CLUSTAL W --- LocARNA 1.4.8 - Local Alignment of RNA DroAna_CAF1_left CT--GATC------ATGGTCATGAATAGTAA----GCAATA-CA-TATGT-CTAT-TTTTAG-ACCAT-AAGCATAT-GGGTGATCAACTCTACCCCTA-AATCCTTGTAGGAGTGAAA- DroEre_CAF1_left TA--TGA--TC---ATGGTCATGAATA---G-----TAAGC-AGCTAGT-CCATT-TGTATAAACAGCTCATTCATT-TAGCCATAGTTACCAACCTTA-ATTTGTTGAAGAACCTATA- DroMel_CAF1_left AC--GAAAAGCT--ATGATCATGGTCAT---------GAAT-AG-TAAA-GCAGC-TAATC-TATTTATATAGCACA-TGCATTTAGTTACCAGCCTTA-CTTTGTTGCAGAACCTATA- DroMoj_CAF1_left TT--CAAC-GAA--AGCTGACCATGGCT--T-----TTATT-TGGAATA-TTTAA-TTTAC-CAATCTATTTTTAAA-CCAACTCAGTTGCA---TTTT-TTTCACTTTTTGGCTACATA DroPer_CAF1_left GG--CCGA------GTG-TGGCCATGCCT-AGTAAATGATC-GA-TTTATTTATA-GAGC-----ATT-AGAGCATTCGGATGAAAATAATCCACTTGA-AATCGTTTAAGAGCACAAA- DroPse_CAF1_left AA--ACCACTAAACGGCCGACTGTGGCC----------ATGCCTAGTAA-ATGATCGATTTATTTATA--GAGC----AT-TAGAGCATTCGGATGAAAAAATCGTTTATGAGCACAAA- DroSec_CAF1_left AA--TGCC------ATGATCATGGTCATG-AATAGTAATGC-AGCTAAT-CTATT-TATGTATATAGC--TTAT----GC-ATTTAGTTACCAGCCTTA-CTTTGTTGCAGAACCTATA- DroVir_CAF1_left TT--GGAC-TC---AATTGCCATAACC---A-----TTAAC-CA-CGGT-GTTAT-TTGCA-TACCAATCTATTTTT-AAACCGCTTGAATTGCACTTT-TATCGCTTATTGACCACTA- DroWil_CAF1_left GT--ATTG------ACCGATAATGGCC---A-----TGAAT-AACTAAT-TAGGT-GTATTTAATAGT--TTTA----TT-TTGGTTTGCCATGTATTT-CAGTTTATAAAGTCCTTGT- DroYak_CAF1_left GCTGTGA--TC---ATGGTCATGAATA---G-----TAAGC-AG-CTTA-TCTAT-TTATA-AACATATGTATCACT-TAGCCTTAGTTACCAACCTTA-ATTTGTTGCAAAACCTATA- DroSim_CAF1_left NN--NNNN------NNNNNNNNNNNNNNN-NN----NNNNN-N--NNNN-NNNNN-NNNNNNNNNNNNNNNNNNNNN-NNNNNNNNNNNNNNNNNNNNN-NNNNNNNNNNNNNNNNNNN- DroAna_CAF1_left ATCTG-A--TACGTTT-ATACGGGGATGTAGCTCAGATGGTAGAACGCTCCCTTATCATGTGAGACGTACTGCTATCGATACCGCGCATCTCCAACTGAGATTTAT--TTTTATTTTTTC DroEre_CAF1_left ATCAA-G--TACCGTT-ATATGGGGATGTAGCTCAGATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTACGGGGATCGATGCCCCGCATCTCCAAGGATATTTCTTTTTT---TCGTATT DroMel_CAF1_left ATCAA-A--TGCCGTT-ATATGGGGATGTAGCTCAGATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTACGGGGATCGATGCCCCGCATCTCCAAGGATGTTTCCT--TT---TTTCTCG DroMoj_CAF1_left GTTGG-G-CATTTCAT-CGAAGGGGATGTAGCTCAGATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTACGGGGATCGATGCCCCGCATCTCCAAGCACATTGTCT--AGA--AGACAAT DroPer_CAF1_left ACCAG-G--TACCGTT-ATATGGGGATGTAGCTCAGATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTACGGGGATCGATGCCCCGCATCTCCAGAATAGATTATT--TTC-TTTTTTTC DroPse_CAF1_left ACCAG-G--TGCCGTT-ATGTGGGGATGTAGCTCAGATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTACGGGGATCGATGCCCCGCATCTCCAGAATAGATTATT--TTC-ATTTTTTC DroSec_CAF1_left ATCAA-G--TACCGTT-ATGTGGGGATGTAGCTCAGATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTACGGGGATCGATGCCCCGCATCTCCAAGGATGTTTCCT--TT---TTTCTCA DroVir_CAF1_left AGCGA-ACCAATTTTC-CGACGGGGATGTAGCTCAGATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTACGGGGATCGATGCCCCGCATCTCCATAAAGAGTGAAT--TT---TTGCATT DroWil_CAF1_left AGATTCG--GTGAAACACCATGGGGATGTAGCTCAGATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTACGGGGATCGATGCCCCGCATCTCCAACTTTGGATTAT--TT---TTTTGTA DroYak_CAF1_left ATCAG-A--TACCGTT-GTATGGGGATGTAGCTCAGATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTACGGGGATCGATGCCCCGCATCTCCAAGGATGTTTATT--TT---CCTTATG DroSim_CAF1_left NNNNN-N--NNNNNNN-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN--NN---NNNNNNN DroAna_CAF1_left CTAATTATTTAT--AGTTCCTTCTAAATA---GTCT-TAACCTTTTTTTTCGAACAAAAAATA-------TTTATCGCAACAAAAGACTTTTTC DroEre_CAF1_left GTGGCACA-TAT--TATGAATA-ACTTTA---TATTTTTTGC-CAAGTTTTTCATAATTTCCCAATTA--CGCTGTTCAA---TTGAAATCGAC DroMel_CAF1_left TATTGTAT-TAA-ATATTTTAT-T-ATTTT-TA-AA-CAAAG-TTTTCACAAGATACCA-AAT--ATGCGCTGAATAATTGAAATCAATTATTT DroMoj_CAF1_left CCTTTTTT-TAC--TCTAATCA-TATTAA---TATA-CAAAT-TGTATGATTCAATACATTTTTGA-A--TCTAAAAAAAATTCTAAATTAAAA DroPer_CAF1_left CTTACCT--TTATACATTTTTT-T-TACCTGCA-AA-TATAT-GCCATACTAGAAATAAAATAATAAA--GAAGCAATAAATAGAGCTTTTAAT DroPse_CAF1_left CTTACCTTTATA--TATTTTGT-TTACCAG-CA-AA-TATAT-GCCATACTAGATATAAAAAGAGCTT--TTAATAAATGTACAGTGGAATCGG DroSec_CAF1_left TATATATAAAAG--TATTTTGA-T-ATCTC-GTATA-TATAA-AAGTATTTTGATATTTTTAAATA----ATTTTTTCACAAGATCCCAAATAT DroVir_CAF1_left GTTTTTAA-ATC--AAACAGCT-TATATA---TACA-CAAAA-ATAATATCTTTCTCTGTGTCTGCTG--CNNNNNNNNNNNNNNNNNNNNNNN DroWil_CAF1_left TTTTATGTTGGT--TTTTTATT-GTTTCAA-GTAAA-ATTTA-AATTTTCAAGATTGCTAATGTTTAATATCTAAAGATTCAAAAGATTTATTT DroYak_CAF1_left GTATTAAA-TAT--TTTAAATA-ACCTTA---TACG-TACGA-CAAATGTTTCATGTTACCAAATAAG--CTCTGTTCAATTGAAGTCGGCAGT DroSim_CAF1_left NNNNNNNN-NNN-NNNNNNNNN-N-NNNN---NNNN-NNNNN-NNNNNNNNNNNNNNNNNNNNNNNNN--NNNNNNNNNNNNNNNNNNNNNNNN