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


DroMoj_CAF1_left   CCTAT--AAAAAATACACAAATAATTAAGAAATAAGTATG-TTAAAGCAATCCT---TGCATGAATAAAAATTTTAA----AAATTG-ATTCGAT--GAATGACGTATAAAAAA-AACA-
DroVir_CAF1_left   ATTGA--TTAATCAATATTAACAAATATTAAATGT-AAACATTA-ATAAAAAA-----AAAAGAAATACAAAC-GAC----GCTTTG-AAAAAAA--AAATAACAAGCGAACGGTTTAA-
DroEre_CAF1_left   CATTACGAGCAGAGGGTCCAAACC--GCTGTCAAT-CATCTGCC-ACCCGATAAGC-GAGCACCAAGAAAAAAAAT-----AGAAGGTAAACCCAGC-AAAAAAAA----TTT-----A-
DroMel_CAF1_left   --------GCAGAGGGTCCAAACC--GCTGTCAAT-CATCTGCC-AACCGATAAGC-GACCCTCAAGAAAAAAAAAAAAAAAGAAGAAAAACCCAGGCAAAAAAAATATATCAA-TATAT
DroSim_CAF1_left   --------GCAGAGGGTCCAAACC--GCTGTCAAT-CATCTGCC-AACCGATAAGC-GACCCTCAAGAAAAAAAAAAACAAAAAGGGAAAACCCAGCCAAAAAATATATATCAA-TCCA-
DroYak_CAF1_left   ATTT--GAGCAGAGGGTCCAAACC--GCTGTCAAT-CATCTGCC-ACACGATAAGCGGACCCTCAAGAAAAAAAAAAA-AAACAG------CCAAAAAAAAAAATATATATCAT-CCGA-

DroMoj_CAF1_left   -----C-GCTGAAGGTTCTACCGAGATTTGAACTCGGATCGCTGGATTCAAAGTCCAGAGTGCTAACCATTACACCATAGAACCAGTCGAGTACCAATCGTCCAGAACTCACAAAAAGAC
DroVir_CAF1_left   -----G-GTTCAAGGTTCTACCGAGATTTGAACTCGGATCGCTGGATTCAAAGTCCAGAGTGCTAACCATTACACCATAGAACCAGCTGTTAGCTTCGCGTCCAAAACTCAGTCAAAGGC
DroEre_CAF1_left   -----A-TGAATAGGTTCTACCGAGATTTGAACTCGGATCGCTGGATTCAAAGTCCAGAGTGCTAACCATTACACCATAGAACCGGATAAATGCGCTGCTGCAAAATTCCAGGCATGCGA
DroMel_CAF1_left   GTATATATATATAGGTTCTACCGAGATTTGAACTCGGATCGCTGGATTCAAAGTCCAGAGTGCTAACCGTTACACCATAGAACCGGATAAATGCGCTGCTGCAAAATTCCAGGCAACCGA
DroSim_CAF1_left   -----C-TTGGTAGGTTCTACCGAGATTTGAACTCGGATCGCTGGATTCAAAGTCCAGAGTGCTAACCGTTACACCATAGAACCGGATAAATGCGCTGTTGCAAAATTCCAGGCAACCGA
DroYak_CAF1_left   -----C-GGACCAGGTTCTACCGAGATTTGAACTCGGATCGCTGGATTCAAAGTCCAGAGTGCTAACCATTACACCATAGAACCGGATAAAAGCGCTGCTGTAAAATTCCAGCCAAATGA

DroMoj_CAF1_left   GA-AACGACGTA-ACAAAGGCATCAGC--GCTCAGCTATAAATAGAAT-CCCG-TTGGTGGTCTCAGTTAACGACGACAGCGGCAGCGGCAGAGACG-TT
DroVir_CAF1_left   ---AGCGACATAAACAGTGGCATCAGC--GCTTAGCTATAAATAGCAT-ACCGGGGGGTGGCCTCAGTTGACGATGGCGGCAGCGTCGCTGCAGGGC-GC
DroEre_CAF1_left   AAAATCAGCGCA-TCTGT--GAGCGAG--CGAGAGAGGTGGAGTGCAGCTCAG-GCTCTGGATTTATAAATAGCCCCTTTCGTCTCGCTCACTCTCA-GT
DroMel_CAF1_left   AA-ATCGGCGCA-TCTGC--AAGCGAG--TTAAAGAGGTGGAGTGCAGCTCAG-GCTCTGGTTTTATAAATAGTCCGGTTCGTCTCGCTCACTCCCACTA
DroSim_CAF1_left   AA-ATCGGCGCA-TCTGC--AGGCGAGAGGGAGAGAGGTGGAGTGCAGCTCAG-GCTCTGGTTTTATAAATAGTCCGGTTCGTCTCGCTCACTCCCAC--
DroYak_CAF1_left   AA-ATCGGCGCA-TCTGT--GAGCGCT--GGAGAGAGGTGGAGTGCAGTTCAG-GCTCTGGTTTTATAAATAGCCCGTTTCGTCCCGCTCACTCCCACTA