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


DroEre_CAF1_left   TTCGTAAGGTAAATCATATTTATATTTTCCGCTTAATT---AAGTAGAGCTCAAGC-CTTATAAACGAATTAAGTAGTATTTAC-GGTGGAGAATTAAATAATTCGTAAAGCCTGTCTTT
DroMel_CAF1_left   TAT-TTACTGTTTTTAACGTAGAGTTCTAGATTTATAA---TCTCAAATGAGGTAT-TCGGATAAAAAACGATTTAGCAACTGTTAACGGTGAACTAAATTATTTGTAAAGCCCGTCTTT
DroSec_CAF1_left   ATTTTTATATTTTCTGCTTTTTTTTA----ACTTATAATCTTAAATTACGTATTCGGATAAAGAACGATTTAACAAATATTAAT-GGTGGAAAATTAAATTATTTGTAAAGCCTGTCTTT
DroSim_CAF1_left   NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN---NNNNNNNNNNNNNNN-NNNNNNNNNNNNNNNNNNNNNNNNNNN-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
DroYak_CAF1_left   CCCGTCATAGTCATAATTATCTTTTCTGCTTAATTAAC---GAAGAGAGTTCAAGT-CTTATAAACGAAATAACAAATATTTAC-TGTAAAGAATTAAATAATTTGTAAAGCCTGTCTCT
DroAna_CAF1_left   GGAGCTTTAGGAAGCTTAA-TGACTGCAATGAATGATT---GTCATGTCTGATG--------AGGTTTTTTTA-AAATATTGAT-ATTTAATAACCATTTATGATTAAAACTCTATAAAC

DroEre_CAF1_left   ATGCCTGTCCTTTTTTTCTG--TGCTACCAGCGGACCGTGTGGCCTAATGGATAAGGCGTCGGACTTCGGATCCGAAGATTGCAGGTTCGAGTCCTGTCACGGTCGAAAAGTAATCTTTT
DroMel_CAF1_left   ATGTTAGTCATATTTTTCAG--AGTTGCCAACTGACCGTGTGGCCTAATGGATAAGGCGTCGGACTTCGGATCCGAAGATTGCAGGTTCGAGTCCTGTCACGGTCGTAAAATTAACTTTT
DroSec_CAF1_left   ATGTTAGTCATATTTTTCGT--AGTTGCCAACTGACCGTGTGGCCTAATGGATAAGGCGTCGGACTTCGGATCCGAAGATTGCAGGTTCGAGTCCTGTCACGGTCGAGACAATAACTTTT
DroSim_CAF1_left   NNNNNNNNNNNNNNNNNNNN--NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNATCCGAAGATTGCAGGTTCGAGTCCTGTCACGGTCGAAACAATAACTTTT
DroYak_CAF1_left   ATGCCAGTCCTATTTTTCGG--AGTTGCCAGCTGACCGTGTGGCCTAATGGATAAGGCGTCGGACTTCGGATCCGAAGATTGCAGGTTCGAGTCCTGTCACGGTCGAAAAATAATCTTTT
DroAna_CAF1_left   AA-----GCTCCTTATTGTTTTAGTTGC---AAGACCGTGTGGCCTAATGGATAAGGCATCGGACTTCTGATCCGAGGATTGCAGGTTCAAGTCCTGTCACGGTCGGAAAAGGGGTTTCT

DroEre_CAF1_left   TTTTT--TAATCTTATA---TTCAATC-TCATTTTATGAAAATGGGATTAAAGGGCATTTGGTTTTGTAGCTCACCTT-CTTGAAGCGC-CTT-CGCTGCGATGAAGA--G-TGCGTCGA
DroMel_CAF1_left   TTCTTTTGTATCCAGAATTTTTTTTAT-TTATTTTATGAAAATGAGATTTGAGGGCATTTGGTTGCATTTATCACACT-TTGTAAGTCTGTAT-CTCACCTT-C-TTG--A-AGCGCCTT
DroSec_CAF1_left   --------------TTT---ATTTT---TTTTTATTTTATAAAA-ATGAGATTT----------GCATTTATCACACC-TTGTAAGTAAGTAT-CTCACCTT-C-TTG--A-AGCGTCTT
DroSim_CAF1_left   TTTAT-----------T------TTTT-TTATTTTATGAAAATGAGATTTGAGCGCATTTGGTTGCATTTATCACACC-TTGTAAGTATGTAT-CTCACCTT-C-TTA--A-AGCGCCTT
DroYak_CAF1_left   TTTTTT-GTAGCTTAAA---TTCAATCCACATTTTATTAAAATGAGATTTAAGGGCATTTGGTCGCATTTATCATGCT-TTGTAAGTCTGTAG-CTCACCTT-T-TTG--A-AGCGCCTT
DroAna_CAF1_left   TTTTGG-TTA--------------AGA-TTTATTCTGTAAGTGGGTCAATAG--GCTTTAGAAGGTAAATAATATTTAAAATTATTTTTGAAAAAATTCCAG-A-CAATCTCTCA-CCTT

DroEre_CAF1_left   -AGCAGTTTCG-AG------------CAG
DroMel_CAF1_left   -CGCTGCGATG-AG------------G--
DroSec_CAF1_left   -CGCTGCGATG-AAGAGTGTGTCGATACA
DroSim_CAF1_left   -CGCTGCGATG-AA------------GA-
DroYak_CAF1_left   -CGCTGCGATG-AA------------GAG
DroAna_CAF1_left   TTTGAA--ACGTCT-------------TC