CLUSTAL W --- LocARNA 1.4.8 - Local Alignment of RNA DroAna_CAF1_left ---ATA-AA-CAAA-------CACTAAAAATGTAAATTTAAATATTTATTTCGAGCCT-CACTCGACTTGTTTGGAAT---ATT-CATTCC-GTACC--GCCCTTA-TCAGTAG------ DroEre_CAF1_left ---ATC-CG-TTTT-------TGTGCTCTTGAGTATCTGA-GCGATAAGA-ACTAGC--CTGAGAACTAATAATAAACTTGACCCTTGTCC-TGACT--GTGC-TG-AT--AGC------ DroMel_CAF1_left ---GATCCA-GCTT-------TATACTCTTGAGTATCTGA-TAGATAAGA-ACTAGC--CTTAGTACTAATAATATACTTGACC-TTTGCC-ACACT--GTTC-TG-AT--CGC------ DroSec_CAF1_left ---GAACCG-GCTT-------TATACTCTTGAGTATCTGA-GAGATAAGA-ACTAGC--CATAGTACTAATAATAAACTTGACC-TTTGCC-ACACT--GTTC-GG-AT--AGA------ DroSim_CAF1_left ---GATATA-ACTT-------TATACTCATGAGTATCTGA-GCGATAAGA-ACTAGC--CTTAGTACTAATAATAAACTTGACC-TTTGCC-ACACT--GTTC-TG-AT--AGC------ DroYak_CAF1_left ---ATG-CG-GTTT-------TGTACTCTTGAGTATCTGA-GCGATAAGA-ACTAGC--CCTAGCACTCATAACAATCTTGACC-CTAGCCCTGACG--GTTC-TA-AT--AGC------ DroPer_CAF1_left ---GCA-AT-ATGC-------CCTTGGGATTTGAACGAGG-CTGAATCGT-TATCTCTTCGGATAGTGCTT------------C-TGTGCTCTCTCTCTCCCT-CTTCT--CTCTCCCTC DroPse_CAF1_left AAGCAA-ATAATTGCAATATGCCCTTGGATTTGAACGAGG-CTCAATCGT-TATCTCT-TGGATAGTGCTT------------C-TCTGTC-TCTCT--CTCT-CT-CG--CTCTCTCT- DroAna_CAF1_left ---ACCTCCATGGTCTG--TGAAGAGCT-TTTGGCGCCAG-CCCCCCAAGTGCCGAAATAGCTCAGTT-GGGAGAGCGTTAGACTGAAGATCTAAAGGTCCCCGGTTCAATCCCGGGTT- DroEre_CAF1_left ---TGTGCCGTGTAGCTTGTATTGAGCT-TTTATCGCCGC-TCGCTCAAGTGCCGAAATAGCTCAGTT-GGGAGAGCGTTAGACTGAAGATCTAAAGGTCCCCGGTTCAATCCCGGGTT- DroMel_CAF1_left ---TATGCCGTGTAGTTTGTCTTGAGCT-TTTATCGCTGA-CCGTTCAAGTGCCGAAATAGCTCAGTT-GGGAGAGCGTTAGACTGAAGATCTAAAGGTCCCCGGTTCAATCCCGGGTT- DroSec_CAF1_left ---AGTGCCTTGTAGTTTGTGTTGAGCT-TTTATCGCTGA-GCATTCAAGTGCCGAAATAGCTCAGTT-GGGAGAGCGTTAGACTGAAGATCTAAAGGTCCCCGGTTCAATCCCGGGTT- DroSim_CAF1_left ---TGTACCTTGCAGTTTGATTTGAGCT-TTTGTCGTTAG-ACGGTCAAGTGCCGAAATAGCTCAGTT-GGGAGAGCGTTAGACTGAAGATCTAAAGGTCCCCGGTTCAATCCCGGGTT- DroYak_CAF1_left ---TGTGCCTTGTAGCTTCTATTGAGCT-TTTATCGCCGC-ACGCTCAAGTGCCGAAATAGCTCAGTT-GGGAGAGCGTTAGACTGAAGATCTAAAGGTCCCCGGTTCAATCCCGGGTT- DroPer_CAF1_left TGTCTCCCTGCGAG---TATAGGGAGCTTTTTGACACCTGTTTGCTCAAGTGCCGAAATAGCTCAGTTGGGGAGAGCGTTAGACTGAAGATCTAAAGGTCCCCGGTTCAATCCCGGGTTT DroPse_CAF1_left -----CTCTGCGCG---TATAGGGAGCT-TTTGACACCTG-TTGCTCAAGTGCCGAAATAGCTCAGTT-GGGAGAGCGTTAGACTGAAGATCTAAAGGTCCCCGGTTCAATCCCGGGTT- DroAna_CAF1_left TCGGCAATCTAAAAAACTT-TTTTTATTTTATTT--TTT-TGTCAA-ATCTTATTTTTAA---ATCTTTTCTTAAA----GT---TTCATCTAATATAATTTCATTAAGTTGA---GTTA DroEre_CAF1_left TCGGCAGCCA-ACATTTT--TTTAATGTATTTTCATTTT-TGTATA-TTCTTTTACTTCA---TGTAAATTGTGTA----TT---TTCATTGTCTATTGTAATGCGGAG-CCA---TTC- DroMel_CAF1_left TCGGCAATAAGAATTTTTTTTTTAATGCATTTTC--TGTTTATATA-TTCTTTTACTTGA---AGTAAATTCTGTA----TT---TTCATTATCTATTGTAATGCCGAA-GCA---TTC- DroSec_CAF1_left TCGGCAATACGGCTTTTT--TTTAATGCATTTTC--TGT-TGTATA-TTCTTTTACTTAA---AGTAAATTCTGTA----TT---TTCATTATCTATTGTAATGCCGAA-GCA---TTC- DroSim_CAF1_left TCGGCAATACGATTTTTT--TTTAATGCATTTTC--TGT-TGCATA-TTCTTTTACTTGA---AGTAAATTCTGTA----TT---TTCATTATCTATTGTAATGCCGAATGCA---TTC- DroYak_CAF1_left TCGGCAAGCCGATTTCTT--TTTTGTGTTATTTT--TTT-AAT-----TCTTTTACTTTA---AGTAAATTCAGTA----TT---TTCATTATCTATTGTAATGCGGAA-CCA---TTT- DroPer_CAF1_left TCGGCAGTCATTAATATT--CTTTTTTCTTTTTA-TATA-T-ATTTTTTGTTGTGCCTCACATTCCACGATTAAATATAATTACGTATGCACTCGAACGCACTTTCTTA-AAAAAAAAA- DroPse_CAF1_left TCGGCAATCATTAATATA--CTTTTTTCTTTTTA-TATA-T-ATTTTTTGTTGTGCCTCACATTCCACGATTAAATATAATTACGTATGCACTCGGAGGCACTTCCTTA-AAA---AAA- DroAna_CAF1_left TCAA-T--TGTCTTGTTAAACTCTTTCATCATTGAAAAGA-C--ATTTCGTATGTCATTTTCCTGGGAAAACTTTTAG-CA DroEre_CAF1_left TGTAGT--TC-CTCATC-----------GTATTTCCCTTCGC--GA-ACTTTCGACATTCTTCGGTGTCTCTATGGGGGAC DroMel_CAF1_left TGTAAT--TC-CGCACC-----------TTATTTCCCTTCGC--GA-ACTTTCGACATTCTTCGGTGTCTGTATCGGGGAC DroSec_CAF1_left TGTAAT--TC-CGCACC-----------TTATTTCCCTTCGC--GA-ACTTTCGACATTCTTCGGTGTCTCTATCGGGAAC DroSim_CAF1_left TGTAAT--TC-CGCACC-----------TTATTTCCCTTCGC--GA-ACTTTCGACATTCTTCGGTGTCTCTATCGGGGA- DroYak_CAF1_left TGTAAT--TT-CTCGCC-----------GTATTTCCCTTCAT--GA-ACTTTCGACATTCTTTGGTGTCTCTATGGAGGAC DroPer_CAF1_left AAAAGAAATA-TATGTA---------AGTCATG--CTTGTGCCTGT-GGGAGAGGAAAGTCGTTGAATTCCTACAA---CA DroPse_CAF1_left AAAAGAAATA-TATGTG---------AGTCATG--CTTGTGCCTGT-AGGAGAGGAAAGTCGTTGAATTCCTACAACAATT