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


DroEre_CAF1_left   TAAGTTTAATC-TTATTTGTTTGACTATA-TTCAAAT------------------CATTCATATGTGTAAA---ATGTAATATTG--TC-CATTTGGGTAAT------------GGT-GA
DroMel_CAF1_left   TTGTGTATATA-T--------TTTGTTAA-CAAG----AACAATA----CTTCATGAAAGTTAGTTGTATATGTAAAT---ATTGTCTT-TTTGGTGTTTGGGT----------GGT-CG
DroSim_CAF1_left   GTTGCTTTACT-A--------TATCTTAT-ATT-----AATGAAA----TTATTATTATTATTATCTATATGTATAAT---ATTGACTT-TTTGGTGTTTGGGTGGTTCGAGTTAAA-TA
DroWil_CAF1_left   TGCGTAAATTA-A--------ATAAACAG-TAAA----TTAAA-A----CTTTAAAATAAAAATAATAATTTACAAAC---ATG---CT-TAAAATATCTAA------------AAA-TA
DroYak_CAF1_left   CTTTTCATAGC-AAATAAAATCAATGTAA-ATTGTTTTGCTAT-ATGCATATGAACGTCATAATATAGTCT-TTTTGT---GTT---TGGCGGTACAAGTTTC-----------TTG-TA
DroGri_CAF1_left   AAATTTGCGCCGCTAGAC-------CTTCGTTCT----CTTTC-A----AAACATAATTATTTTTTAAGCAAA---CG---TTGCATGT-TTCCCTGTTTTGG---------A-TGTGTT

DroEre_CAF1_left   TAAGAGA--GTT---GTTT-GTA-AACAAAAAGAAAAAAAGGAAAGAAAAGATTCCCATACCGGGAATCGAACCCGGGCTTCCTGGGTGAAAGCCAGACGTCCTAGCCACTAGACCATAT
DroMel_CAF1_left   AGTTTAA--TAT---GTGC-AAAAACTGCACAA----AAAGGAA--AA-ATTTTCCCATACCGGGAATCGAACCCGGGCCTTCTGGGTGAAAGCCAGATATCCTAGCCACTAGACCATAT
DroSim_CAF1_left   TGTGCAAAAAAC---TACACACC-TTTTGAAGT----CAAAGAA--AAAATTTTCCCATACCGGGAATCGAACCCGGGCCTTCTGGGTGAAAGCCAGATATCCTAGCCACTAGACCATAT
DroWil_CAF1_left   AGGGCAA--TTC---TATT-TCT-AGAAGTGGA----AAAAAAA--AATTACTTCCCATACCGGGAATCGAACCCGGGCCTTCTGGGTGAAAGCCAGATATCCTAGCCACTAGACCATAT
DroYak_CAF1_left   AATAAAA--ATACACACCT-TTCATTTGGGT-------AAAAAA--GAAGTCTTCCCATACCGGGAATCGAACCCGGGCCTTCTGGGTGAAAGCCAGATATCCTAGCCACTAGACCATAT
DroGri_CAF1_left   TGTTCAAT--CT---TTAA-ACA-AATAAAAAG---AAAAAAAA--TGGTACTTCCCATACCGGGANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

DroEre_CAF1_left   GGGATATTGCATCTG---GTGCATTAAATGCATTTTTTTTA-AATGCAAACAAATATA-TGTATTAGCTTTAAAATGCATTTCTTTGTTTATTAATTGTGAAATATTTA
DroMel_CAF1_left   GGGATACTGTAGCGAAGTCCG--ATTTACGTCTGTATTTTA-AGTGCAAGCACATTAA-TCAGCTTTAAAGTGTATTTACTTCCTTGTTTTTTTACAACCATA-TTCAA
DroSim_CAF1_left   GGGACACTCTGTCGCCGTTTG--ATTTACGTCTGTATTTTA-AGTCCAAGCAAAAAAAATCAGCTTTAAAGTGAATTT--GATTGTTTTGTTTTACAACGATATTCAAA
DroWil_CAF1_left   GGGATACGTTTGAACAATTAT--CAAAAATCAATTTTGTTATCAGGATAGC--AGCAA-ATGCCAACAAACAATAAAACGCAACTAACAATAAAATAAATATATAATAT
DroYak_CAF1_left   GGGACACTGAATCACATGCGA--ATTAATGTAAGTTTTTTA-AGTGCAAGCTTAAAAG-TGAATTTTTATTTGAAAGCGATGTTAAC-GGACTGTGAACAAATATATAT
DroGri_CAF1_left   NNNNNNNNNNNNNNNNNNNNN--NNNNNNNNNNNNNNNNNN-NNNNNNNNNNNNNNNN-NNNNTTATAATATGAATTGG-TTTTGGAACATGAATAAAACCGGAATTTG