CLUSTAL W --- LocARNA 1.4.8 - Local Alignment of RNA


DroAna_CAF1_left   ATTTGACA--TTTTGGG--AGCCACTTTG-TGC-CTGGGCCATCAG-TGCGACT--ATATCTTCTATTAA------AAAAATTGTTTAAAATATAT-GGTATAT--AGTGTTCTATAGCT
DroEre_CAF1_left   TGGGG-GT--CACTCTG--TGCCTGTGCT-GCC-A-GTGGGACGCA-ATCAACAAAATAAAGT-GATAAG------TACAAGTGAATTGCATTGGA-ATAAGTG-ACTTAGAGTGCAGCT
DroGri_CAF1_left   TGTTGCAC--GTGTTGC--ATTCACACCA-TCC-GAGTGATTTGTG-TCCTTTG--AGTGTCGATTTGTG------TTACATCTATACG-GTTATT-TAAAGTG-CTTCTTCTTGGTGCC
DroMel_CAF1_left   G------T--CACTCTG--TGCCTGTGCT-GCC-A-GTGGGACATA-ATCTACAA-ATAAAGT-GATAATCAGTGATATCAGTGAAATACATTGCA-ATGAGTG-CCTTAGAGTGAAGCT
DroMoj_CAF1_left   TTGCACAC--AGCCACA--CAATTGTGAA-TTC-GAGTTCGAACTCCCCGGACT--AGAGAA--TACAAG------TGCAAGTGTCTTGTAAT-GTAAACGTGT-TTTTAAATATTCGCC
DroSec_CAF1_left   TTGGGGGT--CACTCTG--TGCCTGTGCT-GCC-A-GTGGGACATA-ATCTACAA-ATAAAGG-GATAAG------TACCAGTGAATAACATTGAA-ATGAGTG-CCTCAGAGTGTAGCT
DroVir_CAF1_left   CTGTGCCT--GTGCCGC--CTGTGCTGCACAAC-CAACGACGAGAT-GCATACG--TGACCCTGACCGTG------ACCGGGAGTGAAG-TGTAAT-AGCCAGG-ATT-AGATGAACGCC
DroWil_CAF1_left   AGAGACGCTCTGTACCT--AGACTGTTGT-GTC-T-GCGGAATGTC-AACATCA--TGTGTGT-GTG-TG------TGTGTGATATATAGTGACAT-ATTATTA-TAGTAATGGATAATG
DroYak_CAF1_left   GCTTTTGA--CATTTTGGGGGTCACTCTG-TGC-CTGTGCTGCCAG-TAGGACA----TAATC-CACAA-------ATAAAGTGATTTACATTGGA-ATAAGTGAATTGAGAGTGTAGCT
DroPer_CAF1_left   GTGCAACT--GCAACGA--TT-AAGGGTG-TTCCTAATAAGTGTTA-TATTTAG--AGTGTTATATCGA-------AAGTGTTTAAAAGTACGACA-ATCTAAT-CTGTGCTTAAGCCCT
DroPse_CAF1_left   GTGCAACT--GCAACGA--TT-AAGGGTG-TTCCTAATAAGTGTTA-TAATAAA--AGTGTTTTATCGA-------AAGTGTTTAAAAGTACAACA-ATCTAAT-CTGTGCTTAAGCCCT

DroAna_CAF1_left   GCTTAACCGATGCTTTGGCGCTTTAGCTGTATGATAGATTTAA-ATACTTCATAAAGCTAGATTACCAAAGCATTGGCTTCCGCAG-GCCTGTC-TTCAAGG--AATAAAATAATAAT--
DroEre_CAF1_left   GCCTTGCCATTGCTTTGGCGCTTTAGCTGTATGATAGATTTAAACTACTTCATAAAGCTAGATTACCAAAGCATTGGCTTCTGCAG-ATCAATC-TTCAGAA-AGAAAC-TAGGCCCT--
DroGri_CAF1_left   ACATTGCCGTCGCTTTGGCGCTTTAGCTGTATGATAGATTTGA-ATACTTCATAAAGCTAGATTACCAAAGCATCGGCGCCTGTGG-CCAGCTT-AACAAAC-GTTTTCATGAAATTG--
DroMel_CAF1_left   GACTTGCCATTGCTTTGGCGCTTTAGCTGTATGATAGATTTAAACTACTTCATAAAGCTAGATTACCAAAGCATTGGCTTCTGCAG-GTCAATC-GTCAGAA-ACAATT-TAAGATAT--
DroMoj_CAF1_left   CCATTGCCGTTGCTTTGGCGCTTTAGCTGTATGATAGATTTAA-ATACTTCATAAAGCTAGATTACCAAAGCATTGGCTCTGTGGC-CAAACCCCAGCGAAC-T----TGTGAAATAATC
DroSec_CAF1_left   GACTTGCCATTGCTTTGGCGCTTTAGCTGTATGATAGATTTAAACTACTTCATAAAGCTAGATTACCAAAGCATTGGCTTGTGCAG-ATCAATC-GTCAGAA-ACAAAT-TAAGCCAT--
DroVir_CAF1_left   GCACTGCCGTTGCTTTGGCGCTTTAGCTGTATGATAGATTTGA-ATACTTCATAAAGCTAGATTACCAAAGCATTGGCT-CTGTGG-CCAGCTT-AGCAAAG-TTGTGAAACGATTTA--
DroWil_CAF1_left   GTCTTGCCTATGCTTTGGCGCTTTAGCTGTATGATAGATTTGA-CTACTTCATAAAGCTAGATTACCAAAGCATGGGCTCTGGCTG-ACTTAAT-CAACTCA-AGTGTT-TTCTCGAA--
DroYak_CAF1_left   GCCTTGCCATTGCTTTGGCGCTTTAGCTGTATGATAGATTTATACTACTTCATAAAGCTAGATTACCAAAGCATTGGCTTCTGCAG-ATCAATC-ATCAG---ACAAAT-TAGGCCAT--
DroPer_CAF1_left   GCTCTGCTTCTGCTTTGGCGCTTTAGCTGTATGATAGATTTAAAATACTTCATAAAGCTAGATTACCAAAGCATTGGCTCT-GTGGAAACTTCA-TCCAAACAATGAAA-TCCGATCT--
DroPse_CAF1_left   GCTCTGCTTCTGCTTTGGCGCTTTAGCTGTATGATAGATTTAAAATACTTCATAAAGCTAGATTACCAAAGCATTGGCTCT-GTGGAAACTTCA-TCCAAACAATGAAA-TCCGATCT--

DroAna_CAF1_left   --TCATTTA-TATCCT-TATAGTT-TTTTGCTTTAAA-ATGTAT---AATTTATTTATGAGTTGCTCTTTT-GTTTGCACATTATTTGTT------CTT
DroEre_CAF1_left   --GCTTATT-CATTGT-TATTAAT-AATTACACTAAT-TGTTTT---ATTTGTTTAACTTATCAGTTGCTC-TT-TTGTTTGCATATTATT-----TGC
DroGri_CAF1_left   --ATATATA-TATATA-TATATAT-GTGTGTGTGCAA-TAGTTT---ATAAGATTTATGCTATTTATTTGC-TG-CCCTTTGTTTGCCCT------TTT
DroMel_CAF1_left   --GCTTGTT-TATTGT-TATTTAT-TATTACAATTAT-TCTTAA---ATTTGTTTAACTTATATGTTGCTC-TT-TTGTTTGCATATTATT-----TGC
DroMoj_CAF1_left   GAACATGCA-TGTACA-TA--TATATTATTTTTATAA-TATAAT---TTGGTTTGGCTTTTTATTTTGCATATT-ATTTGTTCTTTGGTG------ATT
DroSec_CAF1_left   --GTTTATT-TATTGC-TATTTAT-TATTACATTTATTGTTAAA---TTTGTTTAAACTTATATGTTGCTC-TT-TTGTTTGCATATTATT------TG
DroVir_CAF1_left   ---CATAATTTAACTAATAGTTAA-TAGTTGTACCTG-ATAAAT---ATTAGTT-TATTTGTTGCCTTTTT-AT-TTTGCATATTATTTG------CTC
DroWil_CAF1_left   --AAAGTGG-CAAATT-TAAATTA-ATACGTTTTGTT-TTTTTTGTGTTT-CGTTTTTGTTTTACTGCTTT-TG-CGCTTTATTGTTATA------TGA
DroYak_CAF1_left   --GCTTAGT-TT---T-TATTAAT-TATTTCATTAAT-TTTTAT---ATTTGTTTAACTTATCGGTTGCTC-TT-TTGTTTGCATATTATTTGCTCTTT
DroPer_CAF1_left   --GCGTGTG-CATCTA-ATTATAT--TTTGCTTGCAG-CTTTTG---TTTACTTTGGCCATGTTTTCTTTA-TG-AGTTGATCTTTTGTT------TGC
DroPse_CAF1_left   --GCGTGTG-CACTTA-ATTATAT--TTCGTTTGCAG-CTTTTG---TTTACTTTGGCCATGTTTTCTTTA-TG-AGTTGATCTTTTGTT------TGC