT-ATAGAAAA--GTACCAAGTT---A-AGCCATTTACTT------------TCTATAGCTTAA-ATATTTTCTTTAATTTTCACGACAATTT-GCCAAGAAAA DroYak_CAF1_left GAAATCCTTAGATATTGT-TCTGTCGTTTTAACCTTTTT---T-TTCTTTGTTAAA------------ATTGTTATTTAA-TTTCCCAGAAAAAATTTGAGAAAAAAAA-ATGATTAAAT DroPer_CAF1_left CGAAATT---TATAGAGA-TCTAGCGT----ACGAATCTTCTTTTTTTGGTTAGAG------------TTATTATTTGAA-TGATGAAAAATAGCAATTTAGTTTATCA-ATTTATATTA DroPse_CAF1_left TTGCGACATTTATAGAGA-TCTAACGT----ATGATTTTTT-T-TTTTGTTTAGAG------------TTATTATTTTAA-TGATGAAAAATAGGAATTTAGTTTATCA-ATTTATATAA DroAna_CAF1_left T--------------------TTTAAAAAAACAAAAAAATAGTTTGCCGGGCTCAACCGGGATTTGAACCCGGGACCTCTCGCACCCAAAGCGAGAATCATACCCCTAGACCATTGAGCC DroEre_CAF1_left ---------ATGTGGTTGAACG-G--AACGACAAAAGT-AATACAGCTGGGCTCAACCGGGATTTGAACCCGGGACCTCTCGCACCCAAAGCGAGAATCATACCCCTAGACCATTGAGCC DroMel_CAF1_left AATTTGAACGTGCAGTTGACCGTT--GAACAACAAAAT-AACACAGCTGGGCTCAACCGGGATTTGAACCCGGGACCTCTCGCACCCAAAGCGAGAATCATACCCCTAGACCATTGAGCC DroSec_CAF1_left A--------------------GTT--AAAA--AAAAAT-AATACAGCTGGGCTCAACCGGGATTTGAACCCGGGACCTCTCGCACCCAAAGCGAGAATCATACCCCTAGACCATTGAGCC DroSim_CAF1_left A--------------------GTT--AAAAAAAAAAGT-AATACAGCTGGGCTCAACCGGGATTTGAACCCGGGACCTCTCGCACCCAAAGCGAGAATCATACCCCTAGACCATTGAGCC DroYak_CAF1_left G-----------TGG-----TT-G--AACGACAAAAGT-AATATAGCTGGGCTCAACCGGGATTTGAACCCGGGACCTCTCGCACCCAAAGCGAGAATCATACCCCTAGACCATTGAGCC DroPer_CAF1_left A--------------------G-T--ATTGATAAA-AA-AGTTTAGCCGGGCTCAACCGGGATTTGAACCCGGGACCTCTCGCACCCAAAGCGAGAATCATACCCCTAGACCATTGAGCC DroPse_CAF1_left A----------------------T--ATTGATAAAAAA-AGGTTAGCTGGGCTCAACCGGGATTTGAACCCGGGACCTCTCGCACCCAAAGCGAGAATCATACCCCTAGACCATTGAGCC DroAna_CAF1_left GCATGGACGT-CTGCTGCATTTTTTCAGTTTTGTGC-------CAGACGGTATAT-AAACTTTAGTTATTTAAGTTAAAAATAAAATATATAAGCAAACCA-TCT--GCCTCAGGGGACA DroEre_CAF1_left TCATGCAAGAATCGCCGCTGCTTGCAAGTTTCGATC-------TATGTAGAGCAAAGCATTTTCTTGAAT-ACAATTCGAGGTGAATGGAAATATACCATCTGCCCCAAAGACAAACATA DroMel_CAF1_left TCATAACGAGTAGGCAGCTGTTCGCCAGTTTCCAAC-------TAGGCAAAGCAAGGCATTTTCTTGAGT-AAGCCTCTAAAGACAAACAAAAATCATTGC-TTT--GATGTAACAATCT DroSec_CAF1_left TCATAACGAGTTGGCAACTGTTCGCCACTTTGGAAC-------TAGGCCGAGCAATGCATTTTCTTGAGT-AAGCATTTAAAAGCAAACAAAAATAATTTC-TTT--GATATAACAATCT DroSim_CAF1_left TCATAAAGAGTTGACAGCTGTTCGCCACTTTCGAAC-------TAGGCAGAGCAAAGCATTTTCTTGAGT-AAGCATTTAAAGGCAAACAAAAATAATTTC-TTT--GATATAACAATCT DroYak_CAF1_left TCATGCAGAGTTCGCGGCTGTTAGCCTCTTTCGAAC-------TGAGCAGAGCAAAGCAATTTTATGAAT-GCAATTTGA--GGTGAATAGAAATACACCA-TCT--GACTCTAGAGACA DroPer_CAF1_left TCTTGCCGAGTCATGCCCAGATAACAGTTTTCTATATGTGAGCCAAATAGCACGAA-CAACTAAAACAAG-TAACTATAA-AATCAAATCACAATCAAGAG-GAA--AGTGTTTCTGTAA DroPse_CAF1_left TCTTGCCGAGTCATGCCCAGATAACAGTTTTCTATATGTGAGCCAAATAGCACGAA-CAACTAAAACAAG-TAACTATAAAAATCAAATCACAATCAAGAG-GAA--AGTGTTTCTTTAA DroAna_CAF1_left AATA-TAAATC--AACATTTCAGGTTG-TGTCAACA DroEre_CAF1_left AATA-ATTTCT--TTGATGT---AACA-ATCTTAAA DroMel_CAF1_left AAAA-TATATA--TTTAGTAAACATAG-AACAATAC DroSec_CAF1_left AAAA-TATATA--TTTAATAAACATAG-AACAATAC DroSim_CAF1_left AAAA-TATATA--TTTAATAAACATAG-AACAATAC DroYak_CAF1_left AATG-CAAATACTTTCTCTGATGTAAC-AACCTAAA DroPer_CAF1_left TCTTGTTACCA--CTAAAATAGAAGAAAAACACTGT DroPse_CAF1_left TCTTGTTACCA--CTAAAATAGAAGAC-AAAAACAC