CLUSTAL W --- LocARNA 1.4.8 - Local Alignment of RNA DroAna_CAF1_left C--TGCA-GCTTTTGTTTCG-CATTCGA----T-TCATAAACAGT---CTCCAT-TGATTCAGTTTCT--ATTTTAAGATA-CAAGTGATATTTCATCAGCCA-GTGCCTT-CAACA-GG DroEre_CAF1_left T--TCAC-ACCC-AGAGTTT-CGC--GAAACTCTTC-CAAATTGA---TTTCAGTTCTA-TTTTAAGATAAATGCAAAGGC-GGC-ATTTTA-TC-TCAGCCG-GGAACTT-TAAAA-GG DroGri_CAF1_left T--CAAT-TGAAA-GT-TGTGCTG-ATAACTCT-TTGAATATTGA---TAAGCA-AGTAATAGAGACT--TCTATTTTGAA-ATTTAATTTA-TC-TTAGATT-TGTATGT-CAATT-GC DroMel_CAF1_left C--ACAG-TTTCGCGGAACA-GTC--ACTCTGT-TC-CAAATTGA---TTTCATTTCTA-TTTTAAGATAAATGCAAAGGC-GAA-ATTTTA-TC-GCATCAG-GGAACTT-TAAAA-GG DroMoj_CAF1_left A--ACAA-AGAAACCCATGC-TGA--TAACTTT-GC-TGTTTGATAAGCAAACAGTGTTTGAGCTGCTA-TTGCAAT-AGAATAT-TTAT-C-TTGAA-ATTTGCTA-ATAACAA-T-AG DroPer_CAF1_left G--TGTA-AATTGATAAACA-ATC--TGCCAGA-TA-TTGATGCC--GCTTCGGTGCCTATTTTGGGTGGCTTTTTATCTC-GAACTCGGTC-TC-GGATTCG-GGTTTGA-AATAC-AT DroPse_CAF1_left G--TGTA-AATTGATAAACA-ATC--TGCCAGA-TA-TTGATGCC--GCTTCGGTGCCTATTTTGGGTGGCTTTTTATCTC-GAACTCGGTC-TC-GGATTCG-GGTTTGA-AATAC-AT DroSec_CAF1_left G--GAGC-TGTGTCTACACA-AGC--ACTCAGT-TC-CAAATTGA---TTTCATTTCTA-TTTTAAGATAAATGCAAAGGC-GGA-ATTTTA-TC-GCAGCAG-GGCACTT-CAAAA-GG DroSim_CAF1_left GCGGAGC-TGTGTCT--ACA-AGC--ACTCAGT-TC-CAAATTGA---TTTCATTTCTA-TTTTAAGATAAATGCAAAGGC-GGA-ATTTTA-TC-GCAGCAG-GGCACTT-CAAAA-GG DroVir_CAF1_left G--TAAA-AGACAACAAGCT-GAT--AATTTAG-AA-ATTTGATA--AGCAAACACTT--CGAGCTGCTGCTGTGT-TAAA-ATTTGATTTA-TC-TTAGACT-TTCATAA-CAAAA-AC DroYak_CAF1_left C--CCAACAGTT-TCGCAAA-ACC--GTTTCAT-TT-CAGTTTGA---TTTCATTTCTA-TTTTAAGATAAATGCAAGGGC-GGC-ATTTTA-TC-TGAGTTG-GGAACTT-TAAAA-GG DroWil_CAF1_left A--TAAA-TGTGATAA-ACA-ACC--TC----G-GC-CAATTGAT---TTCATTTCTAT-TTTGATTCATAAATGGGTGGG-GGA-TTTTTT-CC-ATTTCTA-TCTGTAT-TATTTTCA DroAna_CAF1_left C-ACT--CCCAGAGCTT-CA-ACACCAAGTCGGGGGTATAGCTCAGGGGTAGAGCATTCGACTGCAGATCGAGAGGTCCCC-----GGTTCAAATCCGGGTGCCCCCTTTGGTA-ACTTT DroEre_CAF1_left C-GCT--CCAAGTTCGG-GC-AAATCAAGTCGGGGGTATAGCTCAGGGGTAGAGCATTCGACTGCAGATCGAGAGGTCCCC-----GGTTCAAATCCGGGTGCCCCCTGGAACC-ACATT DroGri_CAF1_left A-GCT--CTAACTGCGT-AT-ATTTCA-TTGGGGGGTATAGCTCAGGGGTAGAGCATTCGACTGCAGATCGAGAGGTCCCC-----GGTTCAAATCCGGGTGCCCCCTGGAATT---TGA DroMel_CAF1_left C-GCT--CTGAGTTCGC-CA-TTTTCAAGTCGGGGGTATAGCTCAGGGGTAGAGCATTCGACTGCAGATCGAGAGGTCCCC-----GGTTCAAATCCGGGTGCCCCCTGGAACT-ACATT DroMoj_CAF1_left CTAC---CAATC-TC-G-TT-TTTTCATATTGGGGGTATAGCTCAGGGGTAGAGCATTCGACTGCAGATCGAGAGGTCCCC-----GGTTCAAATCCGGGTGCCCCCTGGAATC-ATATT DroPer_CAF1_left C-TCA--GTGGC-GC-C-TG-TTTTCAAGTTGGGGGTATAGCTCAGGGGTAGAGCATTCGACTGCAGATCGAGAGGCCCCC-----GGTTCAAATCCGGGTGCCCCCTTGGAAC-ACAAC DroPse_CAF1_left C-TCA--GTGGC-GC-C-TG-TTTTCAAGTTGGGGGTATAGCTCAGGGGTAGAGCATTCGACTGCAGATCGAGAGGCCCCC-----GGTTCAAATCCGGGTGCCCCCTTGGAAC-ACAAC DroSec_CAF1_left C-GCT--CTGAGTTCGC-CA-ATTTCAAGTCGGGGGTATAGCTCAGGGGTAGAGCATTCGACTGCAGATCGAGAGGTCCCC-----GGTTCAAATCCGGGTGCCCCCTGGAACT-TTTTT DroSim_CAF1_left C-GCT--CTGAGTTCGC-CA-ATTTCAAGTCGGGGGTATAGCTCAGGGGTAGAGCATTCGACTGCAGATCGAGAGGTCCCC-----GGTTCAAATCCGGGTGCCCCCTGGAACT-AAATT DroVir_CAF1_left A-GCT--CTAAC-TG-T-AAGTTTTTTATATGGGGGTATAGCTCAGGGGTAGAGCATTCGACTGCAGATCGAGAGGTCCCC-----GGTTCAAATCCGGGTGCCCCCTGGAATTCACTTT DroYak_CAF1_left C-GCT--CCGAGTTCGG-GC-AAATCAAGTCGGGGGTATAGCTCAGGGGTAGAGCATTCGACTGCAGATCGAGAGGTCCCC-----GGTTCAAATCCGGGTGCCCCCTGGAACC-ACATT DroWil_CAF1_left C-AGAAAACATGAATGGAGA-GGGGTATGGTGGGGGTTAGGGTCAGAGGTGACACATTCGACTGCAGATTGAGAGGTCACCAACGCAGTTCAAATCCGGTTGCCTTCTAGGAAC-TTTTT DroAna_CAF1_left --TTAATACTTTTTTATGCGA-A--CGCCTGT--C-GAT----TATGAGTTGAATT-G--CATTA-----GAGGTG-TG---CTCCGCCGTCGTGGA--CGTT-GAACTCTGAC---AGA DroEre_CAF1_left --TTTGGTCATGTTTT--TTTGCT-GGCTACT--C-AAGGCTCTTTGTGGACTTAG-GT-GCTTT-----TCAGGC-GG---A-TCGAATT-GAAGCTGTA---TCCGCCAGACG--TGG DroGri_CAF1_left TTTCTTTTTTTTTCTAG--TT-AAATATGTGG--C-G-------TTGACCTCTTGT-G--TGAGA-----TTGGGG-CA---TCGTA--AA-CAACG--CGTG-ACCCGTCCTT---AAG DroMel_CAF1_left --TTTTGCCATATTTTTTTTTGTT-GGCTGCT--C-AAGTCTCTTTGTGGACTTTG-GT-GGACT-----TTTTTG-CA---CGTTGATTG-CGGG---GG--GA-TTAGAGGTGTATC- DroMoj_CAF1_left --TTTTTATATTACTTCCATT-CC-AGCAAAATTT-AAAGGCACATTGGGTCATAA-ACAACTCT-----TGAGCA-A---CCATAAGCTG-CGCC---GCCTGCTTATCTCTTC---CT DroPer_CAF1_left --TTTTTTCACGTCGCTTTTT-TA-TTTCGCC--C-CGGGATTATGGCACCCATTA-AA-GGTGT----------C-CG---TTCCTCCCG-GGAC---AATGACCTATCCTTTC--TCG DroPse_CAF1_left --TTTTTTCACGTCACTTTTT-TA-TTTCGTC--C-CGGGATTATGGCGCCCATTA-AA-GGTGT-----CCTGTC-CG---TTCCTCCCG-GGAC---AATGACCTATCCTCTC--TCG DroSec_CAF1_left --TGCCATATT-TTTGTTTTTTGT-GGCTGCT--C-AAGGCTTTTTGTGGATTTAG-GT-GGACT-----TTTTTG-CT---CGGTGATTG-CGTG---GGGGGGTGGGGTGTCA--CTA DroSim_CAF1_left --TTTTGCCATATTTTTTTTTGGT-GGCTGCT--C-AAGGCTCTTTGTGAACTTAG-GT-GGACT-----TTTTTG-CA---CGGTGATTG-AGTG---GGGGGGTGGGGTGTCA--CTA DroVir_CAF1_left --TATTTATTTTTTATTTTCC-AC-ATTCTCA--A-CAAT------TTTAAGAGCTCAA-TTAAAGGTGTGTGACG-TTGACCTCTGCTCT-GGAT---TTTGGGCAACAACGGG--TCG DroYak_CAF1_left --TTTGATCATATTTT--TTTGTG-GCCTGCT--CTAAGGCTCTTTGTGAACTTGG-GT-GGTTT-----TCAGGG-CG---A-TGGAATT-AAAGGTGTA---TCCGCCAGACG--TGG DroWil_CAF1_left --TTTTTGTTTTTGTCATGGA-T------TAC--C-AGAATTGAAGTGAATTTTAG-TG-AATCC-----CATTAAAGG---TGCGGAGCA-AGGA---CC-----TCATAAACA--ATG DroAna_CAF1_left CCTC--TATGCCCA-CGCATCAAATAACGA----CATATAAA DroEre_CAF1_left CCGATGAACTCGTA-AGAAACAGCGAATAA---AAATGCTTT DroGri_CAF1_left CATC--GCTGCTGC---CTGATTATCTTTC----CATTTTAC DroMel_CAF1_left -CGCCCGACGTGGT-CGAT-GACCCCGTTAACTCGTAGAAAC DroMoj_CAF1_left CTCTC---TCTCTCTCGCTCAA-CA-----------TAATGC DroPer_CAF1_left TAAAGAAGAATACA-TGTGGAATACGTGGT---CATGCCACA DroPse_CAF1_left TAAAGAAGAATACA-TGTGGAATACGTG--------GTCATG DroSec_CAF1_left GAGGTGTATCCGCC-AGACGTGGCCGATGAC----CCCGTAT DroSim_CAF1_left GAGGTGTATCCGCC-AGACGTGGCCGATGAC----CCCGTAT DroVir_CAF1_left TTAACAATTCGTGA-CCATTCATAAG----------CATCGC DroYak_CAF1_left CCGATGAACCCGCA-AAAAACCCTCGCAGC---GAATAAAAA DroWil_CAF1_left CTTAGGAACACGCT-TGCCTACCCCGTTTA---ATGTGCGTT