CLUSTAL W --- LocARNA 1.4.8 - Local Alignment of RNA DroAna_CAF1_left CAATGTT---T-AAATG-AGACAAT-TTGC-AGCCATTTAAATGAGT-CAA-AA---CTA-CT-GCAGATAAAAA-----ATAGTA-GAACAA--AAATGTAT-AA-TCCG--CT-T--- DroEre_CAF1_left AAGTATT---A-ATATATT-GATCG-G--TATAC----GAAATGGTA-TAT-AT---CTATTC-GGA-TCTTAGT-----TATTAA-TATTTA--AAAACGGA-AG-TACAG-AAGA--- DroMel_CAF1_left AATAGAT---A-GGTTTTT-TTAAG-AAATGGCC----TATATCATT-AAT-AT---CTATGG-GCA-TCTAAAT-----TTTAAA-TATTTA--ATAATGGA-AG-GATG--AA-A--- DroMoj_CAF1_left AAAATAA---A-AACAACT-ATATTAAAAAAGTTTT----TACAGGTTAAGAAATTTATTATT-ATT-----TTT-----ATTTTA-TAAAAATCAGTGAAAA-TA-TAAG--AC-AAAA DroSec_CAF1_left TAGATAG---T-TTTTT-A-TTAAG-GATGCTAC-----AGGCCATT-AGT-AT---ATGTTG-GCA-TCTAAAT-----TATAAA-TATTTA--ATAATGGA-AG-GATG--GA-A--- DroSim_CAF1_left CGAAGAG---T-ACTAATA-GGTAG-TTTTTTAT----AAGGGATGG-TAT-AT---ATATTG-GCA-TCTAAAT-----TATAAA-TATTTA--ATAATGGA-AG-GATG--AA-A--- DroVir_CAF1_left ATGTGCT---A-ATAAT-ACAAGAA-TAACTTGC----ACACTAGTA-AAA-AC---ATATTT-ATA-TCTTAAT-----AAAAAA-CAATAA--ACAAACAA-AT-TAAATATA-A--- DroYak_CAF1_left GAAA-AG---TATTAAT-A-GATTC-GTTGGTATAC--GAAATGGTA-TAT-AT---ATATAT-ATA-TTG-GGA-----TATTAA-TTATAA--ATATTTAA-AA-ATGG--AA-A--- DroGri_CAF1_left TAATTTG---A-TTATA-C-AACA----ATAATC----GTTATAATATACAAATGGCATATACATTA-AATATGCAAAAATATTTTAAAT-AA--ATAATTGAGAAAAATAATTG-T--- DroPer_CAF1_left GAAAATAATAA-CCCGC-T-CTCT----CGTCTC----CACATTTGATATGGGTTGCTGGGGGG----GCCGGTC-----TGGCAT-ACTTGC--ACTA------ACAAAAAGAG-A--- DroPse_CAF1_left ATAAT----AA-CCCGC-T-CTCT----CGTCTC----CACATTTGATATGGGATGCTGGGGGGGGT-GCCGGTC-----TGGCAT-ACTTGC--ACTA--A---ACAAAAAGAG-A--- DroAna_CAF1_left ----TT----AAA------TCCTATTACTAGGA---AT-CCTAAGCG--TAGGCCCCGGCGAGATTCGAACTCACGATCTCCTGTTTACTAGACAGGCGCTTTAACCAACTAAGCCACGG DroEre_CAF1_left ----AA----TAA------AAATATTATTATCA---CC-GAATCGTGA-TAGGCCCCGGCGAGATTCGAACTCACGATCTCCTGTTTACTAGACAGGCGCTTTAACCAACTAAGCCACGG DroMel_CAF1_left ----AT----AAA------AAATATAGCAACCA---CC-GAATTGTGA-TAGGCCCCGGCGAGATTCGAACTCACGATCTCCTGTTTACTAGACAGGCGCTTTAACCAACTAAGCCACGG DroMoj_CAF1_left ATTCTT----TTT------TAATATCTCTACTC---TC-AAATAGAGACTAGGCCCCGGCGAGATTCGAACTCACGATCTCCTGTTTACTAGACAGGCGCTTTAACCAACTAAGCCACGG DroSec_CAF1_left --ATAA----AAA------AAATATTGCAATCA---CC-GAATTGTGA-TAGGCCCCGGCGAGATTCGAACTCACGATCTCCTGTTTACTAGACAGGCGCTTTAACCAACTAAGCCACGG DroSim_CAF1_left ----AT----AAA------AAATATTGCAT--A---CC-GATTTGTGA-TAGGCCCCGGCGAGATTCGAACTCACGATCTCCTGTTTACTAGACAGGCGCTTTAACCAACTAAGCCACGG DroVir_CAF1_left ----AA----AAAACGTTGAACGAGTGCCTGCACTTTCGTACAAGCAC-TAGGCCCCGGCGAGATTCGAACTCACGATCTCCTGTTTACTAGACAGGCGCTTTAACCAACTAAGCCACGG DroYak_CAF1_left ----AA----AAA------AAATATTATTATCA---CC-TATTTGTGA-TAGGCCCCGGCGAGATTCGAACTCACGATCTCCTGTTTACTAGACAGGCGCTTTAACCAACTAAGCCACGG DroGri_CAF1_left ----TGCACAGAC------ACACACACTCGTAT---GT-CTT---GCA-TAGGCCCCGACGAGATTCGAACTCATGATCTCCTGTTTACTAGACAGGCGCTTTAACCAACTAAGCCACGG DroPer_CAF1_left ----GG----AAG------TCATATATTTATTA---CT-TGA---CCA-AAGGCCCCGGCGAGATTCGAACTCACGATCTCCTGTTTACTAGACAGGCGCTTTAACCAACTAAGCCACGG DroPse_CAF1_left ----GG----AAG------TCATATATTTATTA---CT-TGA---ACC-AAGGCCCCGGCGAGATTCGAACTCACGATCTCCTGTTTACTAGACAGGCGCTTTAACCAACTAAGCCACGG DroAna_CAF1_left CGCCCTGTTGTTTTAGACCATTTCGGAGGGGT--TCTTAAG-AAATTGG-CCAACA-GAACTGGCACT--TTTCCAA--T--CTATTTTCATCTGGCTAATGG-AAAAACTAAA-TTCAC DroEre_CAF1_left CGCCCACATATCTACAACTT-TTCAGAGGTTCT-TTATGAG-ATTGCAT-ATCTGG-AAA--A--GTAGCGCACTAT--TCACAATTTCCACTTAAAATAATT-AAACTTTGAC-AGTAG DroMel_CAF1_left CGCCCATATACATTGCCCCT-TTCAGAAGTACT-TTATGAG-GTTCCAT-ATTTTG-AAA--A--GTGGAGTACTAT--TCATGATTTCCATTTAAGATAATT-AAACTTTGTC-CATAG DroMoj_CAF1_left CGCCCACGATCGAAAATAGC-GCTAGTGACTCT-GTTTGCA-GATCGAA-TGTGCT-CGA--A--TCTATTTTAAGA--GAGCCCAATCAATCAATTTGATATAATTAGCAGAT-AACAG DroSec_CAF1_left CGCCCATATGTTTTTCATTT-TTCAGAAGTACT-TTATGAG-GTACCAT-ATCTTA-AAA--A--GTATAGCACTAT--TCATGATTTCTACTTAAGATAATT-AAATGTTGTC-CATAG DroSim_CAF1_left CGCCCATATACCTTGCTTTT-TTCACAAGTACT-TCATAAG-GTTCCAT-ATCTTA-AAA--A--GTAGAGCACTAT--TTATGATTTCCACTTAAAATAATT-AAATTTTGTC-TATAG DroVir_CAF1_left CGCCGACATATGCTTCGCGC--GCACATGCCCAGACTTGAAGAT-CGAATGTTTCA-AAA--A--CTATTCTAAAGA--ACTAAATATTCAATTGGGCTAATG-TAAAATCAAT-CAATT DroYak_CAF1_left CGCCCATATATCTCACGCTT-TTCAGAGGTTGT-TTATGAG-GTTCCAT-ATCTTA-TAA--A--GTAGAGCACCAT--TTAAGAGTTCCACTTAAAATAATT-AAATTTTGGC-AATAG DroGri_CAF1_left CGCCCACATATTCGACGCCA-GCGCTTGCCTCT-GTTTGAA-GATCGC--GCGTGTTGAA--A--GCTATTC-CATAGAAATTCACATTCAATTTAG--CTAA-TTTGAAATCAATCAGG DroPer_CAF1_left CGCCCACATATCTCT-GAAG-GAATGTGCTTCT-TCATGAG-GTCTCC--ACCTCTGAGG--A--ACCCGGAACTTTTCCAATCATTTTCAGTTCAA-AAATT-TCATTTAGCT-AATGG DroPse_CAF1_left CGCCCACATATCTCT-GAAG-GAATGTGCTTCT-TCATGAG-GTCTCC--ACCTCTGAGG--A--ACCCGGAACTTTTCCAATCATTTTCAGTTCAA-AAATT-TAATTTAGCT-AATGG DroAna_CAF1_left AGCAACA DroEre_CAF1_left AAACCTC DroMel_CAF1_left ATACTTT DroMoj_CAF1_left ATAC-GA DroSec_CAF1_left ATACTTC DroSim_CAF1_left ATACTTC DroVir_CAF1_left TG-ACAT DroYak_CAF1_left ATACTTC DroGri_CAF1_left TTGTCCA DroPer_CAF1_left AAAATCA DroPse_CAF1_left AAAATCA