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


DroMel_CAF1_left   CAAAGCAATCC-CGCA-TTGATGAAGATGCTTTTTCCCAGAATACTTGGGCTTT--GGCA---AAATAA----------AG--AAAAATAATTCAATTAAAATTTACGGTA--TGCCGAG
DroSec_CAF1_left   TTATTTATGCAAAGCAATCCCGCATTGATGAAGATGCTTTCCCGGAAAACTTA---AAGA---TAGGGA----------TA--TAAAATAATTCAATTAAAATTTACGGT---TGCCGAG
DroSim_CAF1_left   AAA-GCAATCC-CGCA-TTGATGAAGATGCTT--TCCCGGAATACTTGGGCTTT--GACAGAAAAAAGA----------TA--TAAAATAATTCAATTAAAATTTACGGTA--TGCCGAG
DroYak_CAF1_left   GCA----ATCC-CTCA-TTGATGAAGATGCTT--TCCCAGAATACTTAAGCCTCGGGAACCAAGAAAGAGATAAAATAATTCAATTAAAATTTATGGGATAGGCAAGTGGAATGGTAGAC
DroEre_CAF1_left   GCA----ATCC-CGCA-TTGATGAAGATGCTT--TTCCAGAATACTTAAGCCTCGGGAACCAAGAAAGA----------GA--TAAAATAATTCAATTAAAATTTATGGAAA-TGGCAAG

DroMel_CAF1_left   CTGA-AATGTTGAATTTTCCTTCATCGAACGGATTTCGTT------CATTTTTATTTATTATTCATTGGCCCAACTAAATATTTAGCCAGGTCATA-CAAAAATTGAGTTTAGACTCATT
DroSec_CAF1_left   CTGA-AATGTTGAATTTTCCCCCTCCGAAC----TTCTTT------TATTTTTATTTATTAATCATTGGCCCGGTTAAATAAATAACCAGGCCCTA-AAAAAATTGAGTTTAGACTCATT
DroSim_CAF1_left   CTGA-AATGTTGAAATTTCCCCCTTCGAAT----TTCTTT------TATTTTTATTTATTAATCATTGGCCCGGTTAAATAAATAACCAGGCCATAACAAAAATTGAGTTTAGACTCATT
DroYak_CAF1_left   CACATACCTAATAATGTCCAACCTCCGAAC----TTCTGTTCATCATTTTAGTATTTATTAATCAATGGCCCGGCTAAATCAATAGTTAGGCACTAACAAAAATTGAGTTTAGACTCATT
DroEre_CAF1_left   TGGA-ATGGCAGACTAGT----TATCTAAC----AATTCT------ACGTCCGAACTAATTTTCAGCATTATTAATATAATATAATTAA-AATCGT-TGGTCGAGCTACATAAATAGCCA

DroMel_CAF1_left   AGAGTGTTCCTCTCCACGGAAATCTTTAGTAAAAGGCGAAAGATTTATTCGACAATTGAA-GAGAAACCAGAGTAATTTG-CACTACAAA-ATAGTGTAACTCCATACTCAATATTGAAT
DroSec_CAF1_left   AGAGTGTTCCTCTCCACGGAAATCTTTAGTAAAAGGCGAAAGATTTATTCGACAATTGAA-GAGAAACCAGAGTGACTTA-CGCTTTAAC-ATAGTGTAAGTCCTTACTCAATATTGATT
DroSim_CAF1_left   AGAGTGTTCCTCTCCACGGAAATCTTTAGTAAAAGGCGAAAGATTTATTCGACAATTGAA-GAGAAACCAGAGTATCTAA-CAATTCAAC-ATAGTGTAAT-CTTTACTTCATATTGACT
DroYak_CAF1_left   AGAGTGTTCCTCTCCACGGAAATCTTTAGTAAAAGGCGAAAGATTTATTCGACAATTGAA-GAGAAACCAGAGTGACTTAAAACTACGGA-ATAGTGTGCCTCTAGACTCGATATTGTCC
DroEre_CAF1_left   GGCCCTAAGGAAATAGAGATTCTACTCATTAGAGTGTTCCTCCCCACGGAAATCT-TTACTAAAAGGCGAAAGATTTTTT-CGACAATTGAATGTCCAGAA-------TGCCGAATAATT

DroMel_CAF1_left   AGAACCGCTTGGGAATTATATT--GTACCTTTGTTACCTGAATGATTAACAAACTTAAGGGA---GTGTTTTCGA-AAAATC----TGTCTTA
DroSec_CAF1_left   AGAACAGCTTGGGAATTTTAAG--GCAAGCAGTTCGGAGATATAAGTATAAGATTGTGTACC---TTTATGGTTT-TGTTAC----CTGAGTG
DroSim_CAF1_left   AGAACCGCTTGGGAATTTTAAA--CCAGTTCGGAA----ATATAAGTATAAGATTGTGTACC---TTTATGGTTT-TGTTACCTGAATGATTA
DroYak_CAF1_left   AGAACAACTTGGGAATTTTAAA-CGCACGAAATAT-----ATGTAAACTCTGCTACATTTATGGTGTGTTACCTAAGTGAAA----TAAAAAT
DroEre_CAF1_left   CTAAGCGCAGTTC--GAAAATATTAGTAAAAATGGT-----ACAT-TTATGGTTTGT-TACCTGATTGATATAAAAATGTTA----AGGGACC