CLUSTAL W --- LocARNA 1.4.8 - Local Alignment of RNA DroEre_CAF1_left CGGTTTCTTTGC-AA----------TTG-CAA-TTCACTATAAATTTAT-GTGTA-TATT----TAAGGCGGACAGAGTGT-G----TTTTATGATGG-GCG----TGTGATTATTATGT DroGri_CAF1_left GTGTTTCC-AAT-TC----------CAA-TTC-CTGGCGTCGCTGTGTA-A-ACT-GCGGGAAATGTGG---GT-GCAAGA-AGAAATTACA----TT-ATGA--TTGATTCGATTGATT DroMel_CAF1_left GTTTATTT-TCC-GA----------TTG-CAT-TTCACTACAAATATTA-T-ACA-GATT----TGAGGCGGACATAGTGT-G----TTTTATTTATG-ATGG--GCGTGTGAATTATGT DroMoj_CAF1_left CATATTTG-GTC-ACA---------ATT-TAC-TTGATGACTTGCTTCC-A-ATT-CCAT----GTCCGTCTTCAACGAAT-G----TA--ATTTGAG-TGCG--ACCTACATTATGATT DroPer_CAF1_left TC--------CG-TA----------TAG-TA--TCCACCATATAGAGAT-G-CAA-G-TG----CGTGTCGGGGTGTGCTG-C----ATGGT-GGCGG-GGGG--GCGGTGGAGGGGAGG DroPse_CAF1_left TACACCCT-CCG-TA----------TAG-TA--TCCACCATATAGAGAT-G-CAA-G-TG----CGTGTCGGGGTGTGCTG-C----ATGGT-GGCGG-GGGG--GCGGTGGAGGGGTGG DroSec_CAF1_left GTTTCTTT-TCA-GA----------TTG-CAT-TTCACTACAAATATTC-T-ACA-GATT----TGAGGCGGTCAGAGTGT-G----TTTTATTTATG-ATGG--GCGTGTGAATTATGT DroSim_CAF1_left GTTTCTTT-TCA-GA----------TTG-CAT-TTCACTACGAATATTC-T-ACA-GATT----AGAGGCGGACAGAGTGT-G----TTTTATTTATG-ATGG--GCGTGTGAATTATGT DroVir_CAF1_left TTCCGATT-CCA-GC----------CCA-TTC-CAAATTCCA--TTCCT-A-ACTGGGCT----TGATGTAGGTGCAAGGT-A----CGTTATGAATTGATTTTATTGATTGACTGATTG DroWil_CAF1_left TTTTTATT-TTC-TT----------TGG-TTCACCAATAACGAATATCC-A-TCT-CACT----AGAGTTAAAATGAGCGC-G----GTGAAAGAATG-AAGAAGATTCAATTTTTAAAT DroYak_CAF1_left GTTCGCCA-TGG-CTTCTTTTCGGATTG-CAA-TTCACTATAAATTTATAT-GTA-TATT----TGAGGCGGACAGAGTGT-G----TTTTA----TG-ATGG--GCGTGTGA------- DroAna_CAF1_left CTAAAAAA-AAAATA----------TTGACAA-AAAAAAAATTTAATTA-A-ATG-AAAA----ATAATATAAA-TACCGAAG----AAAATGTGCTG-GTGA--GAGTGTCAAAGAGGG DroEre_CAF1_left GG-----------CGGG--AAGTAT-----TACCATGATTTGATGTACGATACATTACGCTAAGCTCATCAAAGCTGGCTGTGATATGCCGCGCAAAGCTG----A-TATGCATTTCACA DroGri_CAF1_left -G-----------ATTG--ATTCGA-----TTCGATTATTTGATGTAGTTTACATTACGCTAAGCTCATCAAAGCTGGCTGTGATATGC-GCGCAAAGCTTTCAAA-AATGCATTTCACA DroMel_CAF1_left GG-----------CGGG--AGGTAT-----TATTATGATTTGATGTACGATACATTACGCTAAGCTCATCAAAGCTGGCTGTGATATGCCGCGCAAAGCGG----A-AATGCATTTCACA DroMoj_CAF1_left GA-----------CTTG--ATTTGA-----TTTGATTGATTGATGTACGTTACATTACGCTAAGCTCATCAAAGCTGGCTGTGATATGCT-CGCAAAGCTTTCA-A-AATGCATTTCACA DroPer_CAF1_left GATACATACGT-ATTAC--GTATAT-----TATGATTGATTGATGTACGATACATTACGCCGAGCTCATCAAAGCTGGCTGTGATATGCG-GGCAAAGCA-----A-AATGCATTTCACA DroPse_CAF1_left GATAC--------ATAC--GTATAT-----TATGATTGATTGATGTACGATACATTACGCCGAGCTCATCAAAGCTGGCTGTGATATGCG-GGCAAAGCA-----A-AATGCATTTCACA DroSec_CAF1_left GG-----------CGGG--AGGTAT-----TATCATGATTTGATGTACGATACATTACGCTAAGCTCATCAAAGCTGGCTGTGATATGCCGCGCAAAGCGG----A-AATGCATTTCACA DroSim_CAF1_left GG-----------CGGG--AGGTAT-----TATCATGATTTGATGTACGATACATTACGCTAAGCTCATCAAAGCTGGCTGTGATATGCCGCGCAAAGCGG----A-AATGCATTTCACA DroVir_CAF1_left AT-----------TGAT--TGATTG-----ATCGATCGATTGATGTACGTGACATTACGCTAAGCTCATCAAAGCTGGCTGTGATATGCG-CGCAAAGCTTTC--A-AATGCATTTCACA DroWil_CAF1_left GA-----------TTTT--TTGATTGATCGATTGATTGATTGATGCAATTCACATTACGCAGAGCTCATCAAAGCTGGCTGTGATATGCTGGATAAAGCAA----ATAATGCATTTCACA DroYak_CAF1_left -T-----------TATT--ATGTAA-----AACCATGATTTGATGTACGATACATTACGCTAAGCTCATCAAAGCTGGCTGTGATATGCCGCGCAAAGCGG----A-AATGCATTTCACA DroAna_CAF1_left CG-----A-GTATTATGATTGATTG-----ATTGATTGATTGATGTACGATACATAACGCTAAGCTCATCAAAGCTGGCTGTGATATGCG-GGCAAAATGG----A-AATGCATTTCACA DroEre_CAF1_left ACCACTTTGAGAGCCCAGCATGAATGCGCCAATATAGTTTTATTGATTGAGGTTTCGGGATATTT-GACTGCGGGA-GTT-T-AGAATTTTCAATTTTGATTTTCA-TGCTCA--TGT-A DroGri_CAF1_left ACCACTTTGAGAGCGCAGCATGAATGTGCCAATCTTAGATA-TGCTTGAAAAATAACGATAAATG-TTCAGATAGA-TAT-AGATATATAGGAGGGGTGGTTGGCTGGGTGGG--TGG-T DroMel_CAF1_left ACCACTTTGAGAGCCCAGCATGAATGCGCCAATATAGTTTTATTGATTGAGGTTTCGGGATACTT-GACTGCGGGA-GTT-C-AGAATTTTCAATTTTGGTTTTCA-TGCTCA--TGT-A DroMoj_CAF1_left GCCTCTTTGAGAGCTCAGCATGAATGTGGCCAATTCTTATGATAGAAAGAGGTACAGG-TATATA-GATAGATAGA-T-A-A-ATATTTTGATGATATTTTGATTT-GTAAAA--GGAGG DroPer_CAF1_left ACCACTTTGTGAGCCCAGCATGAATGTGCCAATAGTTTTG--TAG--ATAGGATTCAGGATCATT-GACTGCGGGA-CTT-T-AGAATTTGCAATTTCGATTAAT---GCTGA--TGT-A DroPse_CAF1_left ACCACTTTGTGAGCCCAGCATGAATGTGCCAATAGTTTTG--TAG--ATAGGATTCAGGATCATT-GACTGCGGGA-CTT-T-AGAATTTGCAATTTCGATTAAT---GCTGA--TGT-A DroSec_CAF1_left ACCACTTTGAGAGCCCAGCATGAATGCGCCAATATAGTTTTATTGATTGA--TTTCGGGATACTT-GACTGCGGGA-GTT-C-AGAATTTTCAATTTTGCTTTTCA-TGATTA--TGT-A DroSim_CAF1_left ACCACTTTGAGAGCCCAGCATGAATGCGCCAATATAGTTTCATTGATTGAGGTTTCGGGATACTT-GACTGCGGGA-GTT-C-AAAATTTTCAATTTTGGTTTTCA-TGCTCA--TGT-A DroVir_CAF1_left ACCACTTTGAGAGCGCAGCATGAATGTGCCAATCTTA-TGGTAAGAAGAA--GACTGATGCATGT-GTGGGATAGATAAA-C-AGTTAGATAGACATTTAAAGGGA-TCAACA--GAG-T DroWil_CAF1_left ACCACTTTGTGAGCTCAGCATGAATGTGTCGTGTGTTTTTCTTT-AATTTTTGGTTGT-TGTTCTATATGTTTGAA-TGC-C-AGCCAATATAAAATATAACTTTT-CGCTAA--TAA-T DroYak_CAF1_left ACCACTTTGAGAGCCCAGCGTGAATGCGCCAATAG--TTTTATTGATTTAGGTTTCGGGATATTT-GACTGCGGGA-TTT-T-AGAATTTTCAATTTTGATTTTCA-TGCTCA--TGT-A DroAna_CAF1_left ACCACTTTGTGAGCCCAGCAGGAATGTGCCAATATTTTTG--TTG--TAATTTTCAGATACAGGA-TTCGGAATCG-GTATC-GGGATAATTGACTGCGGGAGAAT-TACGGAATTTC-C DroEre_CAF1_left ATGATATAAAC-AAA----ATCAGACGCTTG-TTACC--GTT DroGri_CAF1_left TTATCAATTTT-GTT----CAATGATTAATGGTATGA--GGA DroMel_CAF1_left ATGATATAAAC-AAA----ATCAGACACTTG-TTACC--GTT DroMoj_CAF1_left AGGGCACCATGATTT----ATAATTTTGTTC-AATGA--TTT DroPer_CAF1_left ATGATATTAAC-GAAATAAACACTTGCAACG-TTACA--ATA DroPse_CAF1_left ATGATATTAAC-GAAATAAACACTTGCAACG-TTACA--ATA DroSec_CAF1_left ATGATATAAAC-AAA----ATCAGACACTTG-TTACCGTTTT DroSim_CAF1_left ATGATATAAAC-AAA----ATCAGACACTTG-TTACC--GTT DroVir_CAF1_left GGGGGAGAGGG-TTT----GGTTGGTGTGTT-AATTT--TGT DroWil_CAF1_left AGAAATTAGGT-AAG----TTTATATTAACA-TTTTA--AAC DroYak_CAF1_left ATGATATAAAC-AAA----ATCAGAGGCTTT-TTACC--GTT DroAna_CAF1_left AATTTCGATTT-CAA----TGCTGAG-ATGT-GAGAG--AGA