CLUSTAL W --- LocARNA 1.4.8 - Local Alignment of RNA DroAna_CAF1_left TTTTTGACTTA-CG-CCATCA-AA-------ATAA------GC--TTTTGT-TAAAA-----GCTCTCTAAGTTTTCAAGATTTTAAGGGCCAAA--C-GTCGGGA-----GATACTCAT DroEre_CAF1_left CTCTCACATTTTTC-CATTAA-AT-------CGAC------TA--AAAGCT-TATGC--T--GAAAGCTTTCTGCTCAA-ACATAAAGG--GCTTACC-GCTGCAA-----GC-ACTCAG DroGri_CAF1_left AATAAAAAGCT-TT-TTGGGAAAA-------GCTT------TC--CACTGCGTCGAT--A--AAGGGCTATTCTTTCAA-ATCGGTTG--TGCGTAGT-GTGAAAC-----CA--TTTAA DroMel_CAF1_left CTCTATTAAAT-CG-AGAA----A-------AAGC------TTATGCTA-A-AAGCTTTTTCACAAACATAAAG--GGC-TT-ACTGGTGTTAAGAGT-GACAAGA-----GT-ATTCAC DroMoj_CAF1_left GCTTTCACGTG-AA-AAGCTT-TT-------TTGT------TT--TCTCAA-GGGCTGTC--TACTGCTTTTATTTTTA-AC-CGGTTT-TGTAT-AG-TGCAGAG-----GC-CCTTAA DroPer_CAF1_left GAAGATAATCA-AT-AAAATAAAT-------ATAC------AA--AAGCTT-TCTGT-----GCAAAGCTTTTGC-CAA-ATAAAATTCGTCCATAGT-TGCAAAA-----GC-ACTCAA DroPse_CAF1_left GAAGATAATCA-AT-AAAATAAAT-------ATAC------AA--AAGCTT-TCTGT-----GCAAAGCTTTTGC-CAA-ATAAAATTCGTCCATAGT-TGCAAAA-----GC-ACTCAA DroSec_CAF1_left CCAACGCTCTC-ACATTTTTCATTTA--AATCTAC------TA--AAAGCT-TATGC--T--AAAAGCTTTT-TCTCAA-C---------TAAGG-CTTACGT-GGCTAAAGC-ATCCCT DroSim_CAF1_left TCTCACACTTT-TG-CATTAA-AT-------CAAC------TA--AAAGCT-TATGC--T--AAAAGCTTTT-TCTCAA-ACATAAAGGGCTTACAGT-GGCAAGA-----GC-ATTCAC DroVir_CAF1_left TTAGATACAAG-AG-CTTTTG-GC-------GGAA------TT--TATCAA-GGGCCCGA--TTATTTATGTTATTTTG-AA-CCGTCT-TTAAT-AG-TGGAAAA-----GC-TGTTAA DroYak_CAF1_left AAAACGTTCCT-TG-CCAACGCTCTCAGTTTTCTT------TT--AAAGCT-TATGC--T--AAAAGCTTTTTTCTCAA-A---------CATAAAGG-GCTTACC-----GC-ACTCAC DroWil_CAF1_left GATTTGGAATT-TTTCTAAACAAA-------ACAACAAGGGTG-AAAGCTT--TTTT--G--ATAAAGCTTCAGAGAGA------T----GAAAGCTT-GCGTTTG-----TA-GTACAT DroAna_CAF1_left ATAAC-AACTACGACACTAGCTACCCAACAGGGGATGTAGCTCAGATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTACGGGGATCGATACCCCGCATCTC-CAAGTTGAAAAT--CTTT DroEre_CAF1_left GTACA-TTGTACGACATACAGTGTCCATCAGGGGATGTAGCTCAGATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTACGGGGATCGATGCCCCGCATCTC-CAGGTTGATTTT--TTCA DroGri_CAF1_left ATATT-AACTCGACTCACATGTGTTCACATGGGGATGTAGCTCAGATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTACGGGGATCGATGCCCTGCATCTC-CAAATGGTTTTT--TCTA DroMel_CAF1_left CTACA-TTCTACGGCATTCGTATGGTATCAGGGGATGTAGCTCAGATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTACGGGGATCGATGCCCCGCATCTC-CAGTTGACTTTT--TTT- DroMoj_CAF1_left ATAGA-ATCAAAACTACAACGCATTCAACAGGGGATGTAGCTCAGATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTACGGGGATCGATGCCCCGCATCTC-CAAGTGGTTTTT--TTGT DroPer_CAF1_left GTGGA-ACCCAAGACACTATGTTTCCATCAGGGGATGTAGCTCAGATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTACGGGGATCGATGCCCCGCATCTC-CAGGATTTCTTT--TTT- DroPse_CAF1_left GTGGA-ACCCAAGACACAATGTTTCCATCAGGGGATGTAGCTCAGATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTACGGGGATCGATGCCCCGCATCTC-CAGGATTTCTTT--TTTT DroSec_CAF1_left --ACA-TTCTACGACTAAC---TATCATCAG-GGATGTAGCTCAGATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTACGGGGATCGATGCCCCGCATCTC-CAGTTGTCTTTTTTTTCA DroSim_CAF1_left CTACA-CTCTACGACATACGTTTTCCATCAGGGGATGTAGCTCAGATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTACGGGGATCGATGCCCCGCATCTC-CAGTTGATTTTT--TCAC DroVir_CAF1_left GTAGC-AACTCAACTGCAGTGTATATACAAGGGGATGTAGCTCAGATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTACGGGGATCGATGCCCCGCATCTC-CAAGGGATTCTC--TTTT DroYak_CAF1_left GTACA-TTCTACGACATTCATTGTCCGTCAGGGGATGTAGCTCAGATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTACGGGGATCGATGCCCCGCATCTC-CAAGTTGATTTT--TTTC DroWil_CAF1_left ATTACTTTTTGGTCAACCTTGTCGAATTCTGTAGAGTGGTCTAGCTA-ATGGAACGCAAGTTTAACTAGTGAAAGGCTAAGGGTTCAACGCCCAGAGGGTTTCAGGCTGTCTCT--CAAA DroAna_CAF1_left TTGCTTC-CT-TATTTTCTTGTCATAAT-C--T-T--TTTT--TTTTTTTTAACTTTTATTGGGGA-GCACATTT---GCATAAATAACTT--AC-C-CATA----GC-CTGGCACT DroEre_CAF1_left -CAATTTTTT-TTTTTCTTC-GAAACAG-G-AA-C--ATTA--GCATAAGCCACTT-GGCA-GTTT-GATGCACA---TGCTCTC-CCATC--AT-A-GTCGA--CAT-TGTGTCAA DroGri_CAF1_left -CTGTTTTCT-TTTTTTTTA-TTAATTT-T-TT-TGACACT--AAATATGCTGTCA-AGT---TTT-AATTGTCA-A-GCTGCAT-ATTTA--AG-A-GTACT---CA-ATCATCCA DroMel_CAF1_left -TTCACCAAT-TTTTTTTTT-TTTTGTA-A-AA-C--AGGA--ACAT-TAGCATAAGCCA--CTTG-GCAGTTTGATGTACATGC-TCTCC--C--ATCATAG---CC-GACATTTG DroMoj_CAF1_left -TTCTTGATT-TTTTAAAAA-TTTTTTT-T-TC-T--CTTT--TAATATTTGACTA-CGTC-TGAT-TGACAAGC---TATTTAA-GAGAA--TTATTTTGT----GG-AAATATTA DroPer_CAF1_left -TTCATTTTC-TAATCTGGA-ATTTCTTTTTTT-T--TTTC--ATTTTCTCTTCTTTAG---TAAT-GAGTTTTT-GCTAGAGGC-GTATA--TC-A-TGTGC---CC-AAAGTCCG DroPse_CAF1_left -TTCATTTTC-TAATCTGGA-ATTTCTT-T-TT-T--TTTC--ATTTTCTCCTCTTTAG---TAAT-GAGTTTTT-ACTAGAGGC-GTATA--TC-A-TGTAC---CCAAAGTCCGC DroSec_CAF1_left -CCATTTTTTTTTTTTTTTG-TGAACAG-G-AA-C--ATTA--GCATAAGCCACTT-GGC--AGTTTGATGTAAG-----TGCTC-TCCCA--TC-A-TAGCCGACA----TTTGTG DroSim_CAF1_left -CAATTTTTT-TTTTTTTTT-TGTGCAA-C-AGGAACATTA--GCATAAGCCACTT-GGC---AGT-TTGATGT-----ACATGC-TCTCCCATC-A-TAGC----CG-ACATTTGT DroVir_CAF1_left -TTTGTCATG-TTTATATAT-TTTTAAT-C-CC-T--TTAT--ATTTACTCCATTTTGGAT-TGAC-AAGCCATT---AAGATGC-TCTGA--T--ATTTTTG---TC-CCAGCACT DroYak_CAF1_left -ACAATTTTT-TTTTTCTTT-GAAACAG-G-AA-C--ATTA--GCATAAGCCACTA-GTC--ACTTTGATATACA-----TGCTC-TGCCA--TC-A-TAGCCGACAT-TTGTGTCA DroWil_CAF1_left -CCATCTCGC-GATTATTTA-TTTTTTC-A-GT-T--TATTAAATATTTTCCAACAAAT---TA-A-CTTCTTCC-CGTTTGATT-GACAT--GC-T-CTGAC---AT-CATTTGTG