CLUSTAL W --- LocARNA 1.4.8 - Local Alignment of RNA DroEre_CAF1_left CA-TTGTCGTGTATTGTGT-TTTGCACTAT-----C-GCTTA-ATAA--TTG----A-AAT--TAAAGAGGAGGCGAGGGAA-ATAGAGAACGCAA-AAATCCCATT-A-TAATGGAATT DroGri_CAF1_left TC-GCTTAATTATTGAAATTAAAAAGCAAA-----C-CAAAT-TCCA--CAG----T-TCT--GACTAAGTGGACGCCCCAA-A----AATAAAAA-AAA-TA-ATG-G-TAAGACAAGA DroMel_CAF1_left CA-TTGTCGTGTATTGTGT-TTTGCACTAT-----C-GCTTA-ATAA--TTG----A-AAT--TAAAGAGGAGGCGAGGGAA-ATGGAGAACGCAA-AAATCCCATT-A-TAATGGAATT DroMoj_CAF1_left TT-TAAATTAATAATGAA--AGAAAAAAAA-----T-CAAAATCAAAATAAA----ACATG--CCAGAGAGCTGAGTAAGTG-GACGCCCCGAAAA-TGGTAAGACTAT-CTAAATGGAA DroPer_CAF1_left TGTGTTTGCACTATCGCTT-AATAATTGAA-----A-TTAAAGAAAAGAAGG------AAA--AAAAAACGAAACGAAACGA-AACTAAAAGAAAA-AAATCATTCAGT-CCCATTTGAA DroPse_CAF1_left GT-GTTTGCACTATCGCTT-AATAATTGAA-----A-TTAAAGAAAAGAAAG----A-AAA--AAAAAACGAAACGAAACGA-AACTAAAAGAAAA-AAATCATTCAGT-CCCATTTGAA DroSec_CAF1_left CA-TTGTCGTGTATTGTGT-TTTGCACTAT-----C-GCTTA-AAAA--TTG----A-AAT--TAAAGAGGAGGCGAGGGAA-ATGGAGAACGCAA-AAATCCCATT-C-TAATGGAATT DroSim_CAF1_left CA-TTGTCGTGTATTGTGT-TTTGCACTAT-----C-GCTTA-ATAA--TTG----A-AAT--TAAAGAGGAGGCGAGGGAA-ATGGAGAACGCAA-AAATCCCATT-A-TAATGGAATT DroVir_CAF1_left AA-AAAAAATAAAAATAAT-AATAAATAAA-----A-CAAGG-CGAA--CAA----A-ATG--CCAGAGCACTGCCGAGCAA-GTGGACGCCCCAA-AAATGGTAAG-A-CAATGT--GA DroYak_CAF1_left CA-TTGTCGAGTATTGTGT-TTTGCACTAT-----C-GCTTA-ATAA--TTG----A-AAT--TAAAGAGGAGGCAAGGGAA-CTGGAAAACGCAA-AAATCCCATT-A-TAATGGAATT DroAna_CAF1_left GT-TGTTTTCTTGTTTCCC-CCCCCGTTTT--------TG-C-ACTA--TCGC--TT-AATAATTGAAATTAAAAAAGGCGG-CTGGGGGAA--AA-AAACGCCTGA-ATTACAGTGAGT DroWil_CAF1_left TC-CTCGTACGGCATTGTT-TTGTTGTTTCAACTATTTCG-C-ACTA--TCGCATTT-AACAATGGAAATTAAAACGGACAAATAGAAATAA--ATGAAATTAAATT-GAGGCGGATACT DroEre_CAF1_left GGGACTGG------AA-T-TGGAATTCATACTACTGTTTTTAGTGGGTGGGGGTCCAGTGTTTCACATTGATT-TTCTTAGTATTTGTGACTAGATCCACACTCATTAATAACGGTAGTT DroGri_CAF1_left ATAAGGGAAGTGATTT-ATGGATAACCGTATTACTGTTTTTAGTGGGTGAGGGTCCAGTGTTTCACATTGTTT-ATTT--GTATTTGTGACTAGATCCACACTCATTAAAAACGGTAGTT DroMel_CAF1_left GGGACTGGAGCTGGAA-T-TGGAATTCATACTACTGTTTTTAGTGGGTGGGGGTCCAGTGTTTCACATTGATT-TTCTTAGTATTTGTGACTAGATCCACACTCATTAATAACGGTAGTT DroMoj_CAF1_left CGGTTCTGA------T-C-GGAAATACGTACTACTGTTTTTAGTGAGTGAGGGTCCAGTGTTTCACATTGTTT-GCTTAAGTATTTGTGACTAGATCCACACTCATTAAAAACGGTAGTT DroPer_CAF1_left GTGGTTTTA------AGT-TCGCGATCATACTACTGTTTTTAGTGAGTGAGGGTCCAGTGTTTCACATTGATT-TTCTTAGTATTTGTGACTAGATCCACACTCATTAATAACGGTAGTT DroPse_CAF1_left GTGGTTTTA------AGT-TCGCGATCATACTACTGTTTTTAGTGAGTGAGGGTCCAGTGTTTCACATTGATT-TTCTTAGTATTTGTGACTAGATCCACACTCATTAATAACGGTAGTT DroSec_CAF1_left GGGACTGGAGCTGGAA-T-TGGAATTCATACTGCTGTTTTTAGTGGGTGGGGGTCCAGTGTTTCACATTGATT-TTCTTAGTATTTGTGACTAGATCCACACTCATTAATAACGGTAGTT DroSim_CAF1_left GGGACTGGAGCTGGAA-T-TGGAATTCATACTGCTGTTTTTAGTGGGTGGGGGTCCAGTGTTTCACATTGATT-TTCTTAGTATTTGTGACTAGATCCACACTCATTAATAACGGTAGTT DroVir_CAF1_left ACGAGTGGA------T-C-GAATATGCGTACTACTGTTTTTAGTGAGTGAGGGTCCAGTGTTTCACATTCGTTTTTTCAAGTATTTGTGACTAGATCCACACTCATTAACAACGGTAGTT DroYak_CAF1_left GGGACTGGAACTAGAA-T-TGAAATTCATACTACTGTTTTTAGTGGGTGAGGGTCCAGTGCTTCACATTGATT-TTCTTAGTATTTGTGACTAGATCCACACTCATTAATAACGGTAGTT DroAna_CAF1_left GGCGGCGGCGATACTA-A-TACTACTACTACTACTGTTTTTAGTGGGTGAGGGTCCAGTGTTTCACATTGATT-T---CTGTATTTGTGACTAGATCCACACTCATTAATAACGGTAGTT DroWil_CAF1_left ACTACTACTACTACGA-C-TAGAACAACTACTACTGTTTTTAGTGAGTGAGGGTCCAGTGTTTCACATTAAAT-A-TTTAGTATTTGTGACTAGATCCACACTCATTAATAACGGTAGTT DroEre_CAF1_left CAATCATCAA---GCACGT---GTTT--TCTGGACAACCA-TC---GCATGTACTTCCTTCG-AAAAC-CAAAGGGACAAACAGGTGGTGT--TC---TATCAAAAAATTA-AA-AA-G- DroGri_CAF1_left CAATCAACAG--------T---TATT--GCATGACACGCT-AT---GCACGTGTGGTGATTGCTTGGT-GATATTTACAATGCGCTGTGTT--GT---TGGCATAC-AATACAGGGA-A- DroMel_CAF1_left CAATCATCAA---GCACGT---GTTT--TCTTGACAAACT-TC---GCGTGTACTTCATTCG-AAAAG-CAAAGGGACAAACAGGTGGTGA--TC---TTTGAAAAAAAAA-AA-GA-G- DroMoj_CAF1_left CAATCTGCGT---GAAATA---TTTGAATCTAATCAAGCG-AT---GGGTTAAGCTCTCTGT-ACTTT-ATTATTTAAAAAAATATTAGAT-----TTATAGAACG-GA---AGTGA-G- DroPer_CAF1_left CAATCAACAGAATGCACGT---GTTGGCCCCCATCGATA--CG---TATCGATTCGT-------GGAA-GTGTTTCAT---TCACATTTCCGTCCTGCAAATCCCG-TC---CC-GT-T- DroPse_CAF1_left CAATCAACAGAATGCACGT---GTTGGCCCCCATCGATA--CG---TATCGATCCGT-------GGAA-GTGTTTCTTCATTCACATTTCCGTCCTGCAAATCCCG-TC---CC-GT-T- DroSec_CAF1_left CAATCATCAA---GCACGT---GTTT--TCTTGACAAACT-TC---GCGTGTACTTCCTTCG-AAAAG-CAAAGGGACAAACAGGTGGTGA--TC---TTTGAAGA-AA---AA-GA-G- DroSim_CAF1_left CAATCATCAA---GCACGT---GTTT--TCTTGACAAACT-TC---GCGTGTACTTCCTTCG-AAAAG-CAAAGGGACAAACAGGTGGTGA--TC---TTTGAAGA-AA---AA-GA-G- DroVir_CAF1_left CAATCAGCAA---ATAAAC----AAC--ACGGGCCAAATT-GA---GAGAATAACACGATCA-ATTT---AATAACAACGAAATGTGGGTT--GT---AAAATATA-A--T-TG-ACAGC DroYak_CAF1_left CAATCATCAA---GCACGT---GTTT--TCTGGACAAACA-TC---GCATGTACTTCCTTCC-AAAAC-CAAAGGTACAAACAGGTGGTGT--TC---TTAACAGA-AAAA-AA-AA-G- DroAna_CAF1_left CAATCAGCAA---GGCCCACGTGCTG--CCTATACGATATCTGGGGAAATAATATA--TTTT-CC-CTTTAAA-ATTCCCCTCCCCT-TGA--TT---GCATTT-C-CC---T--AT-T- DroWil_CAF1_left CAATCATCGA---AAATAAA-AAAAG---AAACACGT--G-TCATCTAAAGGAAGT--TTAG-TTTTG-CATTTGTTTCTTAAAAACTCTA--AC---GGAAATCA-AC---C--AC-C- DroEre_CAF1_left ACGC--AA----G---GT-AATTAGT---C DroGri_CAF1_left TTTG--TATC-AC---AT-ACAATAC---T DroMel_CAF1_left ACGC--AA----G---GT-AATTAGT---C DroMoj_CAF1_left AACG--CCTG-AT---AA-ATGTCAA---G DroPer_CAF1_left CCTC--CCAT-GTATATT-TCCAAAG---A DroPse_CAF1_left CCTC--CCAT-GT---AT-ATTTCCA---A DroSec_CAF1_left ACGC--AA----G---GT-AATTAGTCAAT DroSim_CAF1_left ACGC--AA----G---GT-AATTAGTCAAT DroVir_CAF1_left TCAT--TTTTTAT---CA-GTTCAGT---T DroYak_CAF1_left ACGC--AA----G---GT-AATTAGTC--A DroAna_CAF1_left AAGGGCCCAA--A---AACAGGTGGT---A DroWil_CAF1_left TGTTT-TTAA--G--CCT-CTCTGTA---T