CLUSTAL W --- LocARNA 1.4.8 - Local Alignment of RNA DroAna_CAF1_left ----T-------------AAATCG--GCATAAATAATTCATTATTGTCGCCTCGTTGGGCATAAATCAAGTCAGCAGAC--ATA---GTTTCTTCGC---TCT--AAA-CGTAGGTAAAA DroEre_CAF1_left ----AGCC--------GTAAATCG--GCATAAATAATTCATTATTGCCGCCTCGTTGCGCATAAATCAAGTCCCTGGTC--ATG---GCCCACACAC---AAG--CAT-CGGCTTTGCGA DroGri_CAF1_left ----AGGTCACACATTCACAGGGA--GCGATAGGGTGAGAGAGATGTCGTTGCCTGTGTGGTAAACTTGAACTTTAGGC----G---GCTTGTAG-T---AGT--CCT-GACTCCTGTCA DroMel_CAF1_left ----AGCC--------GTAAATCG--GCATAAATAATTCATTATTGCCGCCTCGTTGCGCATAAATCAAGTCTCCGGAC--CAG---GCCCACACAC---AAG--CGT-CGGCTAGGCGA DroMoj_CAF1_left ----CGCA--------T---------AAATCAAG-TCAGCCGGTCCAAAGCCAAAACCAGAAACAC---TGTCTTGACAAGTCTCGTCTGACTGAAG---TTA--GCAAATACACACACA DroPer_CAF1_left CGATGCGC--------ATAAATCAAGTCGTTTTGGCCCTGGCC-CGACTCTTCC-AGA------------GCAGCCACA--CAG-----CCACACAC---AAC----T-CA-CAACTCCC DroPse_CAF1_left ----GCGC--------ATAAATCAAGTCGTTTTGGCCCTGGCC-CGACTCTTCC-AGA------------GCAGCCGCA--CAG-----CCACACAC---AGAGGCAT-CA-CAACTCCC DroSec_CAF1_left ----AGCC--------GTAAATCG--GCATAAATAATTTATTATTGCCGCCTCGTTGCGCATAAATCAAGTCTCTGGCC--AAG---GCCCACACAC---AAG--CGT-CGGCTATGCGA DroVir_CAF1_left ----CAGC--------C-AGGCCA--AAGCCAGCAACACTGAGGTCATATAGAGAAGTTGCCTCAG---CAGCAAACTTGAACTTTAGCCAGCACAT---AAA--AGC-CTTGACAGACT DroWil_CAF1_left ----AGTC--------CAAAAACT--GAACTGTGAAGCCAAACTAAC--CCAAGCAGCAGCAGCAGCAAACTCCA-GGTC-CAG---CTCCAG-CTTTGCTTT--TCG-CATGTCTTTCA DroYak_CAF1_left ----ACCC--------GTAAATCG--GCATAAATAATTCATTATTGCCGCCTCGTTGCGCATAAATCAAGTCTCTGGGC--ATG---GCCCTCACAC---AAG--CAT-CGCCTTTGCGA DroSim_CAF1_left ----GCCG--------TACAATCG--GCATAAATAATTCATTATTGCCGCCTCGTTGCGCATAAATCAAGTCTTTGGCC--AAG---GCCCACACAC---AAG--CGT-TCTCTATGCGA DroAna_CAF1_left TGCCAAAA--AAAAGAAAAAAACGTTTCGGTAAAA--TATAAA--ACATTT--A------AAAAGTTGCA----AAAAATGTAC-TTGGAGATGCCGGGGATTGAACCCGGGGCCTCTCA DroEre_CAF1_left TTCCAGCTCTAAACGCATTTAAAGAGCCAAAAATA--TGTAAA--ATACAA--AGGAAAAATGAAAAACA----AAAAATGTAC-TTGGAGATGCCGGGGATTGAACCCGGGGCCTCTCA DroGri_CAF1_left G-CCTACCT-AAACTAAATCAAAAGTCACAAAA-T---ACAAT--GTT-AA--TAAAATAAAAAAAAGCA----AAAAACTGAT-TTGGAGATGCCGGGGATTGAACCCGGGGCCTCTCA DroMel_CAF1_left TACCAGCTCTAAACGCATTTAAAGAACCGAAAATA--TGTAAG--ACACACGAAAAAAAAATTAAAAACA----AAAAATATACTTTGGAGATGCCGGGGATCGAACCCGGGGCCTCTCA DroMoj_CAF1_left C-ACAC-T---AAAC----------TTCGAAATAT--TTAAAT--AAATAT--AAAAATAAT-ATT-GCCA---AAAAAGGTAA-TTGGAGATGCCGGGGATTGAACCCGGGGCCTCTCA DroPer_CAF1_left TCTTT--GATGCGCGTTCCG-GCTC--TAAACATATTTAAAGT--TCCTAA--AAAGAGAAGAAAATACA----AAAAATGTAC-TTGGAGATGCCGGGGATTGAACCCGGGGCCTCTCA DroPse_CAF1_left TCTTT--GATGCGCGTTCCG-GCTC--TAAACATATT------------AA--AAAGAGAAGAAAATACA----AAAAACGTAC-TTGGAGATGCCGGGGATTGAACCCGGGGCCTCTCA DroSec_CAF1_left TACCAGCTCTAAACGCATTTAAAGAGCCGAAAATA--TGTAAG--ACACCC--AAAAAAAT-GAAAAACA----AAAAATGTAC-TTGGAGATGCCGGGGATCGAACCCGGGGCCTCTCA DroVir_CAF1_left G-ACTGCC---TAAGTA--------GAATAAATAC--AAAAACAAAAGTAT--ACCACTAAGAAAA-ACTTG--CAAAAAGTAA-TTGGAGATGCCGGGGATTGAACCCGGGGCCTCTCA DroWil_CAF1_left AACATTTTCAAAATGC---------ACTAAAAACG--AGAAAA--TCTAAA--AAAAAAAACAGTT-TTAAAAAAAAGATAGTA-CTGGAGATGCCGGGGATTGAACCCGGGGCCTCTCA DroYak_CAF1_left TACCAGCTCTAAACGCATTTAAAGAGCCAAAAATA--TGTAAA--ACACAA--AAGAAAAATGAAA-ACAA---AAAAATGTAC-TTGGAGATGCCGGGGATTGAACCCGGGGCCTCTCA DroSim_CAF1_left TACCAGCTCTAAACGCATTTAAAGAGCCGAAAATA--TGTAAG--ACTCAC--NNNNNNNNNNNNN-NNN----NNNNNNNNNN-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN DroAna_CAF1_left CATGCAAAGCGAGCGCTCTACCACTGAGCTACATCCCCGTTGCGA-AACACCCAGCCAAAAT-CGCACTTAG-GGTAGACG-A--GTTTGCTGAGCAAGAAAGGTGGTTGAAATTCC-AG DroEre_CAF1_left CATGCAAAGCGAGCGCTCTACCACTGAGCTACATCCCCGATGAGA-AGCGGTTCGACCAAAA-TGCATTTTGCACTGGGGA-AAGGGGAGTCGATTAAAATCCAAGATTGCAGGACGAAT DroGri_CAF1_left CATGCAAAGCGAGCGCTCTACCACTGAGCTACATCCCCGTTGAAT-ACCTGGCAGCTCAAACCGTTACTTAAGC-CAAATT-CTATTTACACAGTGAAAATTTAGTGATGCAAATTAGAA DroMel_CAF1_left CATGCAAAGCGAGCGCTCTACCACTGAGCTACATCCCCGATGTGA-AACAGCTTGACCAAAA-TGCGTTTTGCATTGGGGG-AAGGGGAGTCGATAAAAAACCTAGATTGCAGGATGAAA DroMoj_CAF1_left CATGCAAAGCGAGCGCTCTACCACTGAGCTACATCCCCATGTTGATGTCTGCCTGCCAAATG-CTGATAAGTCACTCAACC-CCAAATAGACTAGTACAATTCAATGAAGTAG-CTGTTA DroPer_CAF1_left CATGCAAAGCGAGCGCTCTACCACTGAGCTACATCCCCGTTGAGC-GTTTCGCGGTCCAAAG--TCTACAAGGTGTTGTGA-ATGGCAGGGCTAAAGGTGA-GAGGGGTGCACAA-GAAT DroPse_CAF1_left CATGCAAAGCGAGCGCTCTACCACTGAGCTACATCCCCGTTGAGC-GTTTCGCGGTCCAAAG--TGTACAAGGTGTTGTGA-ATGGCAGTGCTAAAGGTGG-GAGGGGTGCACAA-GAAT DroSec_CAF1_left CATGCAAAGCGAGCGCTCTACCACTGAGCTACATCCCCCATGTGA-AACAGCCCGACCAAAA-TGCGTTTTGCATTGGGGA-A-GGGTAGTCGATTTAAAACCTAGATTGCAGGACGAAA DroVir_CAF1_left CATGCAAAGCGAGCGCTCTACCACTGAGCTACATCCCCATTGAAT-ACTCGCCAGCACAAAC-TCTAATTTCAGCAAATGT-GGTTAGTGAACATTAGTGAACATGCGCAATA-AATAAA DroWil_CAF1_left CATGCAAAGCGAGCGCTCTACCACTGAGCTACATCCCCATGTGAC-GAGCGAGCGCTCAAAT-TGCATTTTGGTTGAGCGAGAAAGGGATGCAAAGAGCGCGCAC-GAAAGAC-AGGCAA DroYak_CAF1_left CATGCAAAGCGAGCGCTCTACCACTGAGCTACATCCCCGATGTGA-AACAATCCGACCAAAA-TGCATTTTGCAGTGGGGG-AAGGGGTGTCGATTAAAATCCAT-ATTGCAGGTTGAAA DroSim_CAF1_left NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-NNNNNNNNNNNNNNNN-NNNNNNNNNNNNNNNNNN-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-NNNNNN DroAna_CAF1_left GTGAGAGAGAGA-AAAGGTAG-CTAGCAAAG-GTGGTGGTTATTTC-AT-TCTA DroEre_CAF1_left AGGATATAGGAA-GTTTGAT--TTAGCATTT-AGCACGTATTTTGC-AC-AACA DroGri_CAF1_left GAGTGAATATTA-AACAAATA-AATATACTT-AT-CTTATCTTTTT-AT-CAAT DroMel_CAF1_left AGGATATAGTGA-GATGGATA--CA-CATAT-TTTTTTCAAGCAAAAGA-ATAA DroMoj_CAF1_left AGTG-TTAGGTA-TTGCGAAT-TTCATATTT-TTGTTTTAATATTG-AT-ATTG DroPer_CAF1_left TTTGTATATCTAATAAGTATATACTAGAAAA-CAACTGAAATAAAC-TA-AATG DroPse_CAF1_left TTTGTATATCTAATAATTATATGCTGGA-AG-CAACTGAAATCAAC-GAAATGA DroSec_CAF1_left AGGACATAGTGA-GATGGATA-AGAGCACAT-ATTTTTTAAACAAA-AG-AATA DroVir_CAF1_left ACTG-GTAGCAG-GGTTTCAA-AATTTAAATGAAAAATATATATAT-AT-ATTC DroWil_CAF1_left AACAAAAGGTAA-ATATTAAA-TGCAAATAT-TTAAGAAACAAATA-AT-AAAC DroYak_CAF1_left AGGATATAGGAA-GTTGGATT-AGAGCACAC-ATTTTGTACTACGA-AA-GAAT DroSim_CAF1_left NNNNNNNNNNNN-NNNNNNNN-NNNNNNNNN-NNNNNNNNNNNNNN-NN-NNNN