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


DroEre_CAF1_left   GACC--TCATGCGGTTTCGATTC-GG--TCAAG-GATATT--CTCGC-CATT-GGATATTTCCGCAGCTTCAGTGAGTTT-CGTCGTTA---TGC--AATGAG-TAA-AGCCCA-AGTGT
DroGri_CAF1_left   CAGA--ACTCGAGTGATGTGTGT-GG--TGTGT-GTGGTG--TGTGT-GTGT-GTGTGTGTGTGTGTGTGTGTGTGTGTG-TGTGTGGT--GTGT--ATGTGT-GTG-T-GTGG-TGTGT
DroMel_CAF1_left   AT--------GCGGCTTCGATTC-GG--TCAAG-GATATT--CTCGC-CATT-GGATATTATCGCAACTTCAGTGAGTTT-CGTTGTTACATTGCATAACGACATAA-AGCCCA-AGTGT
DroSec_CAF1_left   GACC--TCATGCGGTTTCGATTC-GG--TCAAG-GATATT--CTCGC-CATT-GGATATTACCGCAACTTCAGTGAGCTT-CGTCGTTA---TGC--AATGAG-TAA-AGCCCA-AGTGT
DroSim_CAF1_left   GACC--TCATGCGGTTTCGATTC-GG--TCAAG-GATATT--CTCGC-CATT-GGATATTACCGCAACTTCAGTGAGCTT-CGACGTTA---TGC--AATGAG-TAA-AGCCCA-AGTGT
DroWil_CAF1_left   ACGT--CTTCACCTAGCCACAAG-GA--TGAAACCGGTTC--G-CGATCGCC-CTTG--GATATCAAATTCTTTATGAAT-T---GACA---TAC--ATTTTG-GAG-TG-CTT-TATTC
DroYak_CAF1_left   GACC--TCATGCGGTTTCGACTC-GG--TCAAG-GATATT--CTCGT-CATT-GGATATTTCCTAAACTTCAGTGAGTTT-CGTCGTTA---TGC--AATGAG-TAA-AGCCCA-AGTGT
DroAna_CAF1_left   ATGCGGTTCCTTTTCGG--TCAAGGATATGTTC-TCCCTTGGATA---TTTC-TTCGAGTTCCTGTCTTCC------CATTAAGATGGT---TAT--GCAATC-GCCTTGCCCAGAGGCT
DroMoj_CAF1_left   CGTT--CCCGATCGTCAGCTGTG-CT--TTGCA-TCTCATTACGC---AAGTTCCGGTTTGTGCGTCAATCGACAATTGCCCTGCGCTC---A----GCGTGC-GGG-ACTCGC-CGTGA
DroPer_CAF1_left   CGGG--TTCGTTTGATG--ACCT-CA--TGCGG-TCACATTTCGGGG-CAGC-GCGCAAAAGGATATTCCC------GTGGTCCCGCCT---TGT--ATGGGG-GATCCATTTTTCTCAG
DroPse_CAF1_left   CGGG--TTCGTTTGATG--ACCT-CA--TCGGG-TCACATTTCGGGG-CAGC-GCGCAAAAGGATATTCCC------GTGGTCCCGCCT---TGT--ATGGGG-GATCCATTTTTCTCAG
DroVir_CAF1_left   GAGT--GCGCTGCGTGCGATCAT-CA--GCTGT-TTTTGCATCTC---ATTA-CGCAAGTTCCGGTTTGGTGTTTTTGATGTCCTGCCA---A-C--ATTCAG-GAC-AACATT-CGTGA

DroEre_CAF1_left   CCTTCATCATTTGGTACGTTTTTCTCCTGGTATCCACTGTAGGCCTATATGTATTTCCACCATAAGGCACGCGGTGAATGCCAAGAGCGAACGCAGTTCTACAAATTAC--TCATA-CCC
DroGri_CAF1_left   GTGCCGTCGTTTGGTACGTTTTTCTCCTGGTATCCACTGTAGGCCTCTATGTTTTTTGACCATAAGGCACGCGGTGAATGCCAAGAGCGAACGAAACTCTACACTTCCA--TTCAAATAT
DroMel_CAF1_left   CCTTCGTCATTTGGTACGTTTTTCTCCTGGTATCCACTGTAGGCCTATATGTATTTCCACCATAAGGCACGCGGTGAATGCCAAGAGCGAACGCAGTTCTACAAATTAC--TCATA-CCC
DroSec_CAF1_left   CCTTCGTCATTTGGTACGTTTTTCTCCTGGTATCCACTGTAGGCCTATATGTATTTCCACCATAAGGCACGCGGTGAATGCCAAGAGCGAACGCAGTTCTACAAATTAC--TCATA-CCC
DroSim_CAF1_left   CCTTCGTCATTTGGTACGTTTTTCTCCTGGTATCCACTGTAGGCCTATATGTATTTCCACCATAAGGCACGCGGTGAATGCCAAGAGCGAACGCAGTTCTACAAATTAC--TCATA-CCC
DroWil_CAF1_left   TCAGAGTCGTTTGGTACGTTTTTCTCCTGGTATCCACTGCAGGCCTATATGTTATTTGACCATAAGGCACGCGGTGAATGCCAAGAGCGAACGAAATTCTACAAAAACC--AAAA--CGC
DroYak_CAF1_left   TCTTCATCATTTGGTACGTTTTTCTCCTGGTATCCACTGTAGGCCTATATGTATTTCCACCATAAGGCACGCGGTGAATGCCAAGAGCGAACGCAGTTCTACAAATTTC--TCATA-CCC
DroAna_CAF1_left   TTTGTGTCGTTTGGTACGTTTTTCTCCTGGTATCCACTGTAGGCCTATATGTATTTCGACCATAAGGCACGCGGTGAATGCCAAGAGCGAACGAAACTCTACAAACTA----------CA
DroMoj_CAF1_left   GTGACGTCGTTTGGTACGTTTTTCTCCTGGTATCCACTGTAGGCCTCTATGAATTTTGACCATAAGGCACGCGGTGAATGCCAAGAGCGAACGAAACTCTACAAAAT------CCA-ACA
DroPer_CAF1_left   TGCTCGTCGTTTGGTACGTTTTTCTCCTGGTATCCACTGTAGGCCTATATGTATTTCGACCATAAGGCACGCGGTGAATGCCAAGAGCGGACGAAACTCTACTATCAA---AAACA-GCA
DroPse_CAF1_left   TGCTCGTCGTTTGGTACGTTTTTCTCCTGGTATCCACTGTAGGCCTATATGTATTTCGACCATAAGGCACGCGGTGAATGCCAAGAGCGGACGAAACTCTACTATCAA---AAACA-GCA
DroVir_CAF1_left   GTGCCGTCGTTTGGTACGTTTTTCTCCTGGTATCCACTGTAGGCCTCTATGAATTTTGACCATAAGGCACGCGGTGAATGCCAAGAGCGAACGAAACTCTACAATTAACAAAAATA-ACA

DroEre_CAF1_left   AATGATA-GACCAA-AAGTGTTTGAAGGCCCTA-AAACT-TCAATAACAAATAAAA-TA-AAC-GAAATTTCACATATT-ACAG-AA-ATT-TACCAA--CGT------GTGGAAAA-AT
DroGri_CAF1_left   A-ACCAGCAAACGA-CTGCTTTAAAGTGTGTGT-GAAGTGAAACTCAAGAAAGCTA-AT-AAA-CATCTT--TGTTTGA-GTAT-AA-ACT-TGATTTGGTTTTGATGTGAAAAGTGCTG
DroMel_CAF1_left   AATAATA-GACAGA-AAGTGTTTAAAAGCCTGA-AATCA-TAATAGACAAATTTGA-AA-TAA-TAAAGA--AATTTGC-GAAA-AG-TGT-TTAAAATTACT------TATGTGGA-AT
DroSec_CAF1_left   AATGATA-GACAGA-AATAATAGACAAATTTC--AAATA-ATAAAGAAATTTA-CC-AAAAGTGTTAAA---AAAATAG-TGAT-GT-TGA-AACATTGTAGC------GAACTTAA-AA
DroSim_CAF1_left   AATGATA-CACCGA-AAGTGTTTAATAGCCCGA-AATCA-TAATAGCCAAATTAAA-AA-TAA-TAAAG---AAATTTG-CCAG-AAGTGT-GAAGAATTAGT------AATGTGGA-AT
DroWil_CAF1_left   AAAAATA-TAAAAA-TAAA-G-AAAACGGACAAAAAAG---AAAA-TTAAATGTTA-AC-AAC-TAAATGT-GAAAGTG-CAAA-TT-AAA-ATCATAAAACA------AAAAGCAA-AA
DroYak_CAF1_left   AATGATA-GACCAA-AACTGCCTGACAGCCCTA-AAACT-TCAGCGACAAATAAAA-TA-AAC-AAGTTTTAAAATAAT-ACAA-AA-GTT-CACTAA---GT------GTGGAAAA-GT
DroAna_CAF1_left   AATGACA-TATTAA-AAATACAAAA--TATATA-TGATT-GGTGCTAATAAAAAGT-GT-TGA-AAATAT--AAAATAG-AAA--TA-ATA-ATGTTTATATA------TATCT--A-AA
DroMoj_CAF1_left   AGCGACC-TCTAAAAAAAGTGAAATAATTCCTA-TGGGT-ATTGCGTAACAATTTTGAT-TTT-GGAATA--ACGAAATCTTGTGCT-TGT-GATTTATTT-T------ATAAT--T-TA
DroPer_CAF1_left   AACGACG-CCAAAA-GTGTTTAAGAAAATGTGA-ATAAA-AGTTTAACAAGGAACA-AT-CCA-GGAAAA--TCCAGAA-GAAG-CC-TGT-ATAAAATAAGG------ATTTT--C-TG
DroPse_CAF1_left   AACGACG-CCAAAA-GTGTTTAAGAAAATGTGA-ATAAA-AGTTTAACAAGGAACA-TT-CCA-GGAAAA--TCCAGAA-AAAG-CC-TGT-ATAAAATGAGG------ATTTT--C-TG
DroVir_CAF1_left   AACGACC-TGACAA-AAAGTGTCCTTAAGTGCA-GAATC-AGTTCAAGCTGAAAGTTCT-TAA-AGAAAA--CACTAGGAAAGCTAA-TCATTTGAGATGT-G------AAGAA--T-TT

DroEre_CAF1_left   AAAGATAGGATAC-----C-GAG
DroGri_CAF1_left   ATTGTGATACGTG-----C-TTA
DroMel_CAF1_left   CATTGTAACCAAC-----A-AAA
DroSec_CAF1_left   CA-AAAATGTTGT-----A-ATT
DroSim_CAF1_left   CATTGTAACATAA-----A-ATA
DroWil_CAF1_left   TGTTATTATCTAT-----T-TTG
DroYak_CAF1_left   AAATATTGAATAC-----TAAGT
DroAna_CAF1_left   GTTATATTTTGAAGCTGTA-ACT
DroMoj_CAF1_left   TTTAATATGAGAA-----GCGTG
DroPer_CAF1_left   CAGAACTTTTGGA-----T-TAA
DroPse_CAF1_left   CAGAACTCTTGGA-----T-TAA
DroVir_CAF1_left   GCTTAACAAACTA-----C-CAG