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


DroMel_CAF1_left   TATTTAGTCAAT-CTCCTA-TATTA-G--TTTCAGTCCCAA-AG--TTTCTGCTAACAGTTATA-----ACTATTAACACCTT-CTGGA--AAAT--TTGTC-CTAAAAA--TAGTGCGT
DroMoj_CAF1_left   AACTATTGTGTC-ACATGA-AATAA-T--ATACATTTGTAG-CAT-ATG-TGTATACATACATG-----CATGTGAACAC-ATATTTAAATTAAAA-ATCTA--AA-ATAAAAAAATAAT
DroPer_CAF1_left   TCGAAGTCTC-C-ATAT-A-TTGAA----TCTGCATAATTC-TT--TGGATAATTGGGGTTCGA-----GTTATGGGAGTTCAACTATA--TAAGA-AAGTA-TTAGTCT--AAAAAAAA
DroPse_CAF1_left   CGTTGAGTCG-C-ATAT-A-TTGAA----TCTGCATAATTC-TT--TGCATAATTGGGGTTCGA-----GTTGTGGGAGTTCAACTATA--TAAGA-AAGTA-TTAGTCT--AAAAAAAA
DroWil_CAF1_left   TTTGATTATT-G-ATTG-AGTATAT----TCAAAACTATAT-TA--AAAACATTCAGTTGTATA-----TAAATGAATGGTGGACTGGT--TAAAA-AAAATTTCA-ATC--CAAAAAAA
DroYak_CAF1_left   CAAAACACAA-T-ATTG-G-TTTCAGTGCAAAGATCTCTGC-CAT-CAC-TTTAAAATGTTAGA-----CAACTACTGTT-TCCCAAAAAATAAAT-GTC-----AGTGA--AGTACATA
DroEre_CAF1_left   GTCAAAACAC-CAATAC-A-ATACA----TCAATACCAAGATCTCTGTCTTCACTAAAAAATATGAAGCGCCTTCTGAAGAAATTTTGT--TCCCAAAAAAA-TAAA-GT-TACGGCTAA

DroMel_CAF1_left   GACGA----CAAAAATA--AGA-CAAAAACTCA-TATTCCCATACCGGGAATTG-AACCCGGGCCTCCCGGGTGAGAGCCGGGTATCCTAACCACTAGACAATATGGGATACGGCTTTGC
DroMoj_CAF1_left   TTAAA----AAAAAAAT---GT-GATAACCACTG-TTTCCCATACCGGGAATTG-AACCCGGGTCTTCCGGGTGAGAGCCGGATATCCTAACCACTAGACAATATGGGATGTACTTCTGA
DroPer_CAF1_left   TATGT----TAAAAAAA----T-GTCATCACACAGCTTCCCATACCGGGAATTG-AACCCGGGCCTTCCGGGTGAGAGCCGGATATCCTAACCACTAGACAATATGGGAGATGTGAGCTG
DroPse_CAF1_left   GATGT----TAAAAAAA----T-GTCAGCACACAGCTTCCCATACCGGGAATTG-AACCCGGGCCTTCCGGGTGAGAGCCGGATATCCTAACCACTAGACAATATGGGAGATGTGAGCTG
DroWil_CAF1_left   AAAAA----AAAGCAAT----T-CACTTGTCATG-TTTCCCATACCGGGAATTG-AACCCGGGCCTTCCGGGTGAGAGCCGGATATCCTAACCACTAGACAATATGGGAGATGCTTTGAC
DroYak_CAF1_left   CATGACTAACAAAAAATCAACTAAGCTTGCTTTGTCTTCCCATACCGGGAATTG-AACCCGGGCCTCCCGGGTGAGAGCCGGGTATCCTAACCACTAGACAATATGGGATGCGTGGAATC
DroEre_CAF1_left   CGAAA----TATAAATA-----AAGCTAGCTTTGCATTTCCATACCGGGAAATGGACGCCGGGCCACCCGGGTGAGAGCCGGGTATCCTAACCACTAGAATATATGGGATACTTTTAAGC

DroMel_CAF1_left   TGTGTCAAGGAACATAT--TCAAACGAAATT--GTCTGGTAGTTATCATT-CTTC-AAATGCAATATGAA-AACTCATATATA--CAATTATATATATTATA
DroMoj_CAF1_left   AAATGCAAAATTCGTTA--TATAGTATAATA--AACATAAACTTTGGCAA-CTACTCTGCTTGGATGGTTAATCCAATTC-AG---ATCTTCTGTTTCATAG
DroPer_CAF1_left   AGGCGTCAAATTTGTAA--TTGAACCAAGTT--TTCAAAAGCAAAGGCAA-TCTT-CAATGAACATGTTC-GTGTTTCATATG--TATTTTAATATACTATA
DroPse_CAF1_left   AGGCGTCAAATTTGTAA--TTGAACCAAGTT--TGCAAAAGCAAAGGCAA-TCTT-CAATGAACATGTTC-GTGTTTCATATG--TATTTTAATATACTATA
DroWil_CAF1_left   AGTGGCCAAATTTAAAT--TC-CGAAGATCGCTTTAATTCTAATTATCGT-TCTT-GATTCAAAAATTAAATTTTAAATTGTT--GAAAATC--TATTTTTA
DroYak_CAF1_left   GAAATCACAT-CTGAAT--ATTTCTTAATAA--TATAAAAATTATAATAA-TTTA-TTTAAA-ATAACACATATATA-CGATATATCTTAAAATTAAAAAAA
DroEre_CAF1_left   TGAGTCAAAGTACAAGTGTCCAGGCAAAAAT--AATG-AATCACATGTAAGTATG-GCTTCAGTAATTAT-TTTTCTGAT-GC---AATACTCATGCATATG