CLUSTAL W --- LocARNA 1.4.8 - Local Alignment of RNA DroAna_CAF1_left GTC--TTTAC----AGATA--TAAAAT--TA-T-----CT-GCTA-AG--AAT-TGAAAGAA-ATATTAT--TTTTCTATTTTTAATAA-ATAG-ATA-AC--ACATAAACCAAATAAAA DroEre_CAF1_left TTT--TCTAA----AGAGGCTCAAAAATACC------ATC-GGAA-CG--TGT-AAATTCGTTAAATATC--GAAATCTAATTTAATAC------------ATATCAAAATCAAATAATA DroGri_CAF1_left AA------ACA-----TAT--CTAAAA--AT-ATGTCATA-ATAA-TG--ATACGAT-ATTT-AATTGAT--TTGCTTTTA-TTAATAGCTTCGAAT--ATTTTCTTGATCTATTCTACT DroMoj_CAF1_left GCG--ATCGT---TTGTCA--AAAAGT--CG-A-----CA-GTAA-AA--ATA-TA-TTTTAGGTAAATA--AGAAATAAG-CTAGCAAAAATA-AAA-GA--ACTTGTATCAAATATAT DroPer_CAF1_left CGTGCAACACCATTAGCGG--TAAAAG--CC-G----TACAAAGA-TGATCTT-CTATTAAATTTATCTT--TAAAT--CAAATAATATTAACAACAA-AA--ATACATACCAATATAAA DroPse_CAF1_left TGC--AACACCATTAGCGG--TAAAAG--CC-T----TACAAAGA-TGATCTT-CTATTAAATTTATCTT--TAAACTGTAAATAATATTAACAACAA-AA--ATACATACCAATATAAA DroSim_CAF1_left CCG--CT---------TTT--CTAAAG--AG-A-GCCAAA-AATA-GC--AAC-CAAACGTG-CAAATTC--GTTAAATTTTTGAATAT-AATT-TAATACGTATTGAATTCAAATAATA DroVir_CAF1_left TGT--AATACA-----AGC--CTACAA--AC-TTGTAATC-GT----C--AGTTTAG-AGAA-AAACTAT--ACAAAATAG-ATCTGTTTAACAATT--TTATTGAATTTTATTCTTGTT DroYak_CAF1_left TTT--CCAAAC---AGACC--CAAAAA--TAGC----CACTAA-A-CG--TGT-AAATACGACCAATTTCTGAAAAT-AATTTCCATACAT----ATT-A-------AAAACAGATAATA DroMel_CAF1_left CTT---CCAAT---T--TT--CTAAAG--AG--AT---CCAAAAATAG--CAACTAA-ACTTGCAAATTC--GTAACATAATTTAATAT-AATT-TAATATGTATTAAAATCAAATGATA DroSec_CAF1_left TCT--TCCGCT---T--TT--CTAAAG--AG--AG---CCAAAAA-AG--CAACCAA-ACGTGTAAATTC--GTTAAATTTTTAAATAT-AATT-TAATACGTATTGAATTCAAATATTA DroAna_CAF1_left --------TATTATT-A---C--ATAATA---A-T-AATAAAAAAT-AA-AAAGTAAATTTTATATCAGGTTCCACCGAGATTTGAACTCGGATCGCAGGATTCAGAGTCCTGAGTGCTA DroEre_CAF1_left TAATTTATAAAGAAC-A---C--TAGTTT---A-C-CTAAATAAAA-AAGAAAAAAAAAGTCCGTATAGGTTCTACCGAGATTTGAACTCGGATCGCAGGATTCAGAGTCCTGAGTGCTA DroGri_CAF1_left --------TTTTATA-T---A-AAATTGT---A-T-TGAAAATACA-AA-AATAATCGAGATAAATCAGGTTCCACCGAGATTTGAACTCGGATCGCAGGATTCAGAGTCCTGAGTGCTA DroMoj_CAF1_left --------TTCAGTAAA---C--AATACTAGAA-ATAAAAAAAAAA-AA-AAAAAGGTCACACCGACAGGTTCCACCGAGATTTGAACTCGGATCGCAGGATTCAGAGTCCTGAGTGCTA DroPer_CAF1_left --------AACAGAATTCATCGTATTAAC---AGA-AATACTATTA-AA-AAAGATAATTTCACTTCAGGTTCTACCGAGATTTGAACTCGGATCGCAGGATTCAGAGTCCTGAGTGCTA DroPse_CAF1_left --------AACAGAATTCATCGTATTAAC---AGA-AATATTATTA-AA-AAACAAAATTTCACTTCAGGTTCTACCGAGATTTGAACTCGGATCGCAGGATTCAGAGTCCTGAGTGCTA DroSim_CAF1_left TTA-----TTAAAAA-A---C--TAAGTT---TAC-TTAATTAAGA-AA-AAAAAAAAATGTAGTCTAGGTTCTACCGAGATTTGAACTCGGATCGCAGGATTCAGAGTCCTGAGTGCTA DroVir_CAF1_left --------TTGCCAA-A---A-GAAGTAA---A-A-ATAAAATAGA-AA-AATAAACTTTAATAATCAGGTTCCACCGAGATTTGAACTCGGATCGCAGGATTCAGAGTCCTGAGTGCTA DroYak_CAF1_left TACC----TTATTAAAAAAAATTAGCAA------C-C-AAAAAAAA-TG-AAAAAAAAACTTAGTATAGGTTCTACCGAGATTTGAACTCGGATCGCAGGATTCAGAGTCCTGAGTGCTA DroMel_CAF1_left --------TTAAAAA-T---C-TAAGTTT---A-C-TTAAAAAAAA-AG-AACAAAAAATGTAGTATAGGTTCTACCGAGATTTGAACTCGGATCGCAGGATTCAGAGTCCTGAGTGCTA DroSec_CAF1_left --------TTAAAGA-A---C-TAAGTTT---A-C-TTAAGAAAAAAAA-AAAAAAAAATTTAGTCTAGGTTCTACCGAGATTTGAACTCGGATCGCAGGATTCAGAGTCCTGAGTGCTA DroAna_CAF1_left ACCATTACACCATGGAACCTCTTTGAAAGATCA-CGCCAAGTGGCAGTT-T-TCTA-AT-GAAGCCGCTTGATCGTAGAGGCCTACA-CGATCAT--AGAAGAGAAAGTTGA---CTAGA DroEre_CAF1_left ACCATTACACCATAGAACCTCTATGAGCGAAAAATGCCAAGAGTTACTT-T-TCCA-GT-GCA-AGTAGACAGATTACCAGCCGAAG-ATCATGG--AAAAGAAAGTTGCTC---AATGA DroGri_CAF1_left ACCATTACACCATGGAACCCCGGTGATCAAGAATCGACAGCAAACAAGCAAAATTT-TA-TTA-CTTTGCATTAAAATAATA--CAA-ATTCTTG--AACTGCTGAGGTAAA---CAAAT DroMoj_CAF1_left ACCATTACACCATGGAACCACTGCGTCGAA-T-TTGCCAATAATCAGTT-T-TGCTTTAGTGA-GGTATTTTGCAGTGTTGACGATC-AGTTTTA--CACAAAAACTTTCAA---CAATC DroPer_CAF1_left ACCATTACACCATAGAACCGCTTTGAACAAGCATCGCTTAGAGGCAGTT-T-TCTA-GT-CAA-GCGATGACCCGCTCTGACACCAC-AGATCGT--AGAAGAGAAAGTTGA---TCAAC DroPse_CAF1_left ACCATTACACCATAGAACCGCTTTGAACAAGCATCGCTTAGAGGCAGTT-T-TCTA-GT-CAA-GCGATGACCCGCTCTGACACCAC-AGATCGT--AGAAGAGAAAGTTGA---TCAAC DroSim_CAF1_left ACCATTACACCATAGAACCTCTANNNNNNNNNNNNNNNNNNNNNNNNNN-N-NNNN-NN-NNN-NNNNNNNNNNNNNNNNNNNNNNN-NNNNNNN--NNNNNNNNNNNNNNN---NNNNN DroVir_CAF1_left ACCATTACACCATGGAACCGTTGAGAAAA--TTTTGTCATAAGTGTAT---TTTGT-AT-CAA-CCAGCAATGTGTATTGAT--CACCAAAATATCTATCTTTCATTAAACA-GACACTA DroYak_CAF1_left ACCATTACACCATAGAACCTCTATGAGCGATGAATGAAAAGAGACACTT-T-TCCA-GT-GCA-TAAAGACAGATAA-GCAC--CGA-AGATCAT--GGAAGAGAAAGTTGCCCACCGAT DroMel_CAF1_left ACCATTACACCATAGAACCTCTATGGGCGAGAAATGCTAAGAGGCACTT-T-TGCA-GT-GCA-AGTAGACAGATTAACAAGCCAAG-ATCATTG--GGAGAAAGTTGCTCA---CTGAT DroSec_CAF1_left ACCATTACACCATAGAACCTCTATGGGTGATGAACGCCAAGAGGCACTT-T-TCCA-GT-GCA-AGTCGACAGATTAATATACGAAG-ATCATTG--GGAGAAAGTTTCTCA---CTGAT DroAna_CAF1_left AATTCCCATCTATTTTTAA DroEre_CAF1_left TATTCCCATCTAATTCTGT DroGri_CAF1_left TCAAAATTTAAATAAACGG DroMoj_CAF1_left TTTTATTTATAAATCTAGT DroPer_CAF1_left AATTTTAGGGCTATTAATA DroPse_CAF1_left AATTTTAGGGCTATTAATA DroSim_CAF1_left NNNNNNNNNNNNNNNNNNN DroVir_CAF1_left TAAAACCAACTCTTTAAGA DroYak_CAF1_left ATTCCCATCTATTTTTGTG DroMel_CAF1_left ATTCAGTTCTATTTCTGTG DroSec_CAF1_left ATTCCCGTCCATTTTTGTG