CLUSTAL W --- LocARNA 1.4.8 - Local Alignment of RNA DroAna_CAF1_left ATGA--G--A---AATTGGCAGTAGCTGTTAAAAGTT-G-GCTAACAGTATCTCT--GTT--AAGCATGGCTCTG-TTAACTTTTTCCAGCTGTT-----AGAAGTG-TTCTAACAG--- DroEre_CAF1_left TTAA--TGCA---AATGGGAAAAAGCCAGTGGCTTGT-G-CGCTGTTAAAAC-TA--GCA--GATACGACCACTG-TTATCT-TTTCCAGCTGTT-----AGAAGCG-TTCTGACTG--- DroGri_CAF1_left GTAA--TTGG---GCGCACTGTTAACTACTGCTTGCT-T-TA-ACACTGCAT-GT--TGTCTGCTGTGAGCACGT-TCTGTTAACATTTCCAGAA-----ACATTCT-ATG--GCCG--- DroMel_CAF1_left TTTA--ATGC---AAATGGAAAAAGCCAACGGCTTGT-G-CGCTGTTAGAAC-TA--GCA--GATACGGACGCTG-TTAACT-TTTCCAGCTGTT-----AGAAGCG-TTCTGACTG--- DroPer_CAF1_left GCCC--TGAG---AACTCCATCAAACTTAACACGATA-T-TTACATAC-ATC-GT--ATG--GTC-------TCTGTTAAGC-TTTTCCAGAATT-----CTGTTAA-GAAACATTCTGT DroPse_CAF1_left GCCC--TGAG---AACTCCAGCAAACTTAACACGATA-T-TTACATAC-ATC-GT--ATG--GTC-------TCTGTTAAGC-TTTTCCAGAATT-----CTGTTAA-GAAGCATTCTGT DroSec_CAF1_left TTAA--TGCA---AATG-GAAAAAGCCAACGGCTTCT-G-CGCTGTTAGAAC-TA--GCA--GATAAGGCCGCTG-TTAATTCTTTCCAGCTGTT-----AGAAGCG-TTCTGACTG--- DroWil_CAF1_left CTTT--TTAGCCTACTG--T-TTTGTGTTTGTGTGTTTCAGT--TCCATTTC-ATTCCGT--TGCTATGTTAATG-CTCTGT-TAAGAATCGTTC-----TGTTA-T-TGCGGAGGG--- DroYak_CAF1_left TTAC--GCCT---GGTT-TAATGCAAATGCGAAAAAA-AGCCAACTGCTTGT-GC--GCT--GTTAGAGCTACTG-TTAACT-TTTCCAGCTGTT-----AGAAGCG-TTCTGACAG--- DroMoj_CAF1_left CTAC--TGCT---TGAATTAACATGGCGCTGTTAATT-T-AACATGACCACT-GT--CGA--CT----GCTGCTG-TTAACA-CTGCCAGTGTTCTGTTAAGAAAAA-TTCTGTT----- DroVir_CAF1_left AGTCACTGCT---TCTTTTTACATTTCCCTGTTAACC-G-TACAATATC--T-GT--TAA--CA----CACGCTG-TTAACA-TTTCCAGCATTC-----TGTTAAGAAGCATTCTG--T DroAna_CAF1_left ---GGGT-TACTTGTATGGCGC-TTTTGCCGCCCGCTTAA-CAGAGCCTCTTTAGCTCAGTGGCAGAGCACTGGTCTTGTAAACCAGGGGTCGTGAGTTCAATCCTCACAGGAGGCAGTC DroEre_CAF1_left ---CGGT-ATGCCCTATTGCGC-TTTGGCCCCCATCTTAA-CAGAGCCTCTTTAGCTCAGTGGCAGAGCACTGGTCTTGTAAACCAGGGGTCGTGAGTTCAATCCTCACAGGAGGCATTG DroGri_CAF1_left ---CTGT-ACATGTTGTTGCTA-ATCAGACAACACGATGGCAAGCGCCTCTTTAGCTCAGTGGCAGAGCACTGGTCTTGTAAACCAGGGGTCGTGAGTTCAATCCTCACAGGAGGCAAAC DroMel_CAF1_left ---CGGT-TATGCCTATTGCGC-TTTGGCCAGCGTTTCAA-CAGAGCCTCTTTAGCTCAGTGGCAGAGCACTGGTCTTGTAAACCAGGGGTCGTGAGTTCAATCCTCACAGGAGGCA--T DroPer_CAF1_left TAGCGCGTAAATGCTATGGGCC-ATCGGACGCCCGTCAAGCAGAGGCCTCTTTAGCTCAGTGGCAGAGCACTGGTCTTGTAAACCAGGGGTCGTGAGTTCAATCCTCACAGGAGGCAATA DroPse_CAF1_left TAGCGCGTAAATGCTATGGGCC-ATCGGACGCCCGTCAAGCAGAGGCCTCTTTAGCTCAGTGGCAGAGCACTGGTCTTGTAAACCAGGGGTCGTGAGTTCAATCCTCACAGGAGGCAACT DroSec_CAF1_left ---CGGT-AATGGGTATTGGGC-TTTGGCCAGCGTTTTAA-CAGAGCCTCTTTAGCTCAGTGGCAGAGCACTGGTCTTGTAAACCAGGGGTCGTGAGTTCAATCCTCACAGGAGGCATTT DroWil_CAF1_left ---CGTA-ATG-GGTATGGCAAGTTAGACAGCGGGTTGGG-CAAAGCCTCTTTAGCTCAGTGGCAGAGCACTGGTCTTGTAAACCAGGGGTCGTGAGTTCAATCCTCACAGGAGGCAAAA DroYak_CAF1_left ---GGGT-AATGGGTATTGCGC-TTTGGCCGGCGTTTTAA-CAGAGCCTCTTTAGCTCAGTGGCAGAGCACTGGTCTTGTAAACCAGGGGTCGTGAGTTCAATCCTCACAGGAGGCATTG DroMoj_CAF1_left -CGCGTA-AAT-GTTGTTGTGA-ATCAGGCAAGAAGCTTGTATGCGCCTCTTTAGCTCAGTGGCAGAGCACTGGTCTTGTAAACCAGGGGTCGTGAGTTCAATCCTCACAGGAGGCAACT DroVir_CAF1_left TGGCGTA-AGT-GTTGTTGCTA-ATCAGACAACATGTTGGCATGCGCCTCTTTAGCTCAGTGGCAGAGCACTGGTCTTGTAAACCAGGGGTCGTGAGTTCAATCCTCACAGGAGGCAACT DroAna_CAF1_left GCCT-ATTGTGATTAA--TAATTTTTTTTTTGTTTACTTAT--TTTAGTTTATTTTTTTCA--ACA--------ACC--AACTAATTACAAGGCTAAAATA-A---------TT----A- DroEre_CAF1_left TACG-AGATTAACTTTTTTTATT--TTTATTTTCTTTTCAT--ATTCGAGTATGTCGTACG--GCA--------AGG--TTGAAAT---AA---TTACCAA-AA--------TT----A- DroGri_CAF1_left TAAA-AAGATCAA--TACATTTTGCTGATTTTTTCTTTTTCTTAATTATTTTTATTGAA-A--TTA--------AGG--ATTCAAT---TA---GTACAAATAC--------TAGTTAA- DroMel_CAF1_left TTGT-ACGAAATCATGTTTTTAT--TTTTATTTTCATATTT---GAATATTTCCTACAAGG--TTG--------AAAC-AATTATC---AAAATTAACTTA-AT--------TC----A- DroPer_CAF1_left GCCA-ATTTTCTT--TTTATTTTCACTTAATATATATTTAC--GCTAATTTTTTTGAATGT--ATTTC-----ATGG--GTTGCAA---AT---TGT-CAG-CA--------AG----G- DroPse_CAF1_left GCCA-ATTTTCTT--TTTATTTTCATTTAATATATATTTAC--GCTAATTTT---GAATGT--ATTTC-----ATGG--GTTGCAA---AT---TGT-CAG-CA--------AG----G- DroSec_CAF1_left GTAC-GAAACTAT--GTTTTTATTTTATTTTCGTATTTCAC--GACAAGGTTGAAACAATT--ATC--------AAA--ATTAACT---TAAT-TCAGTTT-CA--------CT----A- DroWil_CAF1_left ATAT-CCATCAAA--GTTCAAAC-TTTGTGAGAAACTTTTT--TTTCTATTA----TATTTTTTTT--------TTATATATATTA---AT---AATTTAA-TAAACGAAAGGT---CA- DroYak_CAF1_left TAC----GAAATTATGTTTTTTG--TTATTTTTTAATATTT---GAGTATTTC---ATGCG--GCA--------AGG--TTGAAAT---AA---TTATCAA-AA--------TT----A- DroMoj_CAF1_left CGAAAAAACGTTT--GGGAAATATTTTTTGTATTTATTTTC--TGTAATTCATCAATATTT--TAAAT-----GAGT--AATATTT---AT-A-AAT-GAG-TG--------AA----G- DroVir_CAF1_left CGAA-AAACTCGT--GCAAATCGTTTTTTTTATATTTTTA-----AATAAAAAAAATACGT--TAATGTCTCTAGTT--T-----A---AT-A-AAT-TTT-GA--------AT----CA DroAna_CAF1_left -T--AAAA---ATTG----GCTTGA---TTCCGTTTCTGT-A-------AC-ATTTT DroEre_CAF1_left -A--CTTA---GTTC----AGTTTC---GGTATCATTTTG-G-------CG-TTTTA DroGri_CAF1_left -A---TGT----TGC----ATTTTG---AGGGTGATTTAA-C-------AA-TAAAT DroMel_CAF1_left -G--TTTC---ACTA----ACGTTT---TGGCGTTATAAT-T-------AC-CTTTA DroPer_CAF1_left -T--CCAT----ATA----ATTATT---AAAATTAGCTTA-A-----------TTCA DroPse_CAF1_left -T--CCAT----ATA----ATTATT---AAAATTAGCTTA-A-------TT-CAGTT DroSec_CAF1_left -A--CA-T----TTT----GGCGTT---ATAATTACCTTT-A-------TGAATAAA DroWil_CAF1_left -T---AAT----AAT----TATGTT---AAATGCAGGTGTCT-------GT-TATAA DroYak_CAF1_left -G--CTTA---ATTC----GGTTTC---GGTATCATTTTG-GCGTTTTAAT-TACAT DroMoj_CAF1_left ---TATTTATAATGTGTTTAACATT---AGCAGCAAAAAC-A-------TT-TATTC DroVir_CAF1_left AATAAATT----ACTGAACAACTGGTTTAATAAGAAAAAC-A-------TG-CTTTC