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


DroMel_CAF1_left   TCAAGAACAAGAAGCATTTAAATT-TTTAATATTATTTTTCAAAAAAACAAC-TTTTTTCTTTGAA-----AACATACATAAAAAAAAATAAAAA-----AGTTTATAGTTGCCGAAACC
DroSec_CAF1_left   CAATTTATATTTATTT--GTTTTT-TTTGT----CAAGAATATATTTTTTTTGAAGAGTCGAAGTT-----CTTAAAAGTAAAAAAGAATTCACAAGCAAAAATGTGAATTGCCGAAACC
DroSim_CAF1_left   GATATAATATTTCCTG--GAAAGG-CAGTT----ATTTCCATAAAGAGAAATAGATTTCGGTATGG-----AAAATATAATTGCCAAAATAAAATAATTATAAAATGAATTGCCGAAACC
DroEre_CAF1_left   AGACAACTATGTTAAA--GCAAAT-AATTT--------ATAAAAATCGAATT-AAATAACTTAGCTCTAGCTAACAAATAGTTATGAAAAAAAACAAAAAAGTATATTGTTGCCGAAACC
DroYak_CAF1_left   TAAATAAAATTTTAAA--ATTGTATATGTA--------TGTATAAGTTACAA-CTTGGCTGGTACAAATTTCTTTTCACGAAATG-CGAAAAATAAAAAAAAATTCTAATTGCCGAAACC

DroMel_CAF1_left   CGGGATTGAACCGGGGACCTTTAGATCTTCAGTCTAACGCTCTCCCAACTGAGCTATTTCGGCTCCATGAGGATGGGGGCCTCAAGTGTCGTGTAGTCCGGCAGGCTATGCTCTGTCTCT
DroSec_CAF1_left   CGGGATTGAACCGGGGACCTTTAGATCTTCAGTCTAACGCTCTCCCAACTGAGCTATTTCGGCTCCATGACAACGAGGGCCCCAAGTGTTGTGTAGTCCGGCATGCTATGCTCTGTCTCT
DroSim_CAF1_left   CGGGATTGAACCGGGGACCTTTAGATCTTCAGTCTAACGCTCTCCCAACTGAGCTATTTCGGCTCCATGACGATGGGGGCCCCAAGTGTCGTGTAGTCCGGCATGCTATGCTCTGTCTCT
DroEre_CAF1_left   CGGGATTGAACCGGGGACCTTTAGATCTTCAGTCTAACGCTCTCCCAACTGAGCTATTTCGGCGCCATGACGGTGTGGGCCCCAAGTGTCGTGTAGTCCGGCAGGCTATGCTCTGTCTCT
DroYak_CAF1_left   CGGGATTGAACCGGGGACCTTTAGATCTTCAGTCTAACGCTCTCCCAACTGAGCTATTTCGGCGCCATGTAGGTGTGGCCCCCAAGTGTCGTGTAGTCCGGCGGGCTATGCTCTGTCTCT

DroMel_CAF1_left   TTTTCCC-CACTGGTCGCTGAGGA-GCAC--TTCTAATGGGGAGACGACAAAACAAACAAACCGAC-GCCGCATGATAT-TAACG
DroSec_CAF1_left   TTTCCCCACTCCTAATGGGGAGAATACAA--AACAAACAAACCGACGCCCGCATGAT-ATTACAAA-TATTCAGCAGAT-TTA-A
DroSim_CAF1_left   TTTCCCCACTTCTAATGGGGAGACTACAA--AACAAACAAACCCACGTCCGCATGAT-ATTACAAA-TATTCAGTAGAT-CAA-T
DroEre_CAF1_left   TTCCCCC--AATGGTCGGTGCGGA-GCGTGTGTCTAATGGGGAGACTAAA-ATCAAACAAACCTG-TTATGCAAATATTAAGT-A
DroYak_CAF1_left   TTTCCCC--AATGGTCGGTGAGGG-GCGT--TTTTAATGGGGAGACTAAAAAACAAACAAACCAGCGCCTGTTATATAATTAT-T