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


DroMel_CAF1_left   CATCAAAATATTTTTAAAATGTATA-AGAACTGGTT---TCATAGATACTTTCA-AGGCTGGAGCTTTCTGTTGACC--ATGAAAG-AAAC-CTGCTCTTTTCGTGCTGTGAT-ATGAGT
DroMoj_CAF1_left   ATTTTAAGGTAAAAAT-AAATAAAT-GTGATTTAAAACAGTGTCACTACTAATT-TGGTTGCA---TATAGTCGTCTTTATTTAAGAATAC-CGGTTATTCGTTTTGTCATAC-TCAAAT
DroPer_CAF1_left   AAAGAAATAAAATACCTTGGGGAAACTGGTTTGCTT---GCATTATCAAAATCAAAGAGTTTTCTCT-TTGGCCATG--TAACCA--AAAC-TCGTTCGAGGCTGCTGGTAAC-GGAAAT
DroPse_CAF1_left   AAATACCTGCAAGACAATGGGGAAACTGGTTTACTT---GCATTATCAAAATCAAAGAGTTTTCTCT-TTGGCCATG--TAACCA--AAAC-TCGTTCGAGGCTGCTGGTAAC-GGAAAT
DroSec_CAF1_left   CATAAAAATATTTTCAAAATGTATA-AGAACTGGTT---TCATTGCTACTTTCA-AGGCTGGAGCTTTCTGTTGACC--ATGAAAG-AAAC-CTGCTCTTTTCGTGCTGTGAT-ATGAAT
DroSim_CAF1_left   TCCATATAAATATTTTCAAAAGGTA-AAAACTGGTT---TCATTGCTACTTTCA-AGGCTGGAGCTTTCTGTTGACC--ATGAAAG-AAAC-CTGCTCTTTTCGTGCTGTGAT-ATGAGT
DroWil_CAF1_left   CAAATAGCCTTCA-TATTATGTAAG-TTGCCTAATT---TAAATTAAATATTCAATTTAATGTTTAAGTTGGCTAAA--AGTAAAT-AAAC-CAGTTTGTGCTTGGCTATGAGCCAA-AT
DroYak_CAF1_left   CATTAAAACATTTTCAAAATTAATA-TAAACTGGTT---TCATAGCTACTTTCA-AGGCTGGAGCTTTCTGTTGACC--ATGAAAG-AAAC-CTGCACAATTCGTGCGGAAAG-ATGACT
DroGri_CAF1_left   TGAAA--CACAAGAGTGG-AGCT-----------TT-----TTATACAAATTCATCAATAAATAGCT-TTTACGAAC--ATGCTTT-GAAGGTAAATATGCAATATTAAATCG-CTGATT

DroMel_CAF1_left   AAGCTTTTTGACCAA-CGTA-AGACAACTGGCTCGTTGGTCTAGGGGTATGATTTCCGCTTAGGGTGCGGGAGGTCCCGGGTTCAAATCCCGGACGAGCCC-AAGAGAAAA-GAACTTTT
DroMoj_CAF1_left   AGCGTCTTTGGCGAG-ATCG-CTTCAACTGGCTCGTTGGTCTAGGGGTATGATTTCCGCTTAGGGTGCGGGAGGTCCCGGGTTCAAATCCCGGACGAGCCC-AAATAGTAA-AAAACATT
DroPer_CAF1_left   AGGCTTTTGGACGGT-CCAA-CGTTAACCGGCTCGTTGGTCTAGGGGTATGATTTCCGCTTAGGGTGCGGGAGGTCCCGGGTTCAAATCCCGGACGAGCCC-AAGAGAAAT-AACTTTTT
DroPse_CAF1_left   AGGCTTTTGGACGGC-TGAA-CGTTAACCGGCTCGTTGGTCTAGGGGTATGATTTCCGCTTAGGGTGCGGGAGGTCCCGGGTTCAAATCCCGGACGAGCCC-AGGAGAAAC-AACTTTTT
DroSec_CAF1_left   AAGCTTTTTGACCAA-CTTG-TGGCAACTGGCTCGTTGGTCTAGGGGTATGATTTCCGCTTAGGGTGCGGGAGGTCCCGGGTTCAAATCCCGGACGAGCCC-AAGAGAAAA-CACATTTT
DroSim_CAF1_left   AAGCTTTTTGACCAA-CCTG-TGGCAACTGGCTCGTTGGTCTAGGGGTATGATTTCCGCTTAGGGTGCGGGAGGTCCCGGGTTCAAATCCCGGACGAGCCC-AAGAGAAAA-CACTTTTT
DroWil_CAF1_left   GAACACCCT-GCCAGGCCAA-CATCAACTGGCTCGTTGGTCTAGGGGTATGATTTCCGCTTAGGGTGCGGGAGGTCCCGGGTTCAAATCCCCGACGAGCCCCAAGGGGGAA-AAATTTTT
DroYak_CAF1_left   AGGCATTTTGACCGT-CATC-GGGCAACTGGCTCGTTGGTCTAGGGGTATGATTTCCGCTTAGGGTGCGGGAGGTCCCGGGTTCAAATCCCGGACGAGCCC-AAGAGAAAAGAACTTTTT
DroGri_CAF1_left   TGCC-----GCCG----GGCACAGC-GTAGGCTCGTTGGTCTAGGGGTATGATTTCCGCTTAGGGTGCGGGAGGTCCCGGGTTCAAATCCCGGACGAGCCC-AAGCAATT---TATGATT

DroMel_CAF1_left   T---G-TTTCAAATTATAAACTTTGCTTATACTTTTTAT-TTTTGTTGCACAA-ATAACGACTTA-TGGGTAAATAAT-ATTAAC--A--TT-TGTT
DroMoj_CAF1_left   TTTATATTTTTTATTTTTGTTTTTTTATTTCAAACTATA-AAC--AATT-ATT-TATACTTTTTT-TTTAA-TTTTTG-CACAAA--T--AA-CGAC
DroPer_CAF1_left   T---G-TTTTGG-GT-TTTTTGTTGT-CAAATTA-TAAACATTGCTTATAGAA-TTTATTTTTGT-TGCACAAATAACGACTTAA--TGGGTA-AAT
DroPse_CAF1_left   T---G-TTTTGT--T-TTTTTGTTGT-CAAATTA-TAAACATTGCTTATAGAA-TTTATTTTTGT-TGCACAAATAACGACTTAA--TGGGTAAATA
DroSec_CAF1_left   T---G-CTTCAAATTATAAACTTTGCTTATAGTTTTTAT-TTTTGTTGCACAA-ATAACGACTTA-TGGGTAAATAAT-ATTAAC--A--TT-TGTT
DroSim_CAF1_left   T---G-CTTCAAATTATAAACTTTGCTTATAGTTTTTAT-TTTTGTTGCACAA-ATAACGACTTA-TGGGTAAATAAT-ATTAAC--A--TT-TGTT
DroWil_CAF1_left   T---G-TTTTCAAAT-ATATTTTTAATAAACATTTATAG-ATATTTATTGTAT-TCT-TTTTTGT-TTGTTGTTGCACAAATAAC--G--AC-TTAA
DroYak_CAF1_left   T---G-TTTCAAATTATAAACTTTGCTTATAGTTTTTAT-TTTTGTTGCACAA-ATAACGACTTA-TGGGTAAATAAT-ATTAAC--A--TT-T-GT
DroGri_CAF1_left   T---T-ATTTTAACC-AATTT-TAGTTTTTATCAAAAATGAAAGCCATTTTTTTTTTTT-TTTTATCAAACTATAAAC-AATTATTTA--TA-CTTT