CLUSTAL W --- LocARNA 1.4.8 - Local Alignment of RNA DroAna_CAF1_left CCACTTG-CTT--CCTGC--CACCCCACATCACATTACA----TGCAT-ATATCCT-TT--CCTA-TATCCTGA----G-C-AAGGATAT-C-AGAAATAATCCCAGTGATTCAAC-GAG DroEre_CAF1_left GGGCACA-TCA-TCATCA--CTT-ATTCAGCACTCGG------TTCGGCAATGTCC-GT--TGAACTGTTATCC----C-C-CCAGTAATGGTAGTGATT--CACCGACCACGTCGCGA- DroMel_CAF1_left GAACTG--TAC-GGGTAA--TAT----CCCGTCCATCGCC--GC-CAATGATGATT-AG--TGTG---CCAGGCGACCG-A-CCAGCAATGGTAGTGATT--CACCGACCACGTCCGGA- DroMoj_CAF1_left ATTTTCA-AGT--GCTAC--AGT-GCGAGTGTTAGATCT----ACCAC-ATATACA-GA--GCAT-ATATGTAT----A---TGCATATATCATACAAGTATAT-AGAATCCAGATCCAT DroPer_CAF1_left GCCAGT--CCT-CAAACCTGCTC-CCAAGCCAACTCCCAC--TCGCAA-TCCCCAA-AC---ATA-TTTCCATT----T-C-AGTTCCCAGTGATTCAG----TGAATATGTGATTTAG- DroPse_CAF1_left GCCAGT--CCT-CAAACCTGCTC-CCAAGCCAACTTCCAC--TCGCAA-TCCCCAA-AC---TTA-TTTCCATT----T-C-AGTTCCCAGTGATTCAG----TGAATATGTGATTTAG- DroSec_CAF1_left CAATCG--GTT-CGGCAA--TGT-CCGTTGAACTGCACGG--GTACAATGATGATT-AG--TGTG---CCAGGC----G-A-CCAGCAATGGTAGTGATT--CACCGACCACGTCCGGA- DroSim_CAF1_left CAATCG--GTT-CGGCAA--TGT-CCGTTGAACTGCACGG--GTACAATGATGATT-AG--TGTG---CCAGGC----G-A-CCAGCAATGGTAGTGATT--CACCGACCACGTCCGGA- DroVir_CAF1_left GGACAGGCCTC-TTCCGT--AAA-GCAGAACAGTCGATTT--TCTCAA-GTGTTAA-AG--TGAG---AGTGTC----C-A-AAATGATATTGACAGATA--TCTATA-GATATATTTA- DroWil_CAF1_left GTCTTTA-ATT--TTCCT--TTT-TGGTAACCAAAATCG----CAGAC-AAATCGT-GT--CGAA-TGTGTATG----A-A-TTACGCGTAATTCTAACGGTTA-TTGCAATCGCAAAAG DroYak_CAF1_left GCACTCG-GTT-CGGCAA--TGT-CCGTTGAACTGTA------ATCCCCGCCAATG-AT--GAGTGTGACAGTC----G-A-ACAGTAATGGTAGTGATT--CACCGACCATGTCGCGA- DroGri_CAF1_left ATATCGA-AGTTCTC-TT--CAA-ATGGAGGACAGGACGAGTAAGTT--GATGACAGTCAAAACT---AAT-TT----TTAAGTGGC-ACAC-AGTGAAA--TA--TG-AATGGCGCTC- DroAna_CAF1_left CGTTAACGGTGCTTATTGCAGCTGCTGGCCACTGCACAAGATTAGACTT--AAGACTCTTGTGCGTGTGACAGCGGCTATTGTAAGAGGCCATAGAAGCAACCAATCA-ACTGACC-ACC DroEre_CAF1_left ACCAAAAGGTGCTTATTGCAGCTGCTGGCCACTGCACAAGATTAGACTT--AAGACTCTTGTGCGTGTGACAGCGGCTATTGTAAGAGGCCATAGAAGCAACAACCAG-CCATCGTCCCA DroMel_CAF1_left ACCGAAAGGTGCTTATTGCAGCTGCTGGCCACTGCACAAGATTAGACTT--AAGACTCTTGTGCGTGTGACAGCGGCTATTGTAAGAGGCCATAGAAGCAACAGCCAG-CCATTGTTCCA DroMoj_CAF1_left TGGGAACGGTGCTTATTGCAGCTGCTGGCCACTGCACAAGATTAGACTC--AAGACTCTTGTGCGTGTGACAGCGGCTATTGTAAGATGCCAGAGAAGCAACAAATTCTACACAGA-TCA DroPer_CAF1_left CTCGATCGGTACTTATTGCAGCTGCTGGCCACTGCACAAGATTAGATTT--AAGACTCTTGTGCGTGTGACAGCGGCTATTGTAAGAGGCCATATTAGCATCAAAACT-AAACAAACAAA DroPse_CAF1_left CTCGATCGGTACTTATTGCAGCTGCTGGCCACTGCACAAGATTAGATTT--AAGACTCTTGTGCGTGTGACAGCGGCTATTGTAAGAGGCCATATTAGCATCAAAACT-AAACAAACCAA DroSec_CAF1_left ACCGAAAGGTGCTTATTGCAGCTGCTGGCCACTGCACAAGATTAGACTT--AAGACTCTTGTGCGTGTGACAGCGGCTATTGTAAGAGGCCATAGAAGCAACAGCCAG-CCATTGTTCCA DroSim_CAF1_left ACCGAAAGGTGCTTATTGCAGCTGCTGGCCACTGCACAAGATTAGACTT--AAGACTCTTGTGCGTGTGACAGCGGCTATTGTAAGAGGCCATAGAAGCAACAGCCAG-CCATTGTTCCA DroVir_CAF1_left AACGAGCGGTACTTATTGCAGCTGCTGGCCACTGCACAAGATTAGACTC--AAGACTCTTGTGCGTGTGACAGCGGCTATTGTAAGAGACCAGAGAAACAGCGAATAT-TTAACTATTTT DroWil_CAF1_left CAT-AACGGTACTTATTGCAGCTGCTGGCCACTGCACAAGATTAGACTT--AAGACTCTTGTGCGTGTGACAGCGGCTATTGTAAGAGGCCAGAAAACGACCAGAGCACGAAATGA-ACA DroYak_CAF1_left ACCGAAAGGTACTTATTGCAGCTGCTGGCCACTGCACAAGATTAGACTT--AAGACTCTTGTGCGTGTGACAGCGGCTATTGTAAGAGGCCATAGAAGCAACAACCAG-CCATCGTCCCA DroGri_CAF1_left AATAATCGGAGCTTATTGGAGCTGCTGGCCACTGCACAAGATTAGATTCAAAAGACTCTTGTGCGTGTGACAGCGGCTATTGTAAGAGACCAGATAACATCAAGCCAT-ATCAATA-GAA DroAna_CAF1_left AGATCGTCGAGT--C-TCCCACTCGTCC-ACT-TGTCCACTTGTCCCACTCAT-CC-AATCATCCCCTCAGCTA-CTCATTCGC-G-AAGCCCTGC-AAG DroEre_CAF1_left CAATCAA-GACC--C-AGATCGACGGGG-TGC-TCCG-CGGGGTGCCATGCAAGGA-AGCCCTAGAGGCCGCAA-TGCT--AATGCAATTATTA-C-CAA DroMel_CAF1_left TCATCGT-GGTGCCC-AGATTGCCGCA--G-A-GAAGCCGTAGAGATTGCCGC-CT-AATGCAATTATTACCAA-CGTT--TGATG-GAATCAA-ATAAT DroMoj_CAF1_left TGTATTAAGTA---C-GGAGAGACAAT--ACT-AAATTATGTCTACATTATTT-CT-CACTAATCAATTTTTTA-AACAAACTC-T-ATTTACC-A-CCA DroPer_CAF1_left AAAGGAA-GTTG--A-ACGCCTAATGCA-ATC-GATGAGTGTTGGGTTGCTTC-A--GTTTCATTCCAAACGAGGTGCATAAAG-T-GCCCAAT-G-GGA DroPse_CAF1_left AAAGGAA-GTTG--A-ACGCCTAATGCA-ATC-GATGAGTGTTGGGTTGCTTC-A--GTTTCATTCCAAACGAGGTGCATAAAG-T-GCCCAAT-G-GGA DroSec_CAF1_left TCATCGG-GGCC--C-AGATTGCCGCAC-G-A-GAAGCCATAGAGATTGCCGC-CT-AATGCAATTATTACCAA-TGTTTTTGATG-GAATCAA-A-TAA DroSim_CAF1_left TCATCGG-GGCC--C-AGATTGCCGCAC-G-G-GAAGCCATAGAGATTGCCGC-CT-AATGCAATTATTACCAA-CGTTTTAGATG-GAATCAA-A-TAA DroVir_CAF1_left TC--CTA-ATAC--T-AATTGTATATATTATAATAAATGTCTTGCATTGCAGC-TTTTTTTTGTTTTCTCTTAA-ATAC--ATT-T-TCAACCC-A-TGC DroWil_CAF1_left CCAAAACGAAA---ACGGATACATATA--TTC-AAAAATCTTGGACAAAAAGA-AG-CCATAA-AAACACTTTA-ATGGACCTC-A-ACTAATCGG-ATC DroYak_CAF1_left TAATCGA-GACC--C-AGATCGTCGCCC-AGA-GAAGCCCTAGAGGCCGCAATGCT-AATGCAATTATTACAAA-CGTT--TGCCG-AAAACAA-A-TAA DroGri_CAF1_left ACAAATA-TTAT--A-ATAACTAAATCC-A-T-TCCTTCTAAGTGTTCAAATC-TGCATGTATATCAG--TTTT-CTATATTATTA-CAAACAT-G-CCC