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


DroEre_CAF1_left   TTTAAACGAT-CATGACTGCGTA-ATT--TGTTATGAA-AGCATG-T-GTATAATAAAA-GGAGA----AGATAAAATAAAAGT-C--CCAG---CGTAAAAAAAAAAATTCTGTCAGAA
DroGri_CAF1_left   CGATTGTGATCGTT-AATAAATA-ATT--AATTAAAAAACATTCA-T-TTTGTTGATTG-AATTT----TCCTCTAA-AATATA-T--GAAA---AATACAAAAAAAAACTTTGTCAGAA
DroMel_CAF1_left   TAGAATTAGATAAC-TTTAAATT-ATA--ATGACTTCA-TCATAT-C-CAATTAAATAT-ATTTT----TTTTTAAATAGGAAA-A--GTAA---ATAAACAAAAAAAAATTTGTCAGAA
DroMoj_CAF1_left   GAAGCGTATTCAAA-TTACAATT-TTCAATTGCAAATA-TAAATT-A-GTAAAATTTAA---AAA----AAAAAAAAAAATAAA-A--AAAAATTGC---AAAAAAAAACTTTGTCAGAA
DroPer_CAF1_left   TCTCAACTAATCGA-GCATACAT-ACATAAAATAAATT-TTAAAG-C-ATTTTAGAAAA---AGA----AGAAAACTAATAAAA-ATG--AT---ACAAAAAAAAGATGATTTGTCAGAA
DroPse_CAF1_left   TCAACTAATCGAGC-ATACA--T-ACATAAAATAAATT-TTAAAA-C-ATTTTAGAAAA---AAA----AGAAAACTAATAAAA-ATGATAC---AAAAAAAAAAGATGATTTGTCAGAA
DroSec_CAF1_left   GCTTTAAATTATAATGGCTTCTTAAT---TTCCAATGA-AATATATT-TTTA-TAATAATAGGA-----GAAGCAAATAAGCAT-A-TAA-----AATAAGTAAAAAAATTTTGTCAGAA
DroSim_CAF1_left   TTATAATGG-CTTCTTATTTCCT-AT---TTCCAATTA-AATATATT-TTTA-TAATAATAAAA-----AAAGTAAATAACCAT-A-TAAAA---TATATAAAAAAAAATTTTGTCAGAA
DroVir_CAF1_left   ATATGTGGTCAGAGATTTCTCCA-TT---TGCCCGTCA-CATACATTTGCAC--CAAATCAGGG-----TAGAGAAATAATAAT-T--TCAA---AAAATGCAAAAAGCATTTGTCAGAA
DroWil_CAF1_left   TACTCTGTAT-----TTTAACGG-TTGATAAAAAAAAA-GACCGT-A-TAAAAAAATAA---AATTTTGCTACATTTAAAAAAA-A--AAAA---ATAGAAAAAAAAAATTTTGTCAGAA
DroYak_CAF1_left   TAAATTTAAATATA-GTTAAATA-ATA--GAAGGGGAA-AGTAAA-A-GAGTCATATGC-TTCTT----ATAATGTTCTAGTTA-A--AAAA---AAATAAAAAAAAGTTTTTGTCAGAA
DroAna_CAF1_left   TTTTGCAAAGCCCT-CAAAATAA-GTT-TGTACTTCCA-TAGAGA-A-TATA--ATTTTGTAGT-----ATAATAAAGATAAAATA--AATA---AAAATAAAAAAAATATTTGTCAGAA

DroEre_CAF1_left   GTGGGATTCGAACCCACGCCCTCAGAGAGGACCAGAACGCTCGCA----C--GCCCTTCTGCGAAGGGCAAGACT--GAAT-GCCTTGAGTCTGGCGCCTTAGACCGCTCGGCCATCCTG
DroGri_CAF1_left   GTGGGATTCGAACCCACGCCCTCAGAGAGGACCAGAACGCTCATC----G--ACCTTTCTACGAAAGGCAAGACTTTTATC-ATCTTGAGTCTGGCGCCTTAGACCGCTCGGCCATCCTG
DroMel_CAF1_left   GTGGGATTCGAACCCACGCCCTCAGAGAGGACCAGAACGCTCGTAC--AC--GCCCTTCTGCGAAGGGCAAGACT--GAAT-GCCTTGAGTCTGGCGCCTTAGACCGCTCGGCCATCCTG
DroMoj_CAF1_left   GTGGGATTCGAACCCACGCCCTCAGAGAGGACCAGAACGCTCATC---AC-AACCTTTCTATGAAAGGCAAGACT--TTTCAATCTTGAGTCTGGCGCCTTAGACCGCTCGGCCATCCTG
DroPer_CAF1_left   GTGGGATTCGAACCCACGCCCTCAGAGAGGACCAGAACGCTCATACAAAC-GACCCTTCTGGGAAGGGCAAGACTGTTGAT-ATCTTGAGTCTGGCGCCTTAGACCGCTCGGCCATCCTG
DroPse_CAF1_left   GTGGGATTCGAACCCACGCCCTCAGAGAGGACCAGAACGCTCATACAAAC-GACCCTTCTGGGAAGGGCAAGACTGTTGAT-ATCTTGAGTCTGGCGCCTTAGACCGCTCGGCCATCCTG
DroSec_CAF1_left   GTGGGATTCGAACCCACGCCCTCAGAGAGGACCAGAACGCTCACA----C--GCCCTTCTGCGAAGGGCAAGACC--GAAT-GCCTTGAGTCTGGCGCCTTAGACCGCTCGGCCATCCTG
DroSim_CAF1_left   GTGGGATTCGAACCCACGCCCTCAGAGAGGACCAGAACGCTCACA----C--GCCCTTCTGCGAAGGGCAAGACT--GAAT-GCCTTGAGTCTGGCGCCTTAGACCGCTCGGCCATCCTG
DroVir_CAF1_left   GTGGGATTCGAACCCACGCCCTCAGAGAGGACCAGAACGCTCACC----A--ACACTTCTATGAAATGTAAGACT--GTTA-ATCTTGAGTCTGGCGCCTTAGACCGCTCGGCCATCCTG
DroWil_CAF1_left   GTGGGATTCGAACCCACGCCCTCAGAGAGGACCAGAACGCTCAT----AC-CACCTTTCTATGAAAGGCAAGACT--TATC-ATCTTGAGTCTGGCGCCTTAGACCGCTCGGCCATCCTG
DroYak_CAF1_left   GTGGGATTCGAACCCACGCCCTCAGAGAGGACCAGAACGCTCGCA----C--GCCCTTCTGCGAAGGGCAAGACT--GAAT-GCCTTGAGTCTGGCGCCTTAGACCGCTCGGCCATCCTG
DroAna_CAF1_left   GTGGGATTCGAACCCACGCCCTCAGAGAGGACCAGAACGCTCGCA----CAAACCCTTCTGCGAAGGGCAAGACA--TTTT-GCCTTGAGTCTGGCGCCTTAGACCGCTCGGCCATCCTG

DroEre_CAF1_left   ACGAGTTGCGGGCGAGGGCGCAA-A-AACCCGCTTATAAGCTGCGC-GCTTAA-ATTGTGGAAATGCGGGGGGGTTAA-CTTCTAGTGCTGC-GATGATGAT
DroGri_CAF1_left   ACATGAGTATCGACTGTTGCTAAATAAGAACAAGCCAAACTGAACATGAAGTTGGAGTTTTTTT--TT-TACGGCGAT-AACCGT-CACGTA-CTCTCTCTC
DroMel_CAF1_left   ACATGTTACGAATGGGGGCGCAA-A-AACACGTTTATAAGCTGCGGCAGTGAGTTTCCAGTTGAA-AT-TTGGTTGTT-TGTGTATTACCGG-GGGGGTTAT
DroMoj_CAF1_left   ACATGTTGAATGGGGT-TGGCCA-A-ATCGTTGTAATTAACAAACGAAAAAAAGTAAAAGAATTA-AG-CATTAACTTTAAGTTATTTTAAG-AACGGCAAC
DroPer_CAF1_left   ACACGTTGCAAATCGTAGGACTA-A-AGCACTGTCAAAAGCTAAAGTAGGGGATGAGATGACGTC-GC-CAATTACAA-AGGCAACAACAAT-CATGATGAT
DroPse_CAF1_left   ACACGTTGCAAATCGTAGGACTA-A-AGCACTGTCAAAAGCTAAAGTAGGGGATGAGATGACGTC-GC-CAATTACAA-AGGCAACAACAAT-CATGATGAT
DroSec_CAF1_left   ACATGTTGCGGGCCAGCGTGCAA-A-AACAAGCATATAAGCTGCGGCAGTGAATTTGCAGTTGAA-AT-TCGGATGTT-GGTGAATTACCGG-GAGGGTTAT
DroSim_CAF1_left   ACATGTTGCGGGCCAGCGTGCAA-G-AACAAGTTTATAAGCTGCGGCACTGAGTTTGCAGTTGAA-AT-TCGGGTGTT-GGTGAATTACCGG-GAGGGTTAT
DroVir_CAF1_left   ACATGTTAAA-TAGATGTTGCCA-G-AGCGCCGTAATTAAGGGAGCAAGCAGAGTAACAGAACGA-AAATGGAGTTAA-CGTTACTTTAATA-TACTCTCTC
DroWil_CAF1_left   ACATGTTGCGATGGTT-AGGCCA-A-AGCTCGTATACATTACACAATGCTCACACTGAAAGCTAT-TT-TATCTATGTATGTACCTATATAT-TTTTATTTT
DroYak_CAF1_left   ACACGTTGCGGGCGAGGGCGCCA-A-AGCCCGTTTCTAAGCTGCAGCAATGAGTTACCCGTTTAA-AT-TCTGGTGTT-GAGGAAATACAAC-GGTTGGGGA
DroAna_CAF1_left   ACATGTTGCGAACGGAGGCGCCA-A-AGCGTGCTCATAAGCTACAGCC-ACAGATCGGAATGAAA-TC-GGGGTGGAA-AAACAACACGGGGGTGGATTGTT