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


DroEre_CAF1_left   GCAATGGCAACATTTTAAGCTTCATCGGGCATGGAGAGCTCGCC---ACTGGAATAGTTGAGGTAATTGTG----AATGTCCGTGAAAG-ACG-TCTCCA-GGAGAGTTTA--CAGAATT
DroMel_CAF1_left   --A-TGGCAACATTTTAAGCTTCATCGGGCATGGAGAGTTTGCC---ACTGGAATAGTTGAGGGAATTGCGAA-GAATGTCCGTGAAAA-ACG-TCTTCT-GGAGAGTCCA--CAAAATT
DroSec_CAF1_left   --A-TGGCAACATTTTAAGCTTCATCGGGCATGGAGAGCTTGCC---ACTGGAATAGTTGAGGGCATTGCGAA-GAATGTCCGTGAAAA-ACG-TCTCCA-GGAGAGTCCA--CAATATT
DroSim_CAF1_left   --A-TGGCAACATTTTAAGCTTCATCGGGCATGGAGAGCTTGCC---ACTGGAATAGTTGAGGGCATTGCGAA-GAATGTCCGTGAAAA-ACG-TCTCCA-GGAGAGTCCA--CAATATT
DroYak_CAF1_left   CAATTTTAAGCATTTTAAGCTTCATCGGGCATGGAGAGCTTGTC---ACTGAAATAGTTGAGGCAATTGTG----AATGTCCGTGAAAA-TCG-TCTCCA-GGAGGGTCCA--CAAAATT
DroAna_CAF1_left   GGACCGCAATCGGGC-GAGGAATGCCGAGCAGTGACAGCGAAATAGTTGTGGAAAAGGTGAAGAATGTCTGGGGGATATGTTACAAAAAGATATTCTGCTGGCAGTATATTTTCGTTTAT

DroEre_CAF1_left   -CGCTGGTGGGCAAGC----AAAATAACGAGT---ATCCCCTAAA-------AAAGAAAGGGGCACCCGGATTCGAACCGGGGACCTCTCGATCTGTGGTCGAATGCTCTACTTCTGAGC
DroMel_CAF1_left   TCGCTAGTGGGCAAGC----AAAATAACGAGT---ATTGGTTAAAAA--AAAAGTGAAGGGGGCACCCGGATTTGAACCGGGGACCTCTCGATCTGCAGTCGAATGCTCTGCCCCTGAGC
DroSec_CAF1_left   TCGCTGGTGGGCAAAG----AAAATAACGAGT---ATTGCTCAAAAAA-AAAAAAGAAGGGGGCACCCGGATTTGAACCGGGGACCTCTCGATCTGCAGTCGAATGCTCTACCCCTGAGC
DroSim_CAF1_left   TCGCTGGTGGGCAAAC----AAAATAACGAGT---ATTGCTCAAAAA---AAAAAGAAGGGGGCACCCGGATTTGAACCGGGGACCTCTCGATCTGCAGTCGAATGCTCTACCCCTGAGC
DroYak_CAF1_left   TCGC---TGGGCAAAC----AAAAAAACGAGT---ATCCCTTAAA-------AAAGAAGGGGGCACCCGGATTTGAACCGGGGACCTCTCGATCTGCAGTCGAATGCTCTACCCCTGAGC
DroAna_CAF1_left   GAGCGGGAAAGTAATGGTTTATAAAGAATACCATTAAAGGAAAAAAAGCCAAAAAAAAGGGGGCACCCGGATTTGAACCAGGGACCTCTCGATCTGCAGTCGAATGCTCTACCCCTGAGC

DroEre_CAF1_left   TACACCCCCACTTGTGAGGCAAGACTTTAGTGGTGTAGAGGGAAAGC-AAGCCTGCGTTTTGATTTACTTTGATTTTCTTGTCAACTCGTCA--ATACGTAATGCTGCATT-GA-CCCAC
DroMel_CAF1_left   TATACCCCCACTTATGTTAAAAGAGTTTTGAAGTCTACAAGGAGAAC-CATATTTCGTCGGTCTTAACG-TACGTTATGATTTATTTTGATG--TCCTTGTCAACTGGCAAATG-CGTAA
DroSec_CAF1_left   TATACCCCCACTTAAGTTAAAAGAGTTTAAAAGTCGAGAAGCAAAAC-AATATTTCCTTGGCCTTAACA-TACGTTTTGATTTACTTTGATG--TCCTTGCCAACTGGTGAGCA-TATGT
DroSim_CAF1_left   TATACCCCCACTTAAGTTAAAAGAGTTTAGAAGTCGAGAAGGAAAAC-CATATTTCCTTGGCCTTAACT-TACGTTTTGATTTACTTTGATG--TCCTTGTCAACTGGTGAGCA-TATGT
DroYak_CAF1_left   TATACCCCCACTTGCCACGTATAACTTTAGTAGTATAGAAGAAAAAC-AATGTAACGTTGCTCTCAAGCCTACGTTTTGATTTACTTTGTAT--TTCTTGTAAACTTGTCA-AT-TCGTA
DroAna_CAF1_left   TATACCCCCGACTGAAAGAAAGTGGTCTACTACTCGCCAAAAGGAGTTATTATTTTGTAAACCTGGTAG-AGCCGCATGAGA-ACTTATATTTGTTTGCA-ATTCTATTG--CTCGAATG

DroEre_CAF1_left   TGAA
DroMel_CAF1_left   TTAC
DroSec_CAF1_left   GTAC
DroSim_CAF1_left   GTAC
DroYak_CAF1_left   ATGA
DroAna_CAF1_left   ATGC