CLUSTAL W --- LocARNA 1.4.8 - Local Alignment of RNA DroEre_CAF1_left TTT----TAT-------------ATACAGTC---AGGTA-CCTGAAGTAGCGCGCGTGGTGCCAGACATA--TATCTCCATCTCCACCA--TATAAATAAGACAAATGCTCGCA-GGCGA DroGri_CAF1_left CGCGCGCTAA-------------TCAGTGAC---CGGGG-CTGGTTTTGATTATCCCACAGTCAGGTACCTGAAGTAGCGCGCGTGGTG--GCCAGACGCATTCAACAAACGGC-GCCTG DroMel_CAF1_left TTT----TAT-------------ATACAGTC---AGGTA-CCTGAAGTAGCGCGCGTGGTGGCAGACATA--TATCTCCATCTTCACCA--TATAAATAAGCGAAATGCTCGCA-GGCGA DroMoj_CAF1_left GAC-----CG-------------GGGCTGGTTTCGATTATCTCACAGTC-------AGGTACCTGAAGTA--GCGCGCGTGGTGGCTAG-ACGCATT-CAACGCTCTGCTAGCAATTCTA DroSec_CAF1_left TTT-----AT-------------ATACAGTC---AGGTA-CCTGAAGTAGCGCGCGTGGTGGCAGACATA--TATCTCCATCTCCGTCA--TATAAATAAGCCAAATGCTCGCA-GGCGA DroSim_CAF1_left TTT----TAT-------------ATACAGTC---AGGTA-CCTGAAGTAGCGCGCGTGGTGGCAGACATA--TATCTCCATCTCCGCCA--TATAAATAAGCCAAATGCTCGCA-GGCGA DroVir_CAF1_left -------TAA-------------TCAGTGAC---CGGGG-CTGGTTTTGGTTATCCCACAGTCAGGTACCTGAAGTAGCGCGCGTGGTG--GCCAGACGTATTCATCTTAAGCT-TACCA DroYak_CAF1_left TT------AT-------------ATACAGTC---AGGTA-CCTGAAGTAGCGCGCGTGGTGCCAGACATA--TATCTCCAACTCCACGATATATAAATAAGCCAAAAGCTCGCA-GGCGA DroAna_CAF1_left CAG-TGACCGGGGCTGGTTTTTGCAACAGTC---AGGTA-CCTGAAGTAGCGCGCGTGGTGGCAGACATA--TATC--CGCCATACAAA--AGTATATAATGCAAAT-CCTTCA-GAAAA DroEre_CAF1_left G-TCCTCGAA-AGAAATCCC--ATGTGTATCAACTGTCTCCCATGTCTATTGTACTTCATCAGGTGCTCTGGTGTGGTCCGTAACCCGGCACATGTTGAAGTACACTCAATATGAGGCGA DroGri_CAF1_left C-TCAGCA-A-ACAT-CGGC--AAACATTTC--ATGTCTCCCATGTCTATTGTACTTCATCAGGTGCTCTGGTGTCACTCGTAACCCGGCACATGTTGAAGTACACTCAATATGCGGTGA DroMel_CAF1_left G-TCCTCGCC-AGAAATCCC--ATGTGTATCAACTGTCTCCCATGTCTATTGTACTTCATCAGGTGCTCTGGTGTGTCTCGTAACCCGGCACATGTTGAAGTACACTCAATATGAGGCGA DroMoj_CAF1_left G-CATTCTACGCCAGATGGC--AATCTACTTGTGTCTCCCCCATGTCTATTGTACTTCATCAGGTGCTCTGGTGTCAGTGGAAACCCGGCACATGTTGAAGTACACTCAATATGCGGTGA DroSec_CAF1_left GTTCCTCGCC-AGAAATCCC--ATGTGTATCAACTGTCTCCCATGTCTATTGTACTTCATCAGGTGCTCTGGTGTGTCTCGTAACCCGGCACATGTTGAAGTACACTCAATATGAGGCGA DroSim_CAF1_left G-TCCTCGCC-AGAAATCCC--ATGTGTATCA-CTGTCTCCCATGTCTATTGTACTTCATCA-GTGCTCTGGTGTGTCTCGTAACCCGGCACATGCTGAAGTACACTCAATATGAGGCGA DroVir_CAF1_left T-GCCTCC-C-TCAGATGGC--AAACGTTTC--ATGTCTCCCATGTCTATTGTACTTCATCAGGTGCTCTGGTGTGACTTGTAACCCGGCACATGTTGAAGTACACTCAATATGCGTTGA DroYak_CAF1_left G-TCCTCCAA-AGAAACCCC--ATGTGTATCAACTGTCTCCCATGTCTATTGTACTTCATCAGGTGCTCTGGTGTGGCCCGTAACCCGGCACATGTTGAAGTACACTCAATATGAGGCGA DroAna_CAF1_left T-CCCACTCG-AATATGTGTATTTTTGAGAAATATGTCTCCCATGTCTATTGTACTTCATCAGGTGCTCTGGTGTCCACCGTAACCCGGCACATGTTGAAGTACACTCAATATGAGGCGA DroEre_CAF1_left TTTGCATACGAAAGCGACCGGCACAAG----TGTTTACCAGATTACCTAAA-TTAGTAAAAT---ATTAAAGTACTCCTTTCCTTCAGTTCT-TTTTTTTTAAATAAAACGTAAATAA-C DroGri_CAF1_left TTGGCATTTGCT-GCGTTTTAATTAAGAATGTGTATTTAATA----TTTGT-GTATTAATAA--TCTGACTTTAAATAAACA-TTAAATATTAATATGCGAACTCGTTTTCT--TATT-G DroMel_CAF1_left TTTGCATACGAAAGCGACCGATACAAG----TGTTCAACAAATTGCCTAAT-TTAAAGATGA---GTAAAATATAAAAGTACTCTTTTTATT-AAGTTTTTCTTAAAAATAAAATTAT-G DroMoj_CAF1_left TTTGCAGTTGCT-GTT-TCGGCCCGTG----GAACCCCTAGAATATTATGT-CTAAAAATGT---AACTTTTGCAATAAATACTTAAAACAG-AA-CTT-GCAACTTGTTTTCCTTCT-A DroSec_CAF1_left TTTGCATACGAAAGCGACCGATACAAG----TGTTCAACGGATTGGCTAAT-CTAAAGATTA---GTAAAATATTAAAGTACTCTTTTTATT-CAGTTTTCCTTCAATAAAACTTAGG-A DroSim_CAF1_left TTTGCATACGAAAGCGACCGATACAAG----TGTTCAACGGATTGCCTAAT-TTAAAGATTA---GTAAAATATTAAAGTACTCTTTTTATT-CAGTTTTCCTTCAATAAAACGTACA-A DroVir_CAF1_left TTTGCATTTGCT-GTTTGGGTTA----ATAAAGTTCATCAAA----TATTATGTATAATTAA--AAGTTCAAAATAAATATT-GTTAAATGCGCAAATCTACTTCTTATCAT--TGCA-A DroYak_CAF1_left TTTGCATACGAAAGCGACCAATACAAG----TGTTTACC-GATTACCTAAA-TTAAAGATTA---GTAAAATATATAAGTATTATTTTTCGT-CCGGTTATTTTAAAAAAAGCGTACGTA DroAna_CAF1_left ATGTCAAACGAA-GAGTTCTAAAAGTG----ATATTAAACCATT---AATG-TAATATAATTAAATCTATTTTGATGAATAAAAATATTAAA-AATTGTAAACTTTATTCAT--AATA-C DroEre_CAF1_left GAATAAAAGAATG DroGri_CAF1_left GATTGAGT-TGAT DroMel_CAF1_left GCTTCTTAAAACT DroMoj_CAF1_left TCA-TATGTTTTT DroSec_CAF1_left GCTGTTCGTTACA DroSim_CAF1_left GCTGTTTGTTACA DroVir_CAF1_left TATTTGGCTTAGC DroYak_CAF1_left ATAAGCTGTTTAT DroAna_CAF1_left ATCTTTTTGGGAC