CLUSTAL W --- LocARNA 1.4.8 - Local Alignment of RNA DroAna_CAF1_left TTTTTCCAACCTTTCTTTATTTTT-CCTGATCA--ATCC--TT-ATCATTCGTTCG--G-CTATCA-A--G--GAGAATGAAGCTATTTTAGAGACGAA-AACGGAGCTGGTTAGCTCT- DroGri_CAF1_left TTAGAATAAGGAATATTATTTTCT-G---TTGA--AGTAAATTACTCATATTGCTA--TCTGTTTT-T--A--GTCTATTTATATTTAGGAGCATTAAA--TTGGT-GTTGCTTGGCGA- DroMoj_CAF1_left AATGTATTTTTATCAGCACTTTAA-TT-AAACT--CTTTACTTAGT-AATATATGT--T-CTTGCT-G--G--TTCTATTTATAGTTTTAATCGATGAA--ATGGT-GTTGTTTGGGGG- DroPer_CAF1_left AACATTTCAGCGTTCTTTTGATCA-ATTCTCAT--CTGC--TTTT-CTTTTTTTCG--C-CCACGATA--GCAGGCAACTGA-GTCGAA--AAATAGCAACCAGCT-GCAGTTACTTCAT DroPse_CAF1_left AACATTTCAGCTTTCTTTTGATCA-ATTCTCAT--CTGC--TTTT-CTTTTTTTCG--C-CCACGATA--GCAGGCAACTGA-GTCGAA--AAATAGGAACCAACT-GCAGTTACTTCAT DroVir_CAF1_left AACTTTTTATTATATACAACTTTT-TATCAGCG--CTTG--AA-TTTATTAGTTGTTAT-CTGTTT-G-----TTCTATTTA-TAATTCAAAACACGAA-CTTGTT-GTTGCTTGGGGA- DroEre_CAF1_left TTTTGTCTGATCAGTTGTTATCTTTTGTTTTTCTAGGAG--GGGT-CTGGTTTATT--A-TCAGGCT--CTTT---GTGCTCTTACTTT--AAGTAATAACAG-CG-ATAATTAGCTCAT DroMel_CAF1_left TTTTTTCTGATCACTCGTTATTATTGGTTTTTCTAGGAG--TGGT-CAGGTTTATT--A-TCAGCC--CCTTA---ATGTTCTTATTTT--AGGCAGTAACAA-AG-ATAATTAGCTCAT DroSec_CAF1_left TTTTCTGATCAGCCCTTATCATTGGTTTTTCTA--TTAG--CGGT-CTTGTTCATA--T-CTGGATCTTCCTA---ATGTTCTTATTTT--AAGCAGTAACAA-AA-ATAATTAGCTCAT DroSim_CAF1_left TATAAAGTATATTTTTTTCTGATCAGTCCTTAT--CATT--GGTT-TTTCTATTCT--T-CTGCATCTTCCTA---ATGTTCTTATTTT--AAGCAGTAACAA-AA-ATAATTAGCTCAT DroYak_CAF1_left TTCTCTGATCAGTTCTTATTGTTTGTTTTTCTAGAATAG--GGGT-CTGGCTTATT--A-TCAGGCT--CTTC---GTGTTCTTGTTTA--AAGCAGTAACGG-AG-ATAATTAGCTCAT DroAna_CAF1_left -TGGGAGCTCCGTTGGAGCCCGCACCAACACATGGGGATATAGCTCAGTGGTAGAGCATTCGACTGCAGATCGAGAGGTCCCCGGTTCAAACCCGGGTGTCCCCTTAATCACTTT-TT-- DroGri_CAF1_left -CTGTAGCTCCATGTGGTGGAGATCA-CATAATGGGGATATAGCTCAGTGGTAGAGCATTCGACTGCAGATCGAGAGGTCCCCGGTTCAAACCCGGGTGTCCCCTAGGTAAACCTTTT-- DroMoj_CAF1_left -TTTTAGGTGCACTACTCGCGGATCA-CAACATGGGGATATAGCTCAGTGGTAGAGCATTCGACTGCAGATCGAGAGGTCCCCGGTTCAAACCCGGGTGTCCCCTTGGTAAACTTTTTTG DroPer_CAF1_left TAGCGCTCATTTGGAC-GGGTGAAAC-ACGCGTGGGGATATAGCTCAGTGGTAGAGCATTCGACTGCAGATCGAGAGGTCCCCGGTTCAAACCCGGGTGTCCCCTAAGATTACTTTTTTT DroPse_CAF1_left TACCGCTCATTTGGAC-GGGTGAAAC-ACACGTGGGGATATAGCTCAGTGGTAGAGCATTCGACTGCAGATCGAGAGGTCCCCGGTTCAAACCCGGGTGTCCCCTGAGATTACTTTTTT- DroVir_CAF1_left -TTGTAGCTCCATTGGTTGGAGCTGC-AAGTGTGGGGATATAGCTCAGTGGTAGAGCATTCGACTGCAGATCGAGAGGTCCCCGGTTCAAACCCGGGTGTCCCCTTGGTAAACTT-TT-- DroEre_CAF1_left TGGGCCTTTGTTGGAG-CTCGCAGCC-ACACTTGGGGATATAGCTCAGTGGTAGAGCATTCGACTGCAGATCGAGAGGTCCCCGGTTCAAACCCGGGTGTCCCCTTAGTAACATTTTTT- DroMel_CAF1_left GGAACCTTTGTTGGAG-CACGCAGCC-ACACTTGGGGATATAGCTCAGTGGTAGAGCATTCGACTGCAGATCGAGAGGTCCCCGGTTCAAACCCGGGTGTCCCCTAGGTAAACTTTTTT- DroSec_CAF1_left GGGGCCTTTGTTGGAG-CTCGCAGCC-ACTCTTGGGGATATAGCTCAGTGGTAGAGCATTCGACTGCAGATCGAGAGGTCCCCGGTTCAAACCCGGGTGTCCCCTAGGTAAACTTTTTT- DroSim_CAF1_left GGGGCCTTTGTTGGAG-CTCGCAGCC-ACTCTTGGGGATATAGCTCAGTGGTAGAGCATTCGACTGCAGATCGAGAGGTCCCCGGTTCAAACCCGGGTGTCCCCTAGGTAAACTTTTTT- DroYak_CAF1_left GGGGCCTTTGTTGGAG-CTCGCAGCC-ACACTTGGGGATATAGCTCAGTGGTAGAGCATTCGACTGCAGATCGAGAGGTCCCCGGTTCAAACCCGGGTGTCCCCTAGGTAAACTTTTTT- DroAna_CAF1_left -----------TGTTTC-ATACAA-GTTTTAATAATTAACTTTTTT-GCTTTAGC---ATTTACATA--CCAT--AATAATA--CCATTTATT------TT-ATA-AACTGATTTA-AAA DroGri_CAF1_left -----------TGATGT----C------------AATATTCCAATT-TATTTCAA---GGAGAAG----------GGTAATGCGAAAGTTGCTAAGAGAGA-AGGGGAT-AAGGAATGTA DroMoj_CAF1_left CCAGCTTCCCCCATTAA----T----------TTTTTAATTAAAAT-TTAGGGTT---GTAAAAGC---------AATTTAACGGCGTGAATT----GCGA-AAGTGTT-GTGAAATACA DroPer_CAF1_left T-----------TGTTT-T-TCAT--CTGTAAAGGATTCCATG-TG-AAG-AATT---CA-CATGTA--TATATTAAGAATTATCCTATTTTT----TTTCAACTAAGC-TTTTGTCGAA DroPse_CAF1_left ------------TGTTT-T-TCAT--CTGTAAAGGATTCCATG-TG-AAG-AATT---CA-CATGTA--TATATTAAGAATTTTTCTATTTT------TCCATCTAAGG-TTTTGTCGAA DroVir_CAF1_left -----------TGTGTT-G-CCTT-TTGCTTTAATTTTTCATT-TT-GTTTAAAC---AA-AAGAAA--CGGG--TTTGGTA--ACAACTAAA-----CGG-GGT-TACTTTGAAA-GTA DroEre_CAF1_left ------------GCCTTCCACCTACTGTAAATGTACTCATT-G-ATTTTACTAC----ATCTCATACTGGGTA--TTTAGGT--TTTCTTTCA-----TTG-GTC-TTTTTAGGG-AAAT DroMel_CAF1_left ------------CCCATCTGCCTA-ATATTATGGTCTTACTTT-T-GCTACATTTCTTCAT-ATTCA-GTACT--TATGATT--TCTTTTATG-----TT--ACT-AAATTAATT-GTGC DroSec_CAF1_left ------------CCCATCTGCCTA-ATATTATGGTCTAACTTT-TG-CTACATTT---CAA-ATACA-GTACT--TATGATT--TCTTTTATG-----TTC-ATG-TTATTTTAT-GTAA DroSim_CAF1_left ------------CCCATCTGCCTA-ATATTATGGTCTAACTTT-TG-CTACATTT---CAA-ATACA-GTACT--TATGATT--TCTTTTATG-----TTT-ATG-TTATTTTAT-GTAA DroYak_CAF1_left ------------GCCTTCTACACACAGTAGACAGTAGAACA-C-ACACGACACA----GTAGAAGCAATTAAA--CACGGCG--GATCCAGTG-----TAA-TGG-TATGGGCAT-GTTT DroAna_CAF1_left AGTGTTTCTGCT----------AAAAT--ATACTTAAAT--AAAAG DroGri_CAF1_left AA----ATTATAACCTTTTAACAAAGC--CTGCGTAAAT--ATACA DroMoj_CAF1_left AG----ACAATAAA--TAAATTTTTGC--TTGCATATTG--TTTAA DroPer_CAF1_left AA----TTAACA-----TAATGTTCGC--TTAATAATTG--CATTA DroPse_CAF1_left AA----TTAACA-----TAATGGCTGC--TTTATAATTGCATTACG DroVir_CAF1_left TTTTGCACAAAAAT--CACCAAAAAAT--ATATTAATAT--GTGTG DroEre_CAF1_left GTCTG------------TAGTCTCCGT--TTCATCTTGA--CTGTA DroMel_CAF1_left CCTTT------------TTGCCTAAAT--ACCTGTACTA--AAATA DroSec_CAF1_left CTGAA------------TTAATTGTGCCCTTTTTAATGT--AACAT DroSim_CAF1_left CTGAA------------TTAATTGTGCCCTTTTTAATGT--AACAT DroYak_CAF1_left TTCTT------------ACTATGGAGT--TGGACCAATA--CATTG