CLUSTAL W --- LocARNA 1.4.8 - Local Alignment of RNA DroAna_CAF1_left GAATGCGCTAA-----GTTCCC---ATG--AG--TAC--TTTTGTTCCC-A---AACAA--AATCAGAC--AGT---ACCGGGTTCGAT---CC----CCGCTAG---A-AGATTATAA- DroEre_CAF1_left GATGTTGATTC-----TCG--C---GCG--CT--CAT--GATTTTCGAG-T---GGCGG--TTCGAGTGC-CGC---CGAGGTCGGAAT---GA----AAGTGAT---T-TTTCTTAAT- DroGri_CAF1_left GCGTTGAGCTG-----CAACAG--------AA--GAACATT--TTGTTGGTTGTGGTTC--GAGGTTCA--ATT-------CCCATCGGAGAAATGTTTT--TGAGAGT-GTGTGA-AC- DroMel_CAF1_left T---GGCGGTT-----CGAGTG---CCG--CC-GAGGTTGT--GTCGAGAT---GAATA--AAAAAAATA-ATT---CATTCATTTCGTTTTCT----TA--AGAAA-AGAAATTAAGAT DroMoj_CAF1_left GCGTATAGAGT-----TGTCACATCGCGAGAGTAAGTGTTG--TGTCGGCTGAA--GTTCGCGGTTCG-A-ACC---T---CGGTTGAGACCCA----CG--TGCAAGA-TTTT-TATA- DroPer_CAF1_left GCGAGATTTTG-----TTCTTG--------TT--CTGCTCT--GTGCTCTACGCGGTGG--TTCGAATCC-CAC-------CTAGAGACAGAGT----CG--AGAGAGA-AATCTTTTT- DroPse_CAF1_left GCGAGATTTTG-----TTCTTG--------TT--CTGCTCT--GTGCTCTACGCGGTGG--TTCGAATCC-CAC-------CTAGAGACCGAGT----CG--AGAGAGA-AATCTTTTT- DroSec_CAF1_left CTCATGATTTTCGAGTGGCGGT---TCG--AG--TGCCGCT--GAGGTCGG---GGTGA--AATGAAATTCCAT---TCATTTCGTTTT---CT----TA--GTAAA-T-GTATAA---- DroSim_CAF1_left GATTTTCGAGT-----GGCGGT---TCG--AG--TGCCGCC--GAGGTCGG---GATGA--TATGAAATT-CAT---TCATTTCGTTTT---CT----TA--ATAAA-T-ATATGTAGA- DroVir_CAF1_left AGCACATTCAG-----TTGCAG--------TA--CCAGAGG--ACGTTTTGTTCTAGCT--GGCCCGCG--GTT-------CGAGCCTCCGTCA-GACCG--CGAGGTT-TTACA--AA- DroYak_CAF1_left GTTGATTCTCG-----CG-CGC---TCA--TG--ATT------TTCGAG-T---GGTGG--TTCGAGTGC-TGCCGAGGTCGTCGGGAT---GA----AAGGGAT---T-TTTCTTAAT- DroWil_CAF1_left ACCATGCGCTA-----CTTTCA--------CG--CGCCTCG--GTTCAAACCGTGTCGTAGGCTTCAGT----T-------TTTTCTATATATA-GGTAC--ATATATA-ATATA--AT- DroAna_CAF1_left TT-TTAGATTCTTATAT-TATTTGGC-CCGTGACATTA-TTTGTTACAATTTGTCGCCT-TTGGAATTGTTGCACGAGTTCGC---GGGCCCAGAAAGAT----A-ATTCCGG--T-TAA DroEre_CAF1_left AA-TAATATTCCTTGCCTGGGGGGGC-CTGTGAAATCAGTTTGTTGCAATTTGACGTGA-CTGGAATTGTTGCACTA-TTTGC---GGGCCCAGAGAGAT----A-CTTCCGG--ATTAA DroGri_CAF1_left CA-CCA-GTTAATTTATTTCGCCCCG-CAGAAACATAA-TTTGTTGCAATTTGTCGTGC-TTGGAATTGCGGCATTCGCTTTACG-TGGGCCAGAGAAAA-CTTAAATTCCGT--T-TAA DroMel_CAF1_left TTTCTGTTTGTTGGGGTTGGGGGGGC-CTGTGAAATCAGTTTGTTGCAATTTGACGTTA-CTAGAATTGTTGCACTT-TCCGC---GGGCCCAGAGAGAT----A-CTTCCGG--A-TAA DroMoj_CAF1_left ---AAT-TTTATT--------TCGCCCTACAAACATCT-TTCGCTGCAATTTGTCGTGT-TTGGAATTGCTGCAAACGCTTTGCAATGGGCCAG---AGT-AAATGATATTCCGTT-TAA DroPer_CAF1_left ---CTG-TAGTTTGTTGTTGTGTGGC-CTGTGAAATTA-TTTGTTACAATTTGTCGCTCGTTGGAATTGTTGCACTACTTTGC---GGGCCCAGAAAGAA-CTTAGATTCCAT-TT-TAA DroPse_CAF1_left ---CTG-TAGTTTGTTGTTGTGTGGC-CTGTGAAATTA-TTTGTTACAATTTGTCGCTCGTTGGAATTGTTGCACTACTTTGC---GGGCCCAGAAAGAA-CTTAGATTCCAT-TT-TAA DroSec_CAF1_left -------AGATTGTTTGTTGGGGGGC-CTGTGAAATCAGTTTGTTGCAATTTGACATGA-CTGGAATTGCTGCACTT-TTCGC---GGGCCCAGAGAGAT----A-CTTCCGG--A-TAA DroSim_CAF1_left ---TAT-TTTCCGTTTGTTGGGGGGC-CTGTGAAATCAGTTTGTTGCAATTTGACATGA-CTGGAATTGCTGCACTT-TTCGC---GGGCCCAGAGAGAT----A-CTTCCGG--A-TAA DroVir_CAF1_left TT-TTA-TTTACCGTTTATTTCGCCC-CACAAACATCA-TTTGCTGCAATTTGTCGTGT-TTGGAATTGCAGCAAGCGCTTTGCG-TGGGCCAGAGAAAATATGATATTCCGT--T-TAA DroYak_CAF1_left AA-TAATATTCCTTGTTTGGGGGGGC-CTGTGAAATCAGTTTGCTGCAATTTGACGTGA-CTGGAATTGTTGCACTT-TTCGC---GGGCCCAGAGAAAT----A-CTTTCGGTGT-TAA DroWil_CAF1_left AT-T-T-ATTGTTGTTTT-TGGCGCC-CTGTTAATATT-GTTTGGCTACAAATTGTTTC-GTTATTGTTGCCAGATTTTTGAT---GGGGCCAGAATAAA---GAATTTACGT--A-TAA DroAna_CAF1_left TCATAGGCTAA--ATCCCGGTAATCAATACCTTAGTCTATTTCATGC--CCGGCAAACATATTTCTAT-TTTTA--TTTC---TCA--GTGCTTTGATGCCCTTTG--TTTTGCTCG--- DroEre_CAF1_left TCATAGGCTAT--AG-CTGGTCATCAATACCATAGCTTATTTCATGG--CCGGCAGACATATACCCTT-TTTTT--TTGC---ATT-CTCGCTTATTTCACCCTTT--GTTTTGATT--- DroGri_CAF1_left TCATAGACTAA--AA-TCGGTACTCAATACCTTAGCCTATTTCATGC--CCGGAATACAGATCTTTTA-GATAA--TAAT---TGC--AT-GAGTCTCAGTCTCCGGTC--ATCTCT--- DroMel_CAF1_left TCATAGGCTG------CTGGTTTTCAATACCATAGTCTATTTCATGG--CCGGCAAACAAATTTCCTT-TTTGCTTTTGC---CCT--TTGTTTTGATTGCCAAGT--CAACGGTTT--- DroMoj_CAF1_left TCATAGGCTAA--AT-CGGGTACTCAATACCTTAGCCTATTTCATGCCCGGAATACAGTTTGTTTTTT-GATTT--TGTT---TAC-AGC-TA--TTGCTTTTGTGTGTTGTCCATG--- DroPer_CAF1_left TCATAGGCTAA--AA-TTGGTAATCAATACCTTAGTCTATTTCATGC--ATGGAACACAGTTTTCTTT-TTCCT--TTTG---TTG-T----TTGTCTCTCTTGTGTTT--TGCTCT--- DroPse_CAF1_left TCATAGGCTAA--AA-TTGGTAATCAATACCTTAGTCTATTTCATGC--ATGGAACACAGTTTTCTTT-TTTCT--TTTT---CCT-TTT-GTTGTTTGTCTCTTGTTT--TGCTCT--- DroSec_CAF1_left TCATAGGCTG------CTGGTTTTCAATACCATAGCCTATTTCATGG--CCGGCAAACAAATTTCCTT-T------TTGC---CCT--TTGTTTTGATTGCCAAGT--CAACGGTTT--- DroSim_CAF1_left TCATAGGCTG------CTGGTTTTCAATACCATAGCCTATTTCATGG--CCGGCAAACAAATTTCCTT-T------TTGC---CCT--TTGTTTTGATTGCCAAGT--CAACGGTTT--- DroVir_CAF1_left TCATAGACTAA--AA-TCGGTGCTCAATACCTTAGCCTATTTCATGC--CCGGAATACATTTTTATTTTTGTTT--TTTT---CTT--TA-ATACAAGCGCTTGTTGCC--ATGGCA--- DroYak_CAF1_left TCATAGACTATATAT-CTGGTAATCAATACCATAGCCTATTTCATGT--CCGTTTAACATATACCCTT-TTTTT--GTCC---ACT-CGC-ATATTTTGGCCTTTG--TTTTGATTG--- DroWil_CAF1_left TCATACTCTAA--TG-TCTCCATA-ATACGTTTGGAGTATTTCATGC--CCGTCAAACATTTTTGATT-TAACT--TTTTCTTTTACAAAAAATTAATTGCTTTAG--TTGTTTTGTTTA DroAna_CAF1_left CCCTTCTCTCATATAATGCC-AAGGCAACCCCCTT----TTCT-TTTATTTTTCCTTCATTGATAAGGA-GAGG DroEre_CAF1_left GCCAAGGCAACGGTTTGTTG-TCGTTTTCCCCTAT----TTTC-CGCTGATAAGGAGGTTATTGATCCT--GCT DroGri_CAF1_left TC-CCCTCTTTTTTATTATAATTTGCAA-GGTTATTGATCT---GACTATGATGATGATGA---TGAGG-TAAA DroMel_CAF1_left GTTGTCGTTTTCCCTTATTT-TCCGCTGATAAGAAGGTTATTG-ATCCTGCTGGAAATATA---A---G-GCAC DroMoj_CAF1_left GCAACCGA-AGCTCCCCCAT-ACTGCTTTTAGCAAGGTTA----TTGATCTGCGCTAGCGGA--AGTAAC--TG DroPer_CAF1_left ATTCTCCT-CGCTCTATTTTCCTTGTGTATGT-GTGTGTGT-GTGTGTTTTTTCATTGCCAT--GGC------A DroPse_CAF1_left ATTCTCCT-CGCTCTATTTTCCTTGTGTATGTGTGTGTGT----GTGTTTTTTCATTGCCAT--GGCAACCTTT DroSec_CAF1_left GTTGTCGTTCTCCCCTACTT-TTCGCTGATAAGAAGGTTATTG-ATCCTGCTGGAAATATA---AGGCA-TACT DroSim_CAF1_left GTTGTCGTTTTCCCCTACTT-TCCGCTGATAAGGAGGTTATTG-ATCCTGCTGGAAATGGA---AGGCA-CACT DroVir_CAF1_left AAGGGAGCTGCCCTTTGTTATTCAGTTT-TGTGCAGGGTTA---TTGAACGACAGCAAAAC---CTGGC-TGTG DroYak_CAF1_left -CCAAGGCAACGGTTTGTTG-TCGTTTTCCCCTATTTTCCGCT-GATAAGGAGGTTATTGA---TCCTG-CTGG DroWil_CAF1_left TAGGGATTTCTAGCCCAGCG-TTTTTAAAGATT-A-CCTGGAT-TTGAGACCTCTTCTTGA---TTAAA-CAAT