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


DroAna_CAF1_left   AATTTCGT-TGATGCTCTGTTTATATTTTAAATTATCT-AAAAA-GCCACGATTTGCTTG-----TTCATACACT-TTACTGAAATTATA--TTTTAGTATTTGCTTAA-AGAT----TA
DroEre_CAF1_left   TATAGA-A-A-TGCATCCGTACA--TGTAAATGAAGT----TGCTGCTTCTAATTGCCATTCCTACAG-TGTGAT-TG-TGTACGTAT---CTCT-TCACTT----TTT-GTGA--T---
DroGri_CAF1_left   TATCACTA-G-CTCTTTAGACAA-ACTTTAGCTTAAGT-AGTATTTTCGTTTTT-GTCATATTTAAAACTAGTTT-TC-TTCGCATAATT--TGTAAGTTAA---TTTT-AGCT----TA
DroMel_CAF1_left   GATATAGA-A--A-TGCATCAGT--AAAAGTG-AATAAGGCTCCTAATTCTAATATAAATTCGTGATT-TTTAAT-TA-CACACATACAA-TTGT-TAATAT---TTTT-ATTACATGTA
DroMoj_CAF1_left   GATTTGTA-A-TTTAAAT--AAA-AGGCTGTCAGCCA---TTTGTGAACGTAATTTCCATTTGGTTTC-TCTTCT-GA-GTGCTTTCCGTTCAAT-GTTT-----AGCTAGTTT--GCCT
DroPer_CAF1_left   ACACTTTA-G-CTAATACGGAAA-TTCGAATCTTGATTGGTTAAGTGTTGCAAAAGGGTGTTTTT-AA-TGGACA-TA-CACTTTTCGAATATAC-ACTT-G---GGAT-ATTG--AATC
DroPse_CAF1_left   ACACTTTA-G-CTAATACGGAAA-TTCGAATCTAGATTGGTTTAGTGTTGCAAAAGGGTGTTTTTTAA-TAGACA-TA-CACTTTTCGAATTCAC-GCTT-----GGAT-ATTG--AATC
DroSec_CAF1_left   AGCAAAAGCT--ATAAAAATGCA--TAAATGTGAATAAAGCTCCTTGTTCTAATTGTAATTCTTGATT-TTTAAT-TG-CACACATAAAA-TTGT-TAATAT---TTTT-ATTG--TATT
DroVir_CAF1_left   TTACATCT-A-TTATTACAGCATCTATTGTGCTGTATA-AATTT-GACACTGTCTTCCTT-----TAGTCTCACC-TT-CGTTTTTGTGC--TCAAAGCAAAGTTAGTT-TGCT----TA
DroYak_CAF1_left   ATTTCACTTA--AAGTTAACTTA--CTCATGTTAAA-TGACAATCAAAACAATCAAAAATTTTAAAAT-GCCAGTTAT-ATCACTCATAT-TTTG-TGATAT---TTTT-ATTA--TAAC
DroWil_CAF1_left   AGTTGATG-A-CTTATATATGTA--TGTAGATCCAGCT-ATTAGTTTTTGCTAC-TTGGATAATTTAT--TTATC-TA----ATTTTGAT-CAAT-TATTTT---ATAT-ATGT--ATGT

DroAna_CAF1_left   --TTTAACATTCTAGTT-AGTCTTGTGGATACTCTGTCCTGCTATCGCTCACTCAAGGAGGTTGTGATGGATACCATATC-GAAATAACATCACACCCAGGTTGAGTGAGTCAAAGCAAG
DroEre_CAF1_left   --AT---TT-TGTAGTT-AGTTTCGTGGATACTCTGTCCTGCTATCGCTCACTCAAGGAGGTTGTGATGGATACCATATC-GAAATAACATCACACCCAGGTTGAGTGAGTCAAAGCAAG
DroGri_CAF1_left   --TCGCCTGTCGCCTGT-TTTCTTGTGGATATTCTATCCTGCTATCGCTCACTCAAGGAGGTTGTGATGGATACCAAATC-GAAATAACATCACACCCAGGTTGAGTGAGTCAAAGCAAG
DroMel_CAF1_left   TTTCACTGGTGCCAGTT-AGTTTCGTGGATACTCTGTCCTGCTATCGCTCACTCAAGGAGGTTGTGATGGATACCATATC-GAAATAACATCACACCCAGGTTGAGTGAGTCAAAGCAAG
DroMoj_CAF1_left   --AATGGTCTATTGGTTTAGCTTTGTGGATATTCTATCCTGCTATCGCTCACTCAAGGAGGTTGTGATGGATACCGAATC-GAAATAACATCACACCCAGGTTGAGTGAGTCAAAGCAAG
DroPer_CAF1_left   --ACTATTCTGTTGTCC-GGCTTTGTGGATATTCTATCCTGCTATCGCTCACTCAAGGAGGTTGTGATGGATACCATATC-GAAATAACATCACACCCAGGTTGAGTGAGTCAAAGCAAG
DroPse_CAF1_left   --ACTATTCTTTTGTCC-GGCTTTGTGGATATTCTATCCTGCTATCGCTCACTCAAGGAGGTTGTGATGGATACCATATC-GAAATAACATCACACCCAGGTTGAGTGAGTCAAAGCAAG
DroSec_CAF1_left   --ACACTGGTGCCAGTT-AGCTTCGTGGATACTCTGTCCTGCTATCGCTCACTCAAGGAGGTTGTGATGGATACCATATC-GAAATAACATCACACCCAGGTTGAGTGAGTCAAAGCAAG
DroVir_CAF1_left   --ATGCTCAATTGCGTT-GGCTTAGTGGATACTCTATCCTGCTATCGCTCACTCAAGGAGGTTGTGATGGATACCAAATC-GAACTAACATCACACCCAGGTTGAGTGAGTCAAAGCAAG
DroYak_CAF1_left   --TCACTGGTGCCAGTT-AGTTTCGTGGATACTCTGTCCTGCTATCGCTCACTCAAGGAGGTTGTGATGGATACCATATC-GAAATAACATCACACCCAGGTTGAGTGAGTCAAAGCAAG
DroWil_CAF1_left   A-ATAAATCTTTCATTG-AACTTTGTGGATATTCTATCCTGCTATCGCTCACTCAAGGAGGTTGTGATGGATACCATATTATAAATAACATCACACCCAGGTTGAGTGAGTCAAAGCAAG

DroAna_CAF1_left   ACAAAAAGGCTGCTAACTT-TCGTTTCGGATTGGG--GTTCACTGTTTT--GTAAGGACAAGCAA---CTTT------TGGCACTTCATTTCG-G-GGT-AAGTT-TGCCAAGGCTTAGG
DroEre_CAF1_left   ACAAAATGCTGCTA-ACTTTGCATCGGCTTCACTT-TTTTGTCTAGACAAGCAA----CTTTTGG---CACTTCATT-TG-CCA-ACTTTATGCC-GGG-GCTTA-GGTAA----CAAAA
DroGri_CAF1_left   ACAAAATGTTTAGT-TCTTTTATTTTTATTTAATT--TTTTCTCTTTTTTTTTC----CTGTTAC---TTTCTTGCA-CTTTTTCTCAACTTTAA-CGCTTCATT-TGCAT----AAAGT
DroMel_CAF1_left   ACAAAATGCTGCTA-ACTTTGCATCGGTTTCACTT--TTTGTCTAGACAAGCAA----CTTTTGC---CACTTCATT-TG-CCA-ACTTTTTGCC-GGG-GCTTA-GGTAA----CAAAA
DroMoj_CAF1_left   ACAAAATTCTTAGT-TTTCTTGTTGTTTTTATTTTTATTTTTGGCACTTTTGCA----CTTTTTC---GTAACTTTA-AC-ACT-TCATTTGCATAAAG-TTTGA-CGCAT----CACAC
DroPer_CAF1_left   ACAAAATGCGACCC-GAACTTTTTCTCAGTTTTCAGTTTTCACTTGTTCTTTTT----TTTTCTT---TTGTCCAGAGTC-TAG-ACAGTCA-ACTTTT-A-GCACTTCAT----TTGCA
DroPse_CAF1_left   ACAAAATGCGACCC-GAACTTTTTCTCAGTTTTCAGTTTTCACTTGTTCTTTTT----TTTGCTT---TTGTCCAGAGTC-TAG-ACAGTCA-ACTTTT-A-GCACTTCAT----TTGCA
DroSec_CAF1_left   ACAAAATGCTGCTA-ACTTTGCATCGGTTTCACTT--TTTGTCTAGACAAGCAA----CTTTTGC---CACTTCATT-TG-CCA-ACTTTTTGCC-GGG-GCTTA-GGTAA----CAAAA
DroVir_CAF1_left   ACAAAATGTTCGGT-TTATTTTGTCACTTTTGCAC--TTTTTCGTAACTTTAAC----ACTTCAT---TTACATAAA-GTTTGACACGTCACACA-GAC-ACACA-CAAAC----ACAGA
DroYak_CAF1_left   ACAAAATGCTGCTA-ACTTTGCATCGGTTTCACTT--TTTGTCTAGACAAGCAA----CTTTTGG---CACTTCATT-TG-CCA-ACTTTTTGCC-GGG-GCTTA-GGTAA----CAAAA
DroWil_CAF1_left   GCAAAATGTGTTAA-GTTCTATAATTTGGTTTATT--CAGATGATTTCAAATTG----GATACACTTTGAAAACTTT-TC------CCAAAATCC-AAC-ACTTT-CTGTC----TGACT

DroAna_CAF1_left   TGACGATTCAGC--TTCTA
DroEre_CAF1_left   ACAC-A-ACACCAACACCA
DroGri_CAF1_left   TTGAC--GCCTCAAACTCA
DroMel_CAF1_left   ACACTA-ACACCAACAACT
DroMoj_CAF1_left   ACACCC-ACACCC-CCACC
DroPer_CAF1_left   GAACTT-TTGCCA-GGAGC
DroPse_CAF1_left   GAACTT-TTGCCA-GGAGC
DroSec_CAF1_left   ACACCA-ACACCAACAGCT
DroVir_CAF1_left   CCTTCT-TCGACTAAGTCA
DroYak_CAF1_left   ACACCA-ACACTAATACAA
DroWil_CAF1_left   TTTTTT-TTTTTAAAGTTT