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


DroAna_CAF1_left   AAGGTGACTCAACCTTAGGCGTA-A-TATT-C-TATA-TACAAATACTGCT-TATCTAGAAGTTTAGTAAGATTTTATTG---CTAGACTCGGAATAAATAATTTA--A-AACAAATAA-
DroEre_CAF1_left   C-GCAGAGTTCATATTTGATGAA-T-ATCA-AATATT-TGCTCTAATTTAT-TATCGAACTTACTTTTCATTTTGCGTTT---CCAAAAAAACTACAACTTTCTCT--G-AGG-----A-
DroMel_CAF1_left   ACTCT-TCATATTTGATGAATAA-GTTTGC-T-CTCA-TTTATTTATTATT-GAGTTTACTTTTTATTTTGTTTGCGCTT---CCAAAACAATTACAACTTTCTCT--G-ATCAAAAAA-
DroMoj_CAF1_left   CAATATA-TGTAGATAAGTTAATTG-GCGA-AAAATA-AACAATAACATCTATTGTGTGCAGCTTAAATATTTTTATTAT---TAAAAAAAAAAAAATTTCATTTA--T-TATAATAAA-
DroSec_CAF1_left   TAGCACTCTTCATATTTGATGAA-T-AAGC-T-TGCT-CTCATTTATTATT-GAATTTACTTTTCATTTTGTTTGCTGTT---CCAAAACAATTACAACTTTCTCT--G-ATCAAAATA-
DroSim_CAF1_left   TAGCACTCTTCACATTTGATGAA-T-AAGC-T-TGCT-CTCATTTATTATT-GAATTTACTTTTCATTTTGTTTGCGCCT---CCAAAACAATTACAACTTTCTCT--G-ATCAAAAAAA
DroYak_CAF1_left   C-GCACAGTTGAGATTTGATGAA-T-AAGC-TTTGCT-CTCATTTATTTTT-GAGTTTACTTTTCATTTTGTTTGTGTTT---CTAA-AAAACTACAACTTTCTCT--TTAAA-----A-
DroGri_CAF1_left   CTATGTGTAAATCACTCAACGAT-TGCTGTGGCTTGAAGTATAAAATATAA-AATTCTACTTTGAATCTTTCGAGGGTCGCAATTATATTCAGTTTATTATTCAATTTG-CCACACAAA-
DroVir_CAF1_left   TTAATTACCTGGCTTG-GAGGAA-TGTTGT-ACAAAA-TATCTATCGCATA-TATCAAAACAAAGATCGTAT-ATCGATGCAAAGTTTGCTGAGCATTTCTTTTTTCAA-TTTAATAAA-

DroAna_CAF1_left   ---AAAAAATTATTAA----A-CTTGGCAGCGGTGGGATTCGAACCCACGCCTCCGAGGAGACTGGTGCCTTAAACCAGCGCCTTAGACCGCTCGGCCACGCTACCACTGAGTTCCAAGG
DroEre_CAF1_left   -----AAAAAAATCGC----A-TGTGGCAGCGGTGGGATTCGAACCCACGCCTCCGAGGAGACTGGTGCCTTAAACCAGCGCCTTAGACCGCTCGGCCACGCTACCCATAATTGC-GTTC
DroMel_CAF1_left   -----AAAAAAATCTC----A-AGTGGCAGCGGTGGGATTCGAACCCACGCCTCCGAGGAGACTGGTGCCTTAAACCAGCGCCTTAGACCGCTCGGCCACGCTACCCATAATCAT-CGCT
DroMoj_CAF1_left   ----TAAAAAAAAATC----T-CTTGGCAGCGGTGGGATTCGAACCCACGCCTCCGAGGAGACTGGTGCCTTAAACCAGCGCCTTAGACCGCTCGGCCACGCTACCATGTGGCTG-GCCG
DroSec_CAF1_left   ---AAAAAAAAATCCC----A-AGTGGCAGCGGTGGGATTCGAACCCACGCCTCCGAGGAGACTGGTGCCTTAAACCAGCGCCTTAGACCGCTCGGCCACGCTACCCATAATCGC-GGTC
DroSim_CAF1_left   AAAAAAAAAAAATCTC----AAAGTGGCAGCGGTGGGATTCGAACCCACGCCTCCGAGGAGACTGGTGCCTTAAACCAGCGCCTTAGACCGCTCGGCCACGCTACCCATAATCGC-GGTC
DroYak_CAF1_left   -----AAAAAAATCCT----A-AGTGGCAGCGGTGGGATTCGAACCCACGCCTCCGAGGAGACTGGTGCCTTAAACCAGCGCCTTAGACCGCTCGGCCACGCTACCCATAATTGC-GTAC
DroGri_CAF1_left   -----AAAAGAAGCTCAA--A-GTTGGCAGCGGTGGGATTCGAACCCACGCCTCCGAGGAGACTGGTGCCTTAAACCAGCGCCTTAGACCACTCGGCCACGCTACCAAACAGCCG-ATCG
DroVir_CAF1_left   -----AAAAAAATCCCAATCA-CTTGGCAGCGGTGGGATTCGAACCCACGCCTCCGAGGAGACTGGTGCCTTAAACCAGCGCCTTAGACCGCTCGGCCACGCTACCCCGTGTCCG-AGTG

DroAna_CAF1_left   CGACAA-AAA-------ACACTTCT------GATCGAAAGTGACATTTTT-TAT-TTAATTTTTTAAATA----TTATTTTTACAAAAAATAAGCTAAATAAGTGCCTCTCTCGGAAGTT
DroEre_CAF1_left   GGTCAG--AACGCTTTTGCGCTTAT------GATCGCAAGTGCTATATTG-AAA-GTTAAAATATTTATA----GCAAAAGTAACGAACACAATTGGAGGAAGTAATAATAAATATTTAA
DroMel_CAF1_left   GGTCAT--AA-------GCGCTTCT------GATCGCAAGTGCTATATTT-ATA-TTTACCATTTTTATA----GCAAAAATAACAAAAACAATTGTAGGAAACAATAATAAATACTTAA
DroMoj_CAF1_left   CGTTCA-AAT-------ACATTTC-------TCATGCTATATCGCGTTGT-CGCTGTGGGCTTAATTATA----TTTATCAGGCGTACAAAAATATTTCCAATCTTATTGTTGCCTTTAT
DroSec_CAF1_left   CGGCAG--AA-------GCGCTTCT------GATCGCAAGTGCTATATTT-ATA-GTTACTATTTTTATA----GCAAAAATAACGAAAACAATTGTAGGAAATAATAATAAATACTTAC
DroSim_CAF1_left   CGGCAG--AA-------GTGCTTGT------GATCGCAAGTGCTATGTTT-ATA-GTTACTATTTTTATA----GCAAAAATAACGAAAACAATTGTAGGAAATAATAATAAATACTTAC
DroYak_CAF1_left   GGTCAG--AA-------GCGCTTCT------GATCGCAAGTGCTATATTC-ACA-GTTAAAATATTTATA----GCAAAAAATACGATAACAATTGTAGGAAATAATAATAAATATTTCA
DroGri_CAF1_left   AGCCACCAAA-------ATACCCTATACTTTGTCA-CACTTGGCACTTGGCCCG-GTTATTAATAGCCGG-CAATTGTAGCAATACTGTTGCAAC---TACATATTTACACGG-----GG
DroVir_CAF1_left   TCGCTCAAAT-------ATATTGCT------CATA-CTTTTCGTTGTCGCACTT-AACTAAATTGTTGAGACTTTTTATAAAAATGAAAACAATCGCACATAAACAGATTTTTGT--TGC

DroAna_CAF1_left   TATTAAAGAAATCATAA
DroEre_CAF1_left   AAAGCAGTTGGGATGCA
DroMel_CAF1_left   AAAGCAGCTGGGATTGC
DroMoj_CAF1_left   TTATTTTTAAATCATAG
DroSec_CAF1_left   AAAGCAGTTGGGATTGC
DroSim_CAF1_left   AAAGCAGTTGGGATTGC
DroYak_CAF1_left   AAAGCAGCTGAGATCGC
DroGri_CAF1_left   CAAACA---AACAAATA
DroVir_CAF1_left   CTTGCA--CTTGCAACA