CLUSTAL W --- LocARNA 1.4.8 - Local Alignment of RNA DroAna_CAF1_left TT--TAAATAT--GGGGA--TGAAAATAG-TATTTAA--AAT--GATGT-T-G-CGT-TA-T---GGTATT----TTTAAAATAGTCAATGCAT--GTATAGTAAT-----ACAAAATAA DroEre_CAF1_left TG--ATTAAAA--TAATT--CTTTCAAAG-TAAGCGAGGTGTAAAATAA-A-A-CAA-TG-CATAGTCAAA----TAAATTGTTTTCAATAAAA--ATATAACAGT-----ATTTTATAA DroMel_CAF1_left AC--TAAAGTC--TTAGT--ATCAACTAG-ATCCTTTCATGCGAGTTGT-A-A-AAT-AA-AGTCAGAAGT----TAGAAAATATTGTTTAAAT--AAAAAACTGC-----ACTTTTGAA DroMoj_CAF1_left AC--ATAATGT--CAAAATAAGAATATTTTAATGCTGAATGCAGATTAA-TCGTAAA-TGTAATAA-AAGCTG--GCTAATTTATTCAAT------ATTAAATTTAAATAAAATTAATAC DroPer_CAF1_left TG--TCAATCC--AGAGT--CCAAAT-TG-AACTTTA--TTT--GGTGA-A-A-AAC-CG-TATTGCTT---------TCAATGGAATGTTTCTATACTGAGCTCAAATAGAGAACAACA DroPse_CAF1_left TG--TCAATCC--AGAGT--CCAAAT-TA-AACTTTA--TTT--GGTGA-A-A-AAA-CG-TATTGCTT---------TCAATGGAATGTTTCTATACTGAGCTCAAATAGAGAACAACA DroSec_CAF1_left GG--ACTTTTG--AAATT--AGATCCTTT-CATGCGATATAAATAAAGT-C-A-GAA-GT-TGGAAAAAGT----GGTTTTCAATAAAAAATAT--ACACAACTGG-----ACTTTTGAA DroSim_CAF1_left NN--NNNNNNN--NNNNN--NNNNNNNNN-NNNNNNNNNNNNNNNNNNN-N-N-NNN-NN-NNNNNNNNNN----NNNNNNNNNNNNNNNNNNN--NNNNNNNNNN-----NNNNNNNNN DroWil_CAF1_left TTAGACAAATCTAATCAA--TTTGAA-TA-GTTGATA--TAT--TCAAA-A-G-AAA-TT-TAATGTAA---------GTACATATTAAATGCGTTGACTAACTTAAATAAACAATCTAA DroYak_CAF1_left AG--TAAAAGT--ATCAT--CTAGATTCT-TTGAAAGTTAGCGGGGTGT-A-A-TTAATG-GGTAGTTAAA----TAAATGGTTTTCAATAAAG--ATATATCA-A-----ATTTTATAT DroGri_CAF1_left AT--TCTGCAT--TGCGG--TGCTTAATC-AGTAAAT--GAGTCTTGCA---A-AATGTA-CCCAGTTATCAATTTTATTTATGGT-----ATA--ATA-T----------ACTGGTATA DroVir_CAF1_left TA--GGATTAA--TGTGG--GATAAAATA-TATCCAT--TTATTTCATTTT-A-ATTGGT-ATTTGTTTCTAATGTGTATGAAACTAACTTAGT--ATA-T----------ATAATTATT DroAna_CAF1_left AAAT---AAAA-TAAAACTTA--AAAA-ATAATA--AAATAAAAAAAATAAACCCAACTCCGTGACAATGTT-TAT-TTCAACATTGCCGTGACCAGGATTCGAACCTGGGTTACCACGG DroEre_CAF1_left ATAT---CTTT-TAAATTGTT--TTAA-AGTT-A--AAAAAAAAAAAAAAAACCCGACTCCGTGACAATGTT-TAT-TTCAACATTGCCGTGACCAGGATTCGAACCTGGGTTACCACGG DroMel_CAF1_left ATTA---ATCT-TAAATTGTT--GAAA-GGTTTA--AAAAATAAAAAAAAACCCCGACTCCGTGACAATGCA-TAT-TGCAGCATTGCCGTGACCAGGATTCGAACCTGGGTTACCACGG DroMoj_CAF1_left AAAAATATTAAATTTAAATAAAATTAA---TACA--AAAAAGATTGTTCAAATTCGACTCCGTGACAATGCCTCTT-AATAGCATTGCCGTGACCAGGATTCGAACCTGGGTTACCACGG DroPer_CAF1_left AAAA---AGAA-TTATAAATTA-TTCT----G-------ACAAAAAGAAAGACCAAACTCCGTGACAATGCA-TAT-TGCAGCATTGCCGTGACCAGGATTCGAACCTGGGTTACCACGG DroPse_CAF1_left AAAA---AGAA-TTATAAATTA-TTCT----G-------ACAAAAAGAAAGACCAAACTCCGTGACAATGCA-TAT-TGCAGCATTGCCGTGACCAGGATTCGAACCTGGGTTACCACGG DroSec_CAF1_left ATTA---ATCT-TAAATTGTT--GAAA-GGTTTA--TAAAAAATAAAAAAAAACCGACTCCGTGACAATGTT-TGT-TTCAACATTGCCGTGACCAGGATTCGAACCTGGGTTACCACGG DroSim_CAF1_left NNNN---NNNN-NNNNNNNNN--NNNN-NNNNNN--NNNNNNNAAAAAAAAAACCGACTCCGTGACAATGTT-TGT-TTCAACATTGCCGTGACCAGGATTCGAACCTGGGTTACCACGG DroWil_CAF1_left TCAA---TTGT-GAATTAATTC-ACAA----TTT--ATAAAAAAAAAATTAACCTAACTCCGTGACAATGCA-TCT-TGCAGCATTGCCGTGACCAGGATTCGAACCTGGGTTACCACGG DroYak_CAF1_left ATAA---TTTT-AAAAATGTTT-AAAA-GTTTAA--AAATAAAATAAATAAACCCGACTCCGTGACAATGTT-TGT-TTCAACATTGCCGTGACCAGGATTCGAACCTGGGTTACCACGG DroGri_CAF1_left TGA----TAGT-TATTGTTAAT-GCT-CTCAAAA--AAAATTTAAAATTCAACCAGATTCCGTGACAATGTG-CTT-CGAAACATTGCCGTGACCAGGATTCGAACCTGGGTTACCACGG DroVir_CAF1_left ATAT---TAAG-ACATATGTAT-TTTAATATAATAAAAATGAAAAAAAACAATCCGATTCCGTGACAATGCA-GGTTTACAGCATTGCCGTGACCAGGATTCGAACCTGGGTTACCACGG DroAna_CAF1_left CCACAACGTGGGGTCCTAACCACTAGACGATCACGGCTACGTTGGGTTGTTGAATGTAGCCGGCCAAATGGTACATTTAAA-AGAAAATCG-AAAACCTG--ATGCA-ATTTTT-CA-CA DroEre_CAF1_left CCACAACGTGGGGTCCTAACCACTAGACGATCACGGCTACATCGGGTG-ATGTTTGACGGCTGCCAAATTACTATTTTAAA-ACAAATCCGTTTTGATTT--TAGTT-TTATTTATC-GC DroMel_CAF1_left CCACAACGTGGGGTCCTAACCACTAGACGATCACGGCTACATCGGGTG-ATGTTTGACTGCTGCCAAATTACTTTTTTGAA-ACAAATCAGTTTTGACTT--CAATC-TTCAATGTC-CG DroMoj_CAF1_left CCACAACGTGGGGTCCTAACCACTAGACGATCACGGCTACGTCGAATC-TGTAAAGCCTTTGTCTAAATCTTGCTTTTATC-TTAAAT-GACATATATA---TAACG-AACGAACGA-TA DroPer_CAF1_left CCACAACGTGGGGTCCTAACCACTAGACGATCACGGCTACGTTAGGTTGTAGGATTGTGCCAGCCAAAACACCTATATCAA-GAAAATGCCCAAAACCAG--CTATG-CGTTCTCTC-AA DroPse_CAF1_left CCACAACGTGGGGTCCTAACCACTAGACGATCACGGCTACGTTAGGTTGTAGGATTGTGCCAGCCAAAACACCTATATCAA-GAAAATGCCCAAAACCAG--CTATG-CGTTCTCTC-AA DroSec_CAF1_left CCACAACGTGGGGTCCTAACCACTAGACGATCACGGCTACATCGGTTG-ACGTTTCACGGCTGCCAAATTACTTTTTTGAA-AGAAATCAGTTTTAACTT--CAATC-TTCAATCTC-TA DroSim_CAF1_left CCACAACGTGGGGTCCTAACCACTAGACGATCACGGCTACATCGGTTG-ACGTTTGACGGCTGCCAAATTACTTTTTTGAA-AGAAATCAGTTTTAACTT--CAATC-TTCAATCTC-TA DroWil_CAF1_left CCACAACGTGGGGTCCTAACCACTAGACGATCACGGCTATGTGAGGTTGTTGAATCTGGTTTGCCAAATGTCATATTTGTG-AAACTCGCTTGAAACCAGGGCTAAA-GAAACAATA-AT DroYak_CAF1_left CCACAACGTGGGGTCCTAACCACTAGACGATCACGGCTACACCGGGTG-ATGTTGTGCAGCTGCCAAAATACTATTTTAAG-TCAAATCAGTTTTAACTT--CAATC-TTAATGCCAGCG DroGri_CAF1_left CCACAACGTGGGGTCCTAACCACTAGACGATCACGGCTATACCAGTTG-TTCGTGAATGTTGCCCAAATTTCGGTTTTTACAACTAATGAAAAATACATT--CTTTTGTGTTCTCCT-GA DroVir_CAF1_left CCACAACGTGGGGTCCTAACCACTAGACGATCACGGCTACATCGGTTA-TGTTGCCCGACCGACTAAAGTCAGGTCTTACA-ATCAATCACACACATACA--CATTTGTGCATATGT-GA DroAna_CAF1_left GATTATCTAAATAAAA-ATAAT--A---T-TAAAACAAGGTAT-TAAGAT-ATTTTTATA-AAATTTA DroEre_CAF1_left TTCTCTT--AAAATTT-TGGAC--C---T-ATCAGTAAA-TCA-AAAGTA-ATTTTATTTTAACAAAG DroMel_CAF1_left AAGTTTC--TACAAGT-ATCATAGA---T-AATAACAA---TA-TTACTGATTTTATTTA-TCACTTC DroMoj_CAF1_left GATGGGG--ATTATTATAACAATTT---T-AGATGTTA---CTGGTTTCGTAGCAATGAC-ACGGACA DroPer_CAF1_left TATTTTC--CTGATATAATCTGCAA---A-TCGAGTCA---TA-GATGGCGACGGT-AGC-TTCTGTC DroPse_CAF1_left TATTTTC--CTGATATAATCTGCAA---A-TCGAGTCA---TA-GATGGCGACGGT-AGC-TTCTGTC DroSec_CAF1_left AAGTTTC--TATAAAT-AGCATAGA---T-AATAAAAA---TG-TTACTGTTTTATTTAT-TTATCAC DroSim_CAF1_left AAGTTTC--TATAAAT-AGCATAGA---T-AATAAAAA---TG-TTACTGTTTTTATTTA-TCACTTC DroWil_CAF1_left TAGTTTT--CATTTAAAAGAGAAAG---T-AACAACGA---TT-TC-GTCTTGTT--AGC-CTAGCAA DroYak_CAF1_left ATGTTGC--TCTAAAT-AGCATAAA---T-AGTAACAA---TA-CTACTGGTCTTATTT--ATTTATT DroGri_CAF1_left AATTAT---AATTGAAAGAC---AGGTGGCGCTT-AAAT--AA-GT--AT-TGTTTCGTA-TAAAAAT DroVir_CAF1_left AAGACA---GACAAAA-GCTAT-ATGGCT-ATTGAATG---CA-GT-TTG-ATTTTACAA-AATCGCT