CLUSTAL W --- LocARNA 1.4.8 - Local Alignment of RNA DroAna_CAF1_left ATGCAGA---CG-CAGACTTACAGACAC-CAAAGCTT-TTTAA-G-GT-T-TA-CACTGGGA-TAAGTTT--GTA-ATAATAAAGTAAGGGAAA-A-ATATGATT-AATATTTAAAAATA DroEre_CAF1_left TCTTAAAATGCA-CATGCTAATGAAAAACTTTTTAAGAATAAC-T-TA-G-AAATTTGTATA-TATTTTA--TAT--ATAGTTCTTATTTTAAT-G-ATGAAAAG--AAAAATTTATACA DroGri_CAF1_left ACATAGA---CA-CACAGACACCATAGA-TGG-TCGCCAAGGC-GCTT-T-TTTCACGTTTA-CACGTCG--CCGGCAATTACGAAAAAGCCATCA-TATAATTTATTAAAATTGATAAA DroMel_CAF1_left AGTTGAA---GA-TTTAGAAACAATAAG-CTA-ATAAAATCAT-GTAA-A--AATACGTTATCCATCTAT--TCCATTTTCATAAATGCTGAAA-T-AACAAAGAAAAATATTGTATTCA DroMoj_CAF1_left ACACCAC---AGATGGTCGCCCTGAGCG-TGT--TCCCGGTTTACACGGT-GCCAATTTGTG-CATTATA--CATAAAAATATAAAATTTTCAA-A-TTAAAAAAAAAAAAAAAAAAAAA DroSec_CAF1_left ATGCTTA---TT-TACTTCGTTGTTATT-ACT-AAATACGGTT-TTAA-A-AATATGTGTTC-CACTTTC--ATAAATACTTTTGTTTTTTAAT-T-AACCAAGAAAAATATTGTATTCA DroSim_CAF1_left TTATTAA---TA-AATACGGTTTTAAAA-ATA-TGTGTTTCAC-TTTC-A-TAAATGCTGAA-TTGAATT--AAACAAGAAAAAAATTATGTAT-T-CAAAATAAATACTTAAGTATTCA DroVir_CAF1_left ACACGAT---GT-TACTAAATAAGAA-T-TAA-CTATTTATAT-GGTA-A--ATATTGAGGT-CTCAATAATAAATTAATTTACTGATA-ACATTA-ATGAGAAACTGTTAAATAAAAAA DroWil_CAF1_left AAGCAAA---TC-CAAGTGAACAGATGT-TGA-ACCATGGGCT-AAAC-A--AAAAGTTTATGCGGTGAA--TGAAATAAATTTAAAAATTCAT-A-TATCATGAAAAAAGTTTTTTAGA DroYak_CAF1_left AAAACT---CTT-TAAGAATGGGTTAAA-AATGTTTATATATT-T-TA-C-GTTTGTGATGT-TATAAAA--ATATATTCAATTTTCTTATTAA-A-AGAAACGAAAACTATTCAATTCA DroPer_CAF1_left GCAGACA---CA-GAGACACC-ACA-CA-GCC-CGAGATGGTC-GCCA-TGGAGCAGTCTTAGCAATTTT--C---TGGTTTACACGTTGAAAA-GTCTCACAAAAGAG-AATATTTTTC DroPse_CAF1_left ACACAGA---GA-CACCACAC-AGC-CG-GCC-CGAGATGGTC-GCCA-TGGAGCAGCCTCAGCAATTTT--C---TGGTTTACACGTTGAAAA-GTCTCACAAAAGAG-AATATTTTTC DroAna_CAF1_left TAAAAAAAAAGTAATCCGCCCCCGGGTGGACTCGAACCACCAACCTTTCGGTTAACAGCCGAACGCGCTAACCGATTGCGCCACGGAGGCTCAT-GATCA-GGTCGC--GCCAAA---CT DroEre_CAF1_left AAATAAATACTTCAGTCGCCCCCGGGTGGACTCGAACCACCAACCTTTCGGTTAACAGCCGAACGCGCTAACCAATTGCGCCACGGAGGCATTG-AT-CA-GCGAGA--GACAAA--ATT DroGri_CAF1_left ATTAAAAAATCATATCCGCCCCCGGGTGGACTCGAACCACCAACCTTTCGGTTAACAGCCGAACGCGCTAACCAATTGCGCCACGGAGGCAGTT-AGTCA-CCCACC--GGCAAT--ATA DroMel_CAF1_left AAATATATACTTAAGTCGCCCCCGGGTGGACTCGAACCACCAACCTTTCGGTTAACAGCCGAACGCGCTAACCAATTGCGCCACGGAGGCATTG-AT-CA-ACATG--AGACAAA--ATA DroMoj_CAF1_left ATAAAAAATTTGATTTCGCCCCCGGGTGGACTCGAACCACCAACCTTTCGGTTAACAGCCGAACGCGCTAACCGATTGCGCCACGGAGGCAGCTGAT-CT-CATGCT--GGCAGA--ATA DroSec_CAF1_left AAATAAGTATTTAAGTCGCCCCCGGGTGGACTCGAACCACCAACCTTTCGGTTAACAGCCGAACGCGCTAACCAATTGCGCCACGGAGGCATTG-AT-CG-ACAAGA--GACAAA--ATA DroSim_CAF1_left AAATAAATACTTAAGTCGCCCCCGGGTGGACTCGAACCACCAACCTTTCGGTTAACAGCCGAACGCGCTAACCAATTGCGCCACGGAGGCATTG-AT-CA-ACAAGA--GACAAA--ATA DroVir_CAF1_left AAATAAAAAGTTAACTCGCCCCCGGGTGGACTCGAACCACCAACCTTTCGGTTAACAGCCGAACGCGCTAACCGATTGCGCCACGGAGGCAGTT-AA-TG-TCCAGA-GGGCAAA--TTA DroWil_CAF1_left AAAAAAATTATTGGACCGCCCCCGGGTGGACTCGAACCACCAACCTTTCGGTTAACAGCCGAACGCGCTAACCGATTGCGCCACGGAGGCACTT-GT-CCTCCCAGTGAC--TAATACTA DroYak_CAF1_left AAAAAGATACTTCAGTCGCCCCCGGGTGGACTCGAACCACCAACCTTTCGGTTAACAGCCGAACGCGCTAACCAATTGCGCCACGGAGGCATTG-AT-CA-CTAAGA--GACAGA--ATA DroPer_CAF1_left GGCAAAAGATTTGAGCCGCCCCCGGGTGGACTCGAACCACCAACCTTTCGGTTAACAGCCGAACGCGCTAACCAATTGCGCCACGGAGGCCGAT-ATGGA-ACGTCT--GCCTAA--ATA DroPse_CAF1_left GGCAAAAGATTTGAGCCGCCCCCGGGTGGACTCGAACCACCAACCTTTCGGTTAACAGCCGAACGCGCTAACCAATTGCGCCACGGAGGCCGAT-ATGGA-GCGTCT--GCCTAA--ATA DroAna_CAF1_left CAATACTTAAGATAACG--CT--AGATCATAGG-AAAAAGCATCAGT--T--TGTGGGGTTA--TCTAAAA-ATAGAA-ACGTACA--CCGTAA-CATGCTGTTGTGTT-TATCAAAGGC DroEre_CAF1_left GATACATGAAATTA-AG--GC--GAAACAGCGAGAGAGTCCAATTTTT-AAAAAAGTTGCCATAAACTAT--AAATAAAAG-TAGTGTGGCTGA-GATTATGCA--T-T-TACTGCATGT DroGri_CAF1_left TGAAACATAATGCC-CGTTAC--TAAGTTCCGTAAGACGGAACTATTT-ATATTATCTACAA--ATATTAA-TTACTT-ATACACTATATAGAATATCAGCAGTGAT-T-TTTAT---TT DroMel_CAF1_left GCTACTTGAACACA-AG--GC--GAAACAGTGAGAGACTCCGATGATT-AATAAAGAAGAGAG-T-TG-TG-GTTGAG-AT-TATAGAATTTTA-AAATATTTATCA-TATTCGGTTAAT DroMoj_CAF1_left TCAAATATTAGGCC-GA--ACTATAAATAGACATTAA--TAAAGCAAA-CCAAGACGAATTT--ACTATTACGTATTT-TT-TTTAGTCTTATC-TATTTCTTATCA-A-TTCAATAACT DroSec_CAF1_left GCTATTTGAACTTA-CG--GC--GAAACGGTGACAGACTCCGATATTT-AAGAAAGCTATAA--ATAAACA-ATAAAG-AG-CAGTGTCGTTGA-GATTATGGAATT-T-TAACGTATTT DroSim_CAF1_left GTTAGTTGAACTTA-CG--GC--GAAACGGTGAAAGACTCCGATATTT-AAGAAAGCTATAA--ATAAACA-ATAAAG-AG-CAGTGTCGTTGA-GATTATGGAATT-T-TAACGTATTT DroVir_CAF1_left TAAACTTTACACGA-AT--AC--TAAATATAAATGC--TTAA-AGAATAACGAATTATAAAT--TCTTTTTGATATTT-AC-TAAATATTTCCC-TTATCTGTTTCT-T-ATCGTAAGAA DroWil_CAF1_left GTTAATGAATTATC-AA--TT--CAATATGACAGTTAGTCATAGGT-T-TATAATTGCGAATG-T-ATACT-ATATAC-CT-AGATATAGACGG-AAATATGTGGGG-GACTCCC----A DroYak_CAF1_left GCTATTTGAAATTA-GG--AC--GGAACAGCGACAGCGTCTAATTTTT-AAGAAAGCTAAAA--ATGGACA-ATATAT-AT-AATTGTGGTTGA-GCTAATGGAATT-T-TACTGCATGT DroPer_CAF1_left CAAATTTGAAGTCA-GA--TA--AGATTTGCTTGATAGATTATAAATA-CTACCCGTAG-TA--TTAAATATAGCATA-CA-ATAAATACTAGA-TATTATTTATAG-T-GCTTGTCGAT DroPse_CAF1_left CAAATTTGAAGTCA-GA--TA--AGATTTGCTTGATAGATTATAAATA-CTACTCGTAG-TA--TTAAATATAGCATG-CA-ATAAATACTAGA-TATTATTTATAG-T-GCTTGTCGAT DroAna_CAF1_left AAAAGGTT DroEre_CAF1_left AAAATGGG DroGri_CAF1_left CTCTACTC DroMel_CAF1_left GTGTTGTG DroMoj_CAF1_left CTGGATTG DroSec_CAF1_left AACATATT DroSim_CAF1_left AACATATT DroVir_CAF1_left AATCTTTA DroWil_CAF1_left GTTCTTTC DroYak_CAF1_left AAGATGGA DroPer_CAF1_left CAAGATAG DroPse_CAF1_left CAAGATAA