CLUSTAL W --- LocARNA 1.4.8 - Local Alignment of RNA DroAna_CAF1_left AAAAA-TAATA-TTAAGTCCAAAAATATATATTTT-ATCGTTTGGTTATAATTCTCAACTCATTATTCAGCACATGGAGCGTATAAAA--T-GCGGGTTGTA-ACCCGCGTACCTGTGTT DroGri_CAF1_left TATCAGAAAAC--CATT--GGGCTTTGTACTTTACTACTTTACTCTTATAATTCCCAAGTTCTTTTTCCCTGAGGTTTACGTATATAAT-G-ATGACTGGCC-ACAT-ACCTTCTGTGTT DroMoj_CAF1_left TAATC-ACCTT--CTGT--TTGCCTCTCAGCCAGCACATATTCTGTTATAATTCCCAACTGTTTATTCGCCGAGCTTCGCATATAAAAC-GGGGGTTCAGCT-GCGAGCTCATTTGTGTT DroPer_CAF1_left TGAGC-TAGAGTTCTTC--CAGCTGAAAATGTATG-CACTTGCGCTTATAATTCCCAAGTCTTTTTTCTCGGGTATGGCCGTATATAAA-C-GCGTTGCCCG-TCGAACATTAGCGTGTT DroPse_CAF1_left TGAGC-TACAGTTCTTC--CAGCTGAAAATGTATG-CACTTGCGCTTATAATTCCCAAGTCTTTTTTCTCCGGTATGGCCGTATATAAA-C-GCGTTGCCCG-TCGAACACTAGCGTGTT DroVir_CAF1_left CAGTC-GATCT-TGGTG--CAATGCATGGCTAGCG-TGAGTGCGCTTATAATTCCCAAGTGCTGATTCGCTGTCGCTCACGTATATAACTG-GGGTTGAGCCGCAA-GTTGGGTTGTGTT DroEre_CAF1_left AAGTT-GCTGACTGCAT--ATCACTAATTCCCATGCACTGCGTTCTTAAAATTCCCAAGTTCTTATTCCGCAAAGCGTGCGTATAAAA--G-GCGGCAAGCA-TCCAGTGCAAACGTGTT DroMel_CAF1_left AAGTT-GTTATATGCAT--ATCACTAATTTTCATGCAATGGGCTCTTAAAATTCCCAAGTTCTTTTTCCGCATGGAGTGCTTATAAAG--C-GCGACAAGTG-TGTGGTCCAAACGTGTT DroSec_CAF1_left AAGTT-GTTATATGCAT--ATCACTAATTTTCTTGCAAAGCGCTCTTAAAATTCCCAAGTTCTTTTTCCGCACAGCGTGCGTATAAAA--G-GCGGCAAGCG-TGTGGTGCAAACGTGTT DroSim_CAF1_left TAAAA-GTTATATGCAT--ATCACTAATTTTCTTGCAAAGCGCTCTTAAAATTCCCAAGTTCTTTTTCCGCACAGCGTGCGTATAAAA--G-GCGGCAAGCG-TGTGGTGTAAACGTGTT DroYak_CAF1_left ATGTA-GAATTTGCTAT--ATCACTAATTTCCGTGCACTGCGCCCTTAAAATTCCCAAGTTCTTTTTCCGCGAAGCAAGCGTATAAAA--A-GCGGCTGGCA-TTTGGTGCAAACGTGTT DroAna_CAF1_left GTTTGAAAGGAGAGCAAGTTAGCACTCCCCTAGACAAGGATGGAACACATAAACGGTCGGCTGGGCACAAGACAAAGCCGACCACAAGTTTTTTTTAGATAAT-ATAT-TT-TATA-ATA DroGri_CAF1_left GTTTGGAAGGAGAGCAAGTTAGCACTCCCCTAGACAAGGATGGAACACACAAACGAGCGGCTTGGCACAAGACAAGGTCGTTCACAAGTTTTTTTTCTTCCTT-TTTC-CC-CCTT-TCG DroMoj_CAF1_left GTTTGGAAGGAGAGCAAGTTAGCACTCCCCTAGACAAGGATGGAACACACAAACGAACGGCTAGGCACAAGACGATGCCGTTCACAAGTTTTTTTTTTTTTTT-TTAT-AA-TTTT-TAT DroPer_CAF1_left GTTTGGAAGGAGAGCAAGTTAGCACTCCCCTAGACAAGGATGGAACACATAAACGAGCGGCTG-GCACAAGAGAAAGCCGTTCACCAGTTTTTTTTTAAAGGG-CTAT-AC-TTTT-AAT DroPse_CAF1_left GTTTGGAAGGAGAGCAAGTTAGCACTCCCCTAGACAAGGATGGAACACATAAACGAGCGGCTG-GCACAAGAGAAAGCCGTTCACCAGTTTTTTTTAAA-GGG-CTAT-AC-TATT-AAT DroVir_CAF1_left GTTTGGAAGGAGAGCAAGTTAGCACTCCCCTAGACAAGGATGGAACACATAAACGAACGGCGGGGCACAAGACGAAGCCGTTCACACGTTTTTTTTTAT--TA-ATTA-TT-TTAT-TTT DroEre_CAF1_left GTTTGGAAGGAGAGCAAGTTAGCACTCCCCTAGACAAGGATGGAACACATAAATGGTCGGCTAGGCACAAGACAAAGCCGTCCACAATTTTTTTTTTGTTTCG-CATG-GA---AA-TTG DroMel_CAF1_left GTTTGGAAGGAGAGCAAGTTAGCACTCCCCTAGACAAGGATGGAACACATAAACGGTCGGCTAGGCACAGACAAAAGCCGTCCACAAATTTTTTTAAATCTTA--TGA-TAGCTTA-ATG DroSec_CAF1_left GTTTGGAAGGAGAGCAAGTTAGCACTCCCCTAGACAAGGATGGAACACATAAGCGGGCGGCTAGGCACAAGACAAAGCCGTCCACAAATTTTTTTTAGGCCCT--ATTACT---TA-ATG DroSim_CAF1_left GTTTGGAAGGAGAGCAAGTTAGCACTCCCCTAGACAAGGATGGAACACATAAACGGTCGGCTAGGCACAAGACA-AGCCGTCCACAAATTTTTTTTTAGGCCCTATGA-CT---TA-ATG DroYak_CAF1_left GTTTGAAAGGAGAGCAAGTTAGCACTCCCCTAGACAAGGATGGAACACATAAACGGTCGGCTAGGCACAAGACAAAGCCGGCCACAATTTTTTTTAATATTGA--ATT-TAATAGAGAAA DroAna_CAF1_left TAT--AT--T-TTATATGTATATA-CTGTA--AAATG-AATC--ATTAAAACCA--CATAGATGATTTTTTTTTCCACTGAA-AC---CTCTTAAAAT DroGri_CAF1_left GTT--TT--T-CTATTTGATGTAC-TTTAT--TG-TT-GTACGTTCATTCCTTG--AACTTTA-TTC-AGAACACAAACAAATTC---ATTTGCAAAT DroMoj_CAF1_left ATT--TT--T-ATTTTCTATATAT-ATTAA--AT-AT-ATATATATTCCCGAGC--AGTTGCCGCTG-TTAGGTCGATCTTA-AT---GTTTCGATGC DroPer_CAF1_left TAA--AT----TAATTAAATA-TTATACAC--TA-T--AATGATTTAAGTTTTTCATGCTGTT--TT-ATAATTTACACCTA-ATAAATAGCTATGTA DroPse_CAF1_left TAAATATT-A-TACACTATAA-ATTAATTA--TT-AT-ATATTGTAGTGCCATT--TATTTCA--TT-AAAATTTAAGCTTT-TC---ATTCTGTTTT DroVir_CAF1_left ATT--CG--CGTGAGTAAATCGAA-TTGCA--AGTAGTCTAA--AGCATAATGC--GGTTGCCCTTTCTTTTGATTACCCAT-TT---AAATTAAATT DroEre_CAF1_left TTT--TA----CTTAGTAGGAAAA-CAAAAGAAATTG-GTGGAAT-ACATTAAA--TTTTGCAGTTGAAAAAGAAATTCGTT-GA---TACTTATGAC DroMel_CAF1_left CCA--AA----TATCCCTTAATAA-AATAG--AAAAA-A-CACAT-CAAACATA--TACATTTCTATATTCAGAAGCTCTAC-TT---GTCAAATGGT DroSec_CAF1_left CCA--AATATCCTTAATAAAATAT-AAAAC--ACATC-A-AACAT-ATACATTT--CTATATTCAGAAGCTCTGCTTGTCAA--A---TGGTAAAAAT DroSim_CAF1_left CCA--AA----TATCCCTTAATAA-AATATAAAACAC-ATCAAAC-ATATACAT--TTTTATATTCATAAGCTCTACTTGTC-AA---ATGGTAAAAA DroYak_CAF1_left ACA--TA----AAATAAGTAACGT-AAAAA--TATTA-A-AGTGC-TTAAAGAA--ACCATGATGTTTATTATTCAATGGTT--A---AATGTTCTTT