CLUSTAL W --- LocARNA 1.4.8 - Local Alignment of RNA DroAna_CAF1_left ATTCTC-AG-------TTTCTAATTCAA-ATTCAATCTC-GATCCA-AATCCCAATACGA-AATTTATACTTTTATTGTTTCG----GAGT--GAAGTGCCT-TTTTTTAAAA----AAC DroEre_CAF1_left CTCGTG-AT-TCCTGATCCTAAATCCAA-TTCTAATCCC-GATCCG-AATCTA----GTT-GTGAAACACCCATAAGTGCAGC----TGG---TTAGTGCTTGATTTTATGGC----CAA DroGri_CAF1_left AGCAGC-GA-------TCGG-TGCAAAT-ATATAAGCAA-GTGTGT-GTGTGT----GTGCGTGTGTGTAGAGTGTGTGTATATTGAAAAAG-TGAAATAGTGCAACGTATACGAGTCCT DroMel_CAF1_left CG-TGA--------TTCCTGATCCGCAC-ATCTAATCCC-AATCCG-AAACTA----GTTTTTGAAACACCTTTAAGTGCATTTTAATTTTA-ATATTGGTAGTTTTGGTGAC----GAA DroMoj_CAF1_left ACGCAACGA-GCACGGCGCCAGCTTAAA-CGAGAAATCA-AAGAAT-GTAGAA----TAT-ATACTATATATACACATATATG----TTT---AGTGAATCTGTTGTCAAG-T----GTA DroPer_CAF1_left TCAGAC--------CAGACCGTGTGTCC-GTGTGTCTGTGTGACTGTGTGACC----GTG-TGGTGGCATTCCCCTGGGACCTGGCACCTG--GGACCTGGCA-CCTGGGACC----TGG DroPse_CAF1_left ACTCCT-CTCAGACCAGACCGTGTGTCC-GTGTGTCTGTGTGACTGTGTGACC----GTG-TGGTGGCATTCCCCTGGGACCTGGGACC---------TGGCA-CCTGGAACC----TGG DroSec_CAF1_left TCGTGA--------TTCCTGATCCTCAT-TTGTAATCCC-TATCCG-CAACTA----GTT-TTGAAACAAAACCAAGTGCATTTTAATTTTA-ATATTGTTAGTTTTAGTGAC----AAA DroVir_CAF1_left TTTCAT-TA-------TCAGCTGCACAT-CGAGACGCAT-CGACCG-AAATCT----AAGAGTTATATATACATATATAGGCAATGTGTTTTCCCAGTGAATCCCAATGTCGC----ATC DroWil_CAF1_left CAACAA-A--------CAATTTGCAAATGATTTCAACTT-ATAGAA-AATTTA----TAT-TCCTTATTTCGTTTGTGTTTTTTTTTTTTAC-TGTTGTTTTGTGATTATTTT----TAA DroYak_CAF1_left TCCGTC-TC-GTGATTCCTGAACCTCAG-TTCTAATCCC-AATCCG-AATCTA----GTT-GTGAAACACCTTTAAGTGCAGC----TAG---TTAGTGTTTGATTTTATGCC----GAA DroSim_CAF1_left TCGTGA-TT-------CCTGATCCTCAG-TTGTAATCCC-TATCCG-CAACTA----ATT-TTGAAACACCACCAAGTGCATTTTAATGTTA-ATATTGTTAGTTTTAGTGAC----AAN DroAna_CAF1_left AGAAATGTTGCAGTTTCGTTTTGTGACCGACACTAACGGGTATTTT-ACAGG-------ACA-------T---ACA---GG-AT-TACTCGTTTTTGCGATCACAAATCCTGAAATTGCA DroEre_CAF1_left TCCTGTGTTGCAGTTTCGTTTTGTGACCGACACTAACGGGTAATTG-TTTGG-------CCG-----------CCA---GG-AT-TACTCGTTTTTGCGATCACAAATCATGAAATTGCA DroGri_CAF1_left GTGCGTGTTGCAGTTTCGGTTTGTGACCGACACTAACGGGTAGTTA-AAGGG-------CATCCTCGCA----TTCTGCTG-GCTTACTCGTTTTTGCGATCACAAATTCTGAAATTGCA DroMel_CAF1_left TCCTGTGTTGCAGTTTCGTTTTGTGACCGACACTAACGGGTAATTG-TTTGG-------CCG-----------CCA---GG-AT-TACTCGTTTTTGCGATCACAAATTATGAAATTGCA DroMoj_CAF1_left TCCTGTGTTGCAGTTTCGGTTTGTGACCGACACTAACGGGTAGTTG-AGGCA-------TCT-CGTATTCGC-TGT---TT-TA-TACTCGTTTTTGCGATCACAAATTCTGAAATTGCA DroPer_CAF1_left TCCCGTGCTGCAGTTTCATTTTGTGACCGACACTAACGGGTAATGG-C-TGG-------CCG------------CA---GG-AC-TACTCGTTTTTGCGATCACAATAC-TGAAATTGCA DroPse_CAF1_left TCCCGTGCTGCAGTTTCATTTTGTGACCGACACTAACGGGTAATGG-C-TGG-------CCG------------CA---GG-AC-TACTCGTTTTTGCGATCACAATAC-TGAAATTGCA DroSec_CAF1_left TCCTGTGTTGCAGTTTCGTTTTGTGACCGACACTAACGGGTAATTG-TTTGA-------TCA-----------CCA---GG-AT-TACTCGTTTTTGCGATCACAAATCATGAAATTGCA DroVir_CAF1_left CTGTTTGTTGCAGTTTCGGTTTGTGACCGACACTAACGGGTAGTTG-GGGCA-------CCT-CGAATA----CGC---TGTTT-TACTCGTTTTTGCGATCACAAATTCTGAAATTGCA DroWil_CAF1_left TATCCTGTTGCAGTTTCATTTTGTGACCGACACTAACGGGTAGTAACGGGTTAACAAAGTCG----TTTTTCTGGC---CT-TT-TACTCGTTTTTGCGATCACAAATTCTGAAATTGCA DroYak_CAF1_left TCCTGTGTTGCAGTTTCGTTTTGTGACCGACACTAACGGGTAATTG-TTTGG-------TCG-----------CCA---GG-AT-TACTCGTTTTTGCGATCACAAATCATGAAATTGCA DroSim_CAF1_left NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-NNNNN-------NNN-----------NNN---NN-NN-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN DroAna_CAF1_left GCAAAA-AACAGCAAAGAAAACATTGTA-TT--TGGTGTGAA---TT-ATTTTTATTAAA----TTTATTATTCCTTTTGG-AGAATGAGTAG-----GTTT-ATTGGAAAAGTGATTA DroEre_CAF1_left GCAAAA-CGCAACGAAGTCGTGAAGCCA-GT--GAAAAATAATATATATCAGTTT----TGAGTGCATGGAAACTATCAGT-TTGCATTCGAGGATGCATTTA----------TTAAGA DroGri_CAF1_left ACGAAA-ATCAACAAAACCATAAAAAAG-AA--AAACCATAA---AATCTAAAACACAA---------ATTTGATGCGAAT-GAAAAATGGGAGAAGGTTAG-GGATGG-GGGGAAGGG DroMel_CAF1_left GCAAAA-CTCAACGAAATTGTGGAACCA-GT--AAAAATAGATAGAAAATAATATGTTTTGTGTGCTTGTGAACTATAAGT-TTGCATTCTAAGATGCATTT--------------ATC DroMoj_CAF1_left ACGAAA-CGCAACGAAAATGAAAAGTGC-AT--TCCCAAGGAGA-GGGCGCAGGGCGTTC------------AGGGCGAGGGCATCAACAAGAGTTGTGTGC-TCCAGT-GCGAAAAGT DroPer_CAF1_left GCAACG-AGCAGCGAAACTGTGGAATGT-GT--GCAAAAC-AG--TG-TGAAAAGTGATC----TATTAGTGATTAAGGGA-AA-----CAGATTCCAGTGG-AACTGTTTTTTTGTTT DroPse_CAF1_left GCAACG-AGCAGCGAAACTGTGGAATGT-GTGTGCAAAAC-AG--TG-TGAAAAGTGATC----TATTAGTGATTAAGGGA-AA-----CAGACTCAAGTGG-AACTGTTTTTTT--GT DroSec_CAF1_left GCAAAA-CGCAACAAATATATAGAAA-----------ATATATAGAAAATAATAAGTTTTGAGTGATTGTGAACTATAAGT-TTGCATTCTAAAATGCATTTAT------AAAATTGTG DroVir_CAF1_left ACGAAA-AGCAACAAGAAAATTTCTCAA-CG----AACTGAACC-GGGCCGAGGCGGACC--------GGGGTCAATGTGA-GTTCGAGCTG--CGGATCGG-TATTCAGTGATGTGGC DroWil_CAF1_left GCAAAAGATCAACGTATACAACAAACACATA--AAATGATAA---GA-CAGAGTAGACAA----GTGAATA---GATGAAA-GGG--ACGTGTAACATTCA--GTGATA-ACTGTGTGT DroYak_CAF1_left GCAAAA-CGCAACAAAGTCGTGAAACCA-GT--GAATAAT---------CAGTTT----TGTGTGCAAGGAAACTACAACT-TTGCATTCTAAAATGCACTTATTCAGA-CCAAGATGC DroSim_CAF1_left NNNNNN-NNNNNNNNNNNNNNNNNNNNN-NN--NNNNNNN-NN--NN-TATTGGGGGGGT----GACCCCCTCTTCGGTTT-TTGCCATGTAT-----TTTT-CGCCGGTCTTTGTTCA