CLUSTAL W --- LocARNA 1.4.8 - Local Alignment of RNA DroAna_CAF1_left AGGC----GGCCCG---AACCTCTG-TCTCTCCCA--ACTTAAA--ACCTGAACTGGGCTTGGC-TTT-T-ATTCTTTTT-TTTTATATA-TCTACATCTTCAACTTCAAG-TCCAGCAC DroEre_CAF1_left GTGAAAAAGAAACC--TGACTGGGC-TTGGCTTGG-CTT--TAT--GTCT--ACATCT-TCAACTGCA-G-CCCCAGCCG-CAGCTCCTACTCGTTGTATGTGATGATGTT-CCCCCGAC DroGri_CAF1_left GCAG----CAT-TA--ACGGCAGCA-GCAGAAGAGGAAGAAGCA--GCAGCAGCAGTT-ACTTTGTCG-G-ACCAG-TTGGCAACATATG-TTTGGGCTTATCTTAGCCTC-TCTCTTTC DroMel_CAF1_left TGAA-AAAAAAACC--TGACTGGGC-TTGGCTTGG-ACTGGCCT--GGCTCTTCATCT-TCAACTCCA----GCCA-CCA-CAGTTCCTACTCGTTATATGTGATGATGTT-CCCCCGAC DroMoj_CAF1_left TTCC----TGCGTGGCTTT--AGGA-GCAGCAGCA-ACAGCAGC--AGCG--GCAGCA-GTTACTCCG-A-ACCAGTTGG-CAACATCTGTTGGCTGGGCTTATCTTGGTC-CGCTGCGC DroPer_CAF1_left CAGA----ACAGTG--TTGCCAAGC-CAG-CATGC-ACCATCTG--GTCTCGTCTCGT-CTCGGACCTGG-GTTTGGGCT-TGGCTTTATATCTCGTCCCACAACCCCAAC-CCACCTTC DroPse_CAF1_left CAGA----ACAGTG--TTGCCAAGC-CAG-CATGC-ACCATCTG--GTCTCGTCTCGT-CTCGGACCTGG-GTTTGGGCT-TGGCTTTATATCTCGTCCCACAACCCCAAC-CCACCTTC DroSec_CAF1_left AAAA----GAAACC--TGACTGGGC-TTGGCTTGG-CCTGGTCT--GGCTTTATATCT-ACATCTTCA-A-CTCCAGCCG-CAGCTCCTACTCGTTATATGTGATGATGTT-CCCCCGAC DroSim_CAF1_left AAAA----GAAACC--TGACTGGGC-TTGGCTTGG-TCTGGCCT--GGCTTTATATCT-ACATCTTCA-A-CTCCAGCCG-CAGCTCCTACTCGTTATATGTGATGATGTT-CCCCCGAC DroVir_CAF1_left GCAG----CAA-CA--ACAGCAGCA-GCAGCAGCA--GCAGCAAAAGAAGTTACTTCG-GACCAGTTG-GCAACAT-CTGTTGG-GCTTA-TCTTGGTCTGCTCTCTCCCC-TAACTCGC DroYak_CAF1_left CAAA----TGGTGA--AAAAGAAAC-CTGACTGGG-CTTGGCCT--GGCTTTATATCT-ACATCTTCA-A-CTCCAGCCA-CAGCTCCTACTCGTTATATGCGATGATGTT-CCCCCGAC DroWil_CAF1_left GTTG----AGC--A--TGTTGGAATTGTTGTTG-A-TGCGGATG----CG--G-GGGG-A-----GATTT-TGTGTGAAA-CTCTGAAACCCTGGGATGACGAACAAGGTCGTTTCCTTT DroAna_CAF1_left TCTC--CAGTCTCCTACCTTGCGCGCTAATCAGTGACCGGGGCTGGTTTT-----TG--CAACAGTCAGGTACCTGAAGTAGCGCGCGTGGTG-GCAGACATATATCCGCCATA-C--A- DroEre_CAF1_left TGAA--AAGTCTCCTACCTTGCGCGCTAATCAGTGACCGGGGCTGGTTTT-----TTATATACAGTCAGGTACCTGAAGTAGCGCGCGTGGTG-CCAGACATATATCTCCATCT-C--CA DroGri_CAF1_left TTCG--TCGTCGTTTACCGCGCGCGCTAATCAGTGACCGGGGCTGGTTTTGAT--TATCCCACAGTCAGGTACCTGAAGTAGCGCGCGTGGTGGCCAGACGCATTCAACAAACG-G--CG DroMel_CAF1_left TGTA--AAGTCTCCTACCTTGCGCGCTAATCAGTGACCGGGGCTGGTTTT-----TTATATACAGTCAGGTACCTGAAGTAGCGCGCGTGGTG-GCAGACATATATCTCCATCT-T--CA DroMoj_CAF1_left CCGT--CCGTCTTTTACCGTGCGCGCTAATCAGTGACCGGGGCTGGTTTCGAT--TATCTCACAGTCAGGTACCTGAAGTAGCGCGCGTGGTGGCTAGACGCATTCAACGCTCTGC--TA DroPer_CAF1_left TTGA--AAGTCTCCTACCATGCGCGCTAATCAGAGACCGGGGCTGGTTTT-----TTCACTGCAGTCAGGTACCTGAAGTAGCGCGCGTGGTG-CTAGACACGAACATCTGTGTGG--CA DroPse_CAF1_left TTGA--AAGTCTCCTACCATGCGCGCTAATCAGAGACCGGGGCTGGTTTT-----TTCACTGCAGTCAGGTACCTGAAGTAGCGCGCGTGGTG-CTAGACACGAACATCTGTGTGG--CA DroSec_CAF1_left TGAA--AAGTCTCCTACCTTGCGCGCTAATCAGTGACCGGGGCTTGTTTT-----TTATATACAGTCAGGTACCTGAAGTAGCGCGCGTGGTG-GCAGACATATATCTCCATCT-C--CG DroSim_CAF1_left TGAA--AAGTCTCCTACCTTGCGCGCTAATCAGTGACCGGGGCTGGTTTT-----TTATATACAGTCAGGTACCTGAAGTAGCGCGCGTGGTG-GCAGACATATATCTCCATCT-C--CG DroVir_CAF1_left TGCG--CCGTCTTTTACCGTGCGCGCTAATCAGTGACCGGGGCTGGTTTTGGT--TATCCCACAGTCAGGTACCTGAAGTAGCGCGCGTGGTGGCCAGACGTATTCATCTTAAG-C--TT DroYak_CAF1_left TGAACAGAGTCTCCTACCTTGCGCGCTAATCAGTGACCGGGGCTGGTTTT-----TTATATACAGTCAGGTACCTGAAGTAGCGCGCGTGGTG-CCAGACATATATCTCCAACT-CCACG DroWil_CAF1_left CGCC--TTGTCTCTTACCTTGCGCGCTAATCAGTGACCAGGGCTGAGTAATTTTATTCAATACAGTCAGGTACCTGAAGTAGCGCGCGTGGTT-TTAGACCAAGATTCATCGCA-C--GA DroAna_CAF1_left A-AAGT-ATATAATGCAAATCCTTCAGAAAATCCC-A-CTCGAA--TATGTGTATTTTTGAGAAATATGTCTCCCATGTCTATTGT-ACTTCA----TCAG--GT DroEre_CAF1_left C-CATATAAATAAGACAAATGCT-CGCAGGCGAGT-C-CTCGAAAGAAATCCC--ATGTGTATCAACTGTCTCCCATGTCTATTGT-ACTTCA----TCAGG-TG DroGri_CAF1_left C-CTGCTCAGCA-AACATCGGCA-AACATTTCATG-T-CTCCCATGTCTATTG-----TACTTCATCAGGTGCTCTGGTGTCACTC-GTAACCCGGCACATGTTG DroMel_CAF1_left C-CATATAAATAAGCGAAATGCT-CGCAGGCGAGT-C-CTCGCCAGAAATCCC--ATGTGTATCAACTGTCTCCCATGTCTATTGT-ACTTCA----TCAGG-TG DroMoj_CAF1_left G-CAATTCTAGCATTCTA-CGCC-AGATGGCAATC-T-ACTTGTGTCTCCCCC--ATGTCTATTGTACTTCATCAGGTGCTCTGGTGTCAGTG---GAAACC-CG DroPer_CAF1_left T-CATCGTTTCTAGGGAATACTA-TAAATATTCCA-TGTGTCTCCCATGTCTA--TTGTACTTCATCAGGTGCTCTGGTGTGTCCT-GTAACC----CGGCA-CA DroPse_CAF1_left T-CATCGTTTCTAGGGAATACTA-TAAATATTCCA-TGTGTCTCCCATGTCTA--TTGTACTTCATCAGGTGCTCTGGTGTGTCCT-GTAACC----CGGCA-CA DroSec_CAF1_left T-CATATAAATAAGCCAAATGCT-CGCAGGCGAGTTC-CTCGCCAGAAATCCC--ATGTGTATCAACTGTCTCCCATGTCTATTGT-ACTTCA----TCAGG-T- DroSim_CAF1_left C-CATATAAATAAGCCAAATGCT-CGCAGGCGAGT-C-CTCGCCAGAAATCCC--ATGTGTATCA-CTGTCTCCCATGTCTATTGT-ACTTCA----TCAGTGCT DroVir_CAF1_left ACCATGCCTCCC-TCAGATGGCA-AACGTTTCATG-T-CTCCCATGTCTATTG-----TACTTCATCAGGTGCTCTGGTGTGACTT-GTAACCCGGCACATGT-T DroYak_CAF1_left A-TATATAAATAAGCCAAAAGCT-CGCAGGCGAGT-C-CTCCAAAGAAACCCC--ATGTGTATCAACTGTCTCCCATGTCTATTGT-ACTTCA----TCAG---G DroWil_CAF1_left C-GACGGCGACAA--CGACGACA-CAACAAAAAAA-C-CATTTTAATCCATTT--GGGATTTACCCCAAAGTTTTATTTGATTCTC-TTTTTT----TTTTA-TT