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


DroAna_CAF1_left   GTACAAATAT---CACACCCTGACGATAA--CCTTTTTTCCGATTTAGTGCACTGAG-CG---GCGAACAAACACAATCCACCCCT-GTATATTCGAGTATGGCAGGCGCACGTATCAAA
DroMel_CAF1_left   TGTATTTAATTTTCGTTTTTGTTCGTTTG--TATTTGCACCCCGCGATAACAGAATG-TT---TGCTCTACAGAAAATCCACCCTT-G---TGCTGTAGGTTGCTTGCACACGTATCAAA
DroPer_CAF1_left   CTTTTTTTATTATATAACTTTAATTCG----GGTTGG-AATCCGAGGGGGCGGAAAGCGA---GT-GCCGT-GCTACTGCATGGAACA---AGAACCCTAGAGCATGAGTGCGCGTACTT
DroPse_CAF1_left   GCTTTTTTATTATATAACTTTAATTCG----GGTTGG-AATCCGAGGGGGCGGAAAGCGA---GT-GCCGT-GCTACTGCATGGAACA---AGAACCCTAGAGCATGAGTGCGCGTACTT
DroSec_CAF1_left   GTATTTAATATTTCGTTTTTGTTCGTTTG--GATTTGCACCCCGCGATAACAGAATG-TT---TGCTCTATAGAAAATCCACCCTT-G---TGCAGTGGGTTGCGTGCGCACGTATCAAA
DroSim_CAF1_left   ATTTAATATTT--CGTTTTTGTTCGTTTGTGTATTTGCACCCCGCGATTACAGAATG-TT---TGCTCTATAGAAAATCCACCCTT-G---TGCTGTGGGTTGCGTGCGCACGTATCAAA
DroYak_CAF1_left   TTGTATTTAAT--AATTCGTTTTTGTTTG--TATTTTCACCCCTCGATAACAGTATG-TGTT-TGCTATACAGAAAATCCACCCCT-G---TGCTGTGGGTTGCGTGCGCACGTATCAAA
DroEre_CAF1_left   TTTAATATTT---CGCTTTTGGTCGTTTG--TACTTTCACCCCTCGATAACAGTATG-TGTTTTGCTTTACAGAAAATCCACCCTT-G---TGCTGTGGGTTGCGTGCGCACGTATCAAA

DroAna_CAF1_left   TGTTTTCCAGCTTAAGCCAGGTTACATCAAGTGACCGTGTGGCCTAATGGATAAGGCGTCGGACTTCGGATCCGAAGATTGCAGGTTCGAGTCCTGTCACGGTCGAAATTTGGA-TTTGA
DroMel_CAF1_left   TGTTTTCGAGTTTAAGCGTGCTTGGAACAAGCGACCGTGTGGCCTAATGGATAAGGCGTCGGACTTCGGATCCGAAGATTGCAGGTTCGAGTCCTGTCACGGTCGAAACCAA-AGTATT-
DroPer_CAF1_left   -ATTCCC--GTTTAAAACGACAATACACAAGCGACCGTGTGGCCTAATGGATAAGGCGTCGGACTTCGGATCCGAAGATTGCAGGTTCGAGTCCTGTCACGGTCGAATAGAA-AGTATC-
DroPse_CAF1_left   -ATTCCC--GTTTAAAACGACAATACACAAGCGACCGTGTGGCCTAATGGATAAGGCGTCGGACTTCGGATCCGAAGATTGCAGGTTCGAGTCCTGTCACGGTCGAACACAA-AGTATC-
DroSec_CAF1_left   TGTTTTCGAGTTTAAGCGTGCTTGAAACAAGCGACCGTGTGGCCTAATGGATAAGGCGTCGGACTTCGGATCCGAAGATTGCAGGTTCGAGTCCTGTCACGGTCGACACCAA-AGTAAA-
DroSim_CAF1_left   TGTTTTCGAGTTTAAGCGTGCTTGAAACAAGCGACCGTGTGGCCTAATGGATAAGGCGTCGGACTTCGGATCCGAAGATTGCAGGTTCGAGTCCTGTCACGGTCGACACCAA-AGTAAA-
DroYak_CAF1_left   TGTTTTCGAGTTTAAGCCTGCTTGGAACAAGCGACCGTGTGGCCTAATGGATAAGGCGTCGGACTTCGGATCCGAAGATTGCAGGTTCGAGTCCTGTCACGGTCGACACTAA-AGTAAT-
DroEre_CAF1_left   TGTTTTCGAGTTTAAGCCTGCTTGGAACAAGCGACCGTGTGGCCTAATGGATAAGGCGTCGGACTTCGGATCCGAAGATTGCAGGTTCGAGTCCTGTCACGGTCGACACTAA-AGTAAT-

DroAna_CAF1_left   TTTTTTTATATTTTATTTATTTTTATTT-T-TTTATTTTCACTATACTATGTTTTACGCGA-------AGTGTGTTTCTTTTCCTAATATTTTGTTCCAAAAT------TAGAAAAT-AT
DroMel_CAF1_left   ATTT--------TTT-----TTTTGTGA-G-AAACTT-ATGTTTTGT-TCTTTAAAA---AATTCAATTTGT----TGCAAAC-TAAAACCATAAAATAAATC------AACAAAAA-CA
DroPer_CAF1_left   CTTTTTT-CGCTTTTTTTTCTTTTTCAGTCAACAAAT-ATTACTCTCAAGTGCCTAAAATA-------ATTT----TTCCTTC-ATCAAAATAATTTAAACAG------AAGAAAAA-CA
DroPse_CAF1_left   TTTTTTT-CGCTTTTTTTTCTTTTTCAGTCAACCAAT-ATTACTCTCAAGTGCCTAAAATA-------ATTT----TTCCTTC-ATCAAAAGAATTTAAATAG------AAGAAAAA-CA
DroSec_CAF1_left   TTTTTTTTCTTTTTTTTATTTTTTTTGA-A-AGAAAT-TTGTTTTTTTTTTTAATTAAGT--------TTGT----TGCAAAC-TAAAATCATAAAGTAAATATACATAAACAAAAA-AA
DroSim_CAF1_left   TTTTTTTTTTCTTTTTTTATTTTTTTTG-A-AAGAAA--ATTGAATTTTGTTCTTAAAAAAATTAAATTTGT----TGCGAAC-TAAAATCATAAAGTAAATA------CACA-AAACCA
DroYak_CAF1_left   ATTTTTTTCTTTTTTTATTTTTTTGTAG-G-AAATTT-CTGTTTCTTTTTCTCAAAAAAAAACTAATAATGC----TGCATAT-TAAAATCGTAAAGTAAATC------CACACAGGCCA
DroEre_CAF1_left   TTTTTTT-TTTTTTTTACTTTTTTGTAAGAAAATTCT-TACTTTCTCAAAAAAAA-------CTAAATATGC----TGCATTT-TAATTTGGTAAAGTAAATC------CACATAGG-CA

DroAna_CAF1_left   -AAGCAATAATAA-T--ATTTTTAC
DroMel_CAF1_left   -ACAAAAATTTTA-A--GGTTCACT
DroPer_CAF1_left   AAATATAGCTGGGGAGATTATATTC
DroPse_CAF1_left   AAATATAGCGGGGGAGATTATTTTC
DroSec_CAF1_left   -AAAAAGATACAC-T--TGGCTAAT
DroSim_CAF1_left   -AAAAAAAC-TTT-A-AGATGCACT
DroYak_CAF1_left   -AAATAAAT-TAA-A------AGAT
DroEre_CAF1_left   -AAAAAGTTAAATAA--TACACTTG