CLUSTAL W --- LocARNA 1.4.8 - Local Alignment of RNA DroAna_CAF1_left TAAA-----A----TA-GTT---T-TATT--T-TTC--TATGAATAAAT-------GTGTTTAAAATGCATAGCAA-ACGTGATGT-T--GAAGTTGTTAAA-ATAAAAAA-T-AAATAA DroEre_CAF1_left CTAC-----G----AT--AA---A-ACTT--G-TTA--TTTTCGGTCGA-------CCAAACAAATGGAGCATGAT-TTCGTTAGAAC--AATGGAATGATC-ATT-TATT-TTATTTCC DroMel_CAF1_left GTGC-----TGCAAAAAAAA---A-ACTT--G-TTA--TTTTCGGTCGA-------GCAAACAAATTGGGCCCGAT-TTTTTTAGAAC--CAT---CTGATC-ATT-AT---T-TTTTCG DroMoj_CAF1_left TTAGTGCTGC----GA-TTTGTGATTGTGGAATTTA--TCCACGTGTGATATGTGATGCCAAGCATTGAGCAAGAT-GCACTCTTATA--AATATTATATTA-AAA-TAAAAA-A-TAAA DroPer_CAF1_left TAGA-----G----AA-GGA-----AAAATTT-AAA--AATTTAGTAACACGAAAATTCAACTAAATGCACTGGAA-GCAAAATTAGA--AAAAATACAATA-AAA-TCGA-G-T-TGAA DroPse_CAF1_left TAGA-----G----AA-GGA-----AAAATTT-AAA--AATTTAGTAACACGAAAATTCAACTAAATGCACTGGAA-GCAAAATTAGA--AAAAATACAATA-AAA-TCGA-G-T-TGAA DroSec_CAF1_left CTGC-----A----AA-AAA---A-ACTT--G-TTA--TTTTCGGTCGA-------GCAAACAAATGGAACACGAC-TTCTTTAGAAC--AATCGCTCGATC-ATT-CCTT-T-TCTTCC DroSim_CAF1_left TGCA-----A----AA-AAA---A-ACTT--G-TTA--TTTTCGGTCGA-------GCAAACAAATGGAGCACGAT-TTCTTTAGAAC--AATCGCTCGATC-ATT-CCTT-T-TCTTCC DroVir_CAF1_left TGTA-----T----AC-AGG-----TGGCTCG-AAA--GCTCTTCAAACAGTAACACG-TGCTAACATGTCTTCAAGCGTAACAGTTC--AAATCGAATTGA-ATA-TAAT-T-A-TAAA DroYak_CAF1_left TTCT-----T----AA--CA---C-ACGT--G-CTA--CGATAAAACTT-------GTTAG-TTTCGGTCAACGAT-TTCGTTAGAACCAGAATGAATGATC-ATT-CTTT-T-TCTTCC DroGri_CAF1_left AATG-----T----GT-GTG-----TGTAT-A-TATGCTCTGTATTTGCAGTTCGAAAGCTCTTCAACCAATAGTG-TGT--AA-ATA--AATTTCGAGAAACGT--GTAA-C-TTTTAT DroAna_CAF1_left ATAATAA-AGAAAAAA-GTATATT-TCGATTCAGGTTCCACCGAGATTTGAACTCGGATCGCAGGATTCAGAGTCCTGAGTGCTAACCATTACACCATGGAACCTCACTGATCGTGCTCT DroEre_CAF1_left GATTAAA-AGAAAAAA-TGA-A-----C-TTCAGGTTCCACCGAGATTTGAACTCGGATCGCAGGATTCAGAGTCCTGAGTGCTAACCATTACACCATGGAACCTCACTGATCTCCCGTT DroMel_CAF1_left AGTTAAA-AGAAAAAA-CTA-ATT-TCA-TTCAGGTTCCACCGAGATTTGAACTCGGATCGCAGGATTCAGAGTCCTGAGTGCTAACCATTACACCATGGAACCTCGCTGATCTTCCAAT DroMoj_CAF1_left TAATACAAAAATTAGA-CTG-ATA-TAG-TCCAGGTTCCACCGAGATTTGAACTCGGATCGCAGGATTCAGAGTCCTGAGTGCTAACCATTACACCATGGAACCGATGCGATCGTTT-GT DroPer_CAF1_left AGAGAAA-A-AAAAGA-TTT-TCAGAAA-TCAAGGTTCCACCGAGATTTGAACTCGGATCGCAGGATTCAGAGTCCTGAGTGCTAACCATTACACCATGGAACCTCTCTGAACGCCG-TG DroPse_CAF1_left AGAGAAA-AAAAAAGA-TTT-TCAGAAA-TCAAGGTTCCACCGAGATTTGAACTCGGATCGCAGGATTCAGAGTCCTGAGTGCTAACCATTACACCATGGAACCTCTCTGAACGCCG-TG DroSec_CAF1_left AGTTAAA-AGAAAAAA-GTA-ATT-TCA-ATCAGGTTCCACCGAGATTTGAACTCGGATCGCAGGATTCAGAGTCCTGAGTGCTAACCATTACACCATGGAACCTCGCTGATCTTCCGCT DroSim_CAF1_left AGTTAAA-AGAAAAAA-ATA-ATT-TCA-TTCAGGTTCCACCGAGATTTGAACTCGGATCGCAGGATTCAGAGTCCTGAGTGCTAACCATTACACCATGGAACCTAGCTGATCTTCCGCT DroVir_CAF1_left AAAAAAA-ATAAAAGAAGAA-T-TCGAA-CTCAGGTTCCACCGAGATTTGAACTCGGATCGCAGGATTCAGAGTCCTGAGTGCTAACCATTACACCATGGAACCCATACGATCTCCA-CC DroYak_CAF1_left AGTTAAA-AGAAAAAA-GTA-ATC-TCA-ATCAGGTTCCACCGAGATTTGAACTCGGATCGCAGGATTCAGAGTCCTGAGTGCTAACCATTACACCATGGAACCTCGCTGATCTCCCATT DroGri_CAF1_left AAAAAAA-AAGGAAAG-ATC-GCT-AAG-CTCAGGTTCCACCGAGATTTGAACTCGGATCGCAGGATTCAGAGTCCTGAGTGCTAACCATTACACCATGGAACCCATATGGTCTTCCAAT DroAna_CAF1_left AGTCTTTACAGATATAAAATTATCTGCTAAGAATT----GAAA-GAAATATTA-T-TTTTCTATTTT-TAATAAATAGAT--AACACATAAACCAAATAAAATATTA-TT-ACATAATAA DroEre_CAF1_left TTTCTAAAGAGGCTCAAAAATACCATCGGAA-CGT----GTAA-ATTCGTTAA-A-TATCGAAATCT-AATTTAATACATATCAAAATCAAATAATATAATTTATAA-AG-AACACTA-- DroMel_CAF1_left TTTCTAAAGAGATCCAAAAATAGCAACTAAA-CTT----GCAA-ATTCGTAAC-A-TAATTTAATAT-AATTTAATATGTATTAAAATCAAATGATATTAAAAATCTAAG-TTTACTT-- DroMoj_CAF1_left CAAAA--AGTCGA-----CAGTA---A-AAA-TAT----A-TTTT-AGGTAAATA-AGAAATAAGCT-AGCAAAAATAA--AAGAACTTGTATCAAATATATTTCAG-TAAACAATAC-- DroPer_CAF1_left CAACA--CCATTA-----GCGGT---A-AAA-GCC----GTACAA-AGATGATCTTCTATTAAATTT-ATCTTTAAATC--AAATAATATTAACAACAAAAATAC-A-TA-CCAATAT-- DroPse_CAF1_left CAACA--CCATTA-----GCGGT---A-AAA-GCC----TTACAA-AGATGATCTTCTATTAAATTT-ATCTTTAAACTGTAAATAATATTAACAACAAAAATAC-A-TA-CCAATAT-- DroSec_CAF1_left TTTCTAAAGAGAGCCAAAAA-AGCAACCAAA-CGT----GTAA-ATTCGTTAA-A-TTTTTAAATAT-AATTTAATACGTATTGAATTCAAA---TATTATTAAAGAACT-AAGTTTA-- DroSim_CAF1_left TTTCTAAAGAGAGCCAAAAATAGCAACCAAA-CGT----GCAA-ATTCGTTAA-A-TTTTTGAATAT-AATTTAATACGTATTGAATTCAAATAATATTATTAAAAAACT-AAGTTTA-- DroVir_CAF1_left AAAAA--ATTTTG-TAATACAAGCCTACAAA-CTT----GTAA-TCGTCAGTTTAGA--GAAAAACT-ATACAAAATAGATCTGTTTAACAATTT-TATTG-AATTT-TATTCTTGTT-- DroYak_CAF1_left TTTCCAAACAGACCCAAAAATAGCCACTAAA-CGT----GTAA-ATACGACCA-A-TTTCTGAAAATAATTTCCATACATATTAAAAACAGATAATATACCTTATTAAA--AAAAATT-- DroGri_CAF1_left AAAAAATAGATAG-------TAA---A-AAT-TTATGGTGAAA-TAGATAAA----AAGTGCTCAAT-ACCTTGTAAAATTTATTTTATATAAATT--TAGCTTA-A-A--TATTTTC-- DroAna_CAF1_left TAA---TAAAAAA--TAAAAAGTAA DroEre_CAF1_left GTTT--ACCTAAA--TAAAAAAGAA DroMel_CAF1_left AAA---AAAAAAG--AACAAAAAAT DroMoj_CAF1_left TAG---AAATAAA--AAAAAAAAAA DroPer_CAF1_left AAA---AACAGAATTCATCGTATTA DroPse_CAF1_left AAA---AACAGAA--TTCATCGTAT DroSec_CAF1_left CTTAAGAAAAAAA--AAAAAAAAAA DroSim_CAF1_left CTTA---ATTAAG--AAAAAAAAAA DroVir_CAF1_left TTG---CCAAAAG--AAGTAAAAAT DroYak_CAF1_left AGC---AACCAAA--AAAAATGAAA DroGri_CAF1_left GAT---AAACAAT--TTAAATATAT