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


DroAna_CAF1_left   TTTTGCGA-ACCACTGTTTTTCGGTGTGCTTATAATTCCCAACCGCTTCTGGCGCAGGCGCCAT-GTAGTTCTCAG-CCAA-GAGCTGGCAA-AAG-TACTCTGGCTTCTCTTCAGTTGT
DroEre_CAF1_left   TTAATGAG-AAGCTACCGCGCTGGTGTGCTTATAATTCCCAACATGTTATAGCAGCCGCCGCATGGAGTAGCTGAT-GAAA-A-TGATCATT-CGG-CACTCTGGTTTCTCTTCAATTGT
DroGri_CAF1_left   TTAGCATT-TATTTGCCAA-CCAAGCTGCGTATAATTCCCAAACAGTTCTAGCAGCAACTGCGTAGTACAGTTTGA-AATT-G-GCGGCGTA-TGGCTACTCTGGCTTCTCTTCAGTTGT
DroMel_CAF1_left   TTAGCGCG-AACTGACCGAGCCGGTGTGCATATAATTCCCAACGTGTTAAAGCAGTCACTGAATAGAGTAGCTGAT-AAAA-A-TTGTTGAA-AGG-CACTCTGGTTTCTCTTCAATTGT
DroMoj_CAF1_left   ATTTCGTC-TACTCTCGACACTGCGCGCGCTGTAATTCCCAAACGGTTGTGGCACTGAGAGCATGGTA-TGCCGCC-GTTG-T-GCTTTGGTTCGG-TACTCTGGCTTCTCTTCAGTTGT
DroPer_CAF1_left   AGCTGGTG-GCGAAACTGGCTGTATGTGCTTATAATTCCCAACTGGTTCTAGCACGGGCTGTATGGTATGGCTCAA-GTTT-G-CTGTGTAC-CGG-TACTCTGGCTTCTCTTCAGTTGT
DroSec_CAF1_left   TTAGCGCG-AAGTGACCGAGCCGGTGTGCGTATAATTCCCAACGTGTTCAAGCAGTCACTGCATAGAGTAGCTGAT-AAAA-A-TTGTGGTA-AGG-CACTCTGGTTTCTCTTCAATTGT
DroSim_CAF1_left   TTAGCGCA-TAGTGACCGAGCCGGTGTGCATATAATTCCCAACGTGTTAAAGCAGTCACTGCATAGAGTAGCTGAT-AAAA-A-TTGTGGTA-AGG-CACTCTGGTTTCTCTTCAATTGT
DroVir_CAF1_left   GTGTGCTT-TCGTTAACCGTCAGTCGCGCTG-TAATTCTCAAATGGTTCTGTCGGCGGCTGCATGGTGTCGTCGCT-GTTCAG-CATTTTCA-AAT-CACTCTGGCTTCTCTTCAGTTGT
DroWil_CAF1_left   TATGAATA-TTTTCATTTGT-TGATTGCATTATAATTCCCAACCAACTCTGGCATTGTGCGCATGGTATGACTCTAACTGG-C-ACTGGAAT-AGT-TACTCTGGCTTCTCTTCAGTTGT
DroYak_CAF1_left   TCAGCGCG-AGGCGACCGTGCCGGTGTGCGAATAATTCCCAACATGTTAAAGCAGTCCCCGCATGGAGTAGCTGAT-AAAA-A-TTGTTGTC-AGG-CACTCTGGTTTCTCTTCAATTGT
DroPse_CAF1_left   CTGGTGGCGAAACTGGC-TGTATGTGCCCTTATAATTCCCAACTGGTTCTAGCGCGGGCTGTATGGTATCGCTCAA-GTTT-G-CGATGTAT-CGG-TACTCTGGCTTCTCTTCAGTTGT

DroAna_CAF1_left   CGAATAAATCTTTCGCCTTTTACTAAAGATTTCCGTGGAGAGGAGCACTCTAATGAGTCTAAAATAATTTTTTAGTAGTGCC-CTGTCGTAAGACT-GGGGCCAT-A-ATAAATAAATAT
DroEre_CAF1_left   CGAATAAATCTTTCGCCTTTTACTAAAGATTTCCGTGGAGAGGAACACTCTAATGAGTCTAAAATAAT-TTTTAGTAGTGCC-CTGTCGCAAGACT-GGGGCCAT-C-AGAAATACATAT
DroGri_CAF1_left   CGAATAAATCTTTCGCCTTTTACTAAAGATTTCCGTGGAGAGGAGCACTCTAATGAGTCTAAAATAAT-TTTTTGCAGTGCC-T-GATTCCCATC---GGGCCATGAATAATGCATTTAA
DroMel_CAF1_left   CGAATAAATCTTTCGCCTTTTACTAAAGATTTCCGTGGAGAGGAACACTCTAATGAGTCTAAAATAAT-TTTTAGTAGTGCC-CTGTCGCAAGACT-GGGGCCAT-A-AAAAATAAATTT
DroMoj_CAF1_left   CGAATAAATCTTTCGCCTTTTACTAAAGATTTCCGTGGAGAGGAGCACTCTAATGAGTCTAAAATAAT-TTTTGCTAGTGCC-TGATTGCAAAAT--CGGGCCAT-T-AATCAATTCATA
DroPer_CAF1_left   CGAATAAATCTTTCGCCTTTTACTAAAGATTTCCGTGGAGAGGGGCACTCTAATGAGTCTAAATTAAT-TTTTTGTAGTGCC-CTGTCGCAAGACTTGGGGCCAT-A-AATGATAAATGT
DroSec_CAF1_left   CGAATAAATCTTTCGCCTTTTACTAAAGATTTCCGTGGAGAGGAACACTCTAATGAGTCTAAAATAAT-TTTTAGTAGTGCC-CTGTCGCAAGACT-GGGGCCAT-C-AAAAATAAATGT
DroSim_CAF1_left   CGAATAAATCTTTCGCCTTTTACTAAAGATTTCCGTGGAGAGGAACACTCTAATGAGTCTAAAATAAT-TTTTAGTAGTGCC-CTGTCGCAAGACT-GGGGCCAT-C-AAAAATAAATGT
DroVir_CAF1_left   CGAATAAATCTTTCGCCTTTTACTAAAGATTTCCGTGGAGAGGAGCACTCTAATGAGTCTAAAATAAT-TTTTGCTAGTGCC-CGATTGCAAAAT--TGGGCCAT-T-AATTAATACATA
DroWil_CAF1_left   CGAATAAATCTTTCGCCTTTTACTAAAGATTTCCGTGGAGAGGAGCACTCTAATGAGTCTAAAATAATTTTTTGTTAGTGCCCTTGTTGCAAAAC--GGGGCCAT-A-ATTAATACATTT
DroYak_CAF1_left   CGAATAAATCTTTCGCCTTTTACTAAAGATTTCCGTGGAGAGGAACACTCTAATGAGTCTAAAATAATTTTTTAGTAGTGCC-CTGTCGCAAGACT-GGGGCCAT-T-AAAAATAAATAT
DroPse_CAF1_left   CGAATAAATCTTTCGCCTTTTACTAAAGATTTCCGTGGAGAGGGGCACTCTAATGAGTCTAAATTAAT-TTTTTGTAGTGCC-CTGTCGCAAGACTTGGGGCCAT-A-AATGATAAATGT

DroAna_CAF1_left   GAATTTAGTTGTAAGAAATAA--GA-AAAAA-CATTCATT-TTTGTA-TTTTT-TTTTTAATAGTTTTTATT-TTAACTA-----C--GTAATTACAACTCT
DroEre_CAF1_left   GAAGAAATAT-TTAGAATTGG-AAT-TAT-A-TTAAAACA-ATGGTTTGTTTA-TTTT--TAAAGTTTGTTT-TTATTTTA-A-CT--ACG-TAATTACAAC
DroGri_CAF1_left   ACATTGAAAA-TAGTTTTAAT-TGT-TTTTAAAGTTTTTA-TTTTTAA-CTAA-ATAA--TTACAACGTATA-ATACA-AA-TTTT--ATAGTT----AAAA
DroMel_CAF1_left   AAAATAATAT-TAGAATTGTA-ATG-GAA-C-GCATTAAA-ACTACTT-CTTG-TATG--TTTTTAACGTTT-GTTTTTAT-T-TT--AACTACGTAATTAC
DroMoj_CAF1_left   AAAAATATAG-TTATACTGC-AAAC-TAG-A-GTTCGCAT-TTGTTTTGACGT-GT-T--TTTATTTTAACT-AA-ATAAT-TACA--ACGTATAATACAAA
DroPer_CAF1_left   TATTAGGAGG-AGAGATGTATC-GCCCTG-A-CTATTCCTGAAACTGA-AAGC-C--T--TGGAGAAATCAT-CG-CTCCACC-CCCAGCTTTT--GGTCAA
DroSec_CAF1_left   AGAGTAAATT-TAAGAATTCT-TGT-ATT-C-TTTATATG-TAAAGGA-ACGT-ATTA--AAACTACTGCTT-GTATGTTT-T-TA--ACGTTTGTTTTTAT
DroSim_CAF1_left   AAAGTAAATT-TAAGAATTCT-TGT-ATT-C-TTTATATG-TAAAGGA-ACGT-ATTA--AAACGACTGCTT-GTATGTTT-T-TA--ACGTTTGTTTTTAT
DroVir_CAF1_left   TACA-ATCAA-TCAGTTAATA-ATA-TAA-T-GTTTTT-T-AAACATACACACATACA--TTTTGAATTGTT-TATTTTAA-C-TA--AATAATTACAACGT
DroWil_CAF1_left   GCACAATTAA-AAACAATAAA-AGA-GAA-T-TTCCAAAC-GAATTTA-AACA-TATG--TATTTTGTTTCT-CTTTGCCA-T-GC--CGAAAAAAAATTAT
DroYak_CAF1_left   AAAGTAAATT-CTTGAAATTGAAAA-TAC-A-TGCTGTTT-TCTTGTTGTCAA-TA-G--AATGGAATTAAAACT-CCATT-TTGT--ATGTTTTTTAAG--
DroPse_CAF1_left   TATAAAGAGG-AGAGATGTAT-GGC-C-----CTGACTAT-TCAGAGAGCTGGAAACT--GAAAGCCTTGGA-GAAATCAT-CGCT--CCACCCCCAGATTT