CLUSTAL W --- LocARNA 1.4.8 - Local Alignment of RNA DroAna_CAF1_left TT-----T--GA-GGGGATTCTTGTAG-CACAC--T-TGT-TGGC-GTAGCATTA-------TC--CTTTAACTC-GC-GTC-GCGGATTTGGAT--TATC-----G-TATTTTT-TATC DroEre_CAF1_left AC-------GAACACTTGTTGGCTTAG-C--AT--C-CAA-TCGTTA-TCCCCAA-------T---CGTTATCGC-AC-ACGTAGACATTCGC-A-------------TCGAGCGGGGTC DroGri_CAF1_left GG-----T--GG-GCTTGGTTCGCTCA-CAGTC--T-GCA-GATG-TATGCAAGA-------A---TAAAATAAT-GA-GAT-ACAAACACTTGTT-GGCTT------TGTTGTAATATT DroMel_CAF1_left TC-----ACAAACACTTGTTGGTTTAG-C--AT--C-CAA-TCGTTA-TGCCCAA-------TT--CGCGAACTG-GC-TTT-CTGCATTCGC-A-------------TCGAGCGGGGTC DroPer_CAF1_left TC-----C--AA-ATAGTACGAGCCGA-A-CAC--T-TGT-TGGG-C-ACATGGG-------GC--TGGGGGCTG-GG-GCT-GCACATAGGC-GG-GGTAC------ATACGAGTATGT DroPse_CAF1_left AG---------------TACGAGCCGA-A-CAC--T-TGT-TGGG-C-CCATGGGGCTGGGGGC--TGGGGGCTG-GG-TCT-GCACATAGGC-GG-GGTAC------ATACGAGTATGT DroSec_CAF1_left TTGGATCACGAACACTTGTTGGCTTAG-C--AT--C-CAA-TCGTTA-TACCCAA-------TT--CGCGAACTG-CC-TTT-CTGCATTCGC-A-------------TCCAGCGGGGTC DroSim_CAF1_left GG--ATCACGAACACTTGTTGGTTTAG-C--ATATC-CAA-TCGTTA-TACCCAA-------TT--CGCGAACTG-CC-TTT-CTGCATTCGC-A-------------TCCAGCGGGGTC DroVir_CAF1_left TG-----G--GT-TGGTCTTTACGTAT-C--GA--A-GC--GACG-TTATCTATC-------A---C--CGTAAT-AA-GAT-GCAAACACTTGTT-GGGTTTGTTGTAGTCCTGTTT-A DroWil_CAF1_left CT-----T--CA-TCCATTATGCGTATGC-AGT--TGTTC-GC-T-C-TCTCTCG-------GT--CGCTCGCTC-TCTGTC-TCT-GTTGGC-TG-GTACT------CCCAGAGTGTGT DroYak_CAF1_left CG--------AACACTTGTTGGCTTAG-C--AT--C-CAA-TCGTTA-TCCCCAA-------TT--CGCGAACTG-GC-TTT-CTACGTTCGC-A-------------TCGAGCGGGGTC DroMoj_CAF1_left CA-----A-ACACTTGTTGGTTGTGTT-T--GT--TGTAGTCCTG-TTTACCGGT-------GCGGCGACTCAACACC-TAT-AAATTTTGTT-TCCGTTTT------TTTTTTTTTTTT DroAna_CAF1_left G-TAG-----AA--AAATCAGTTT-CAATCGGAATCTAGGCTTATTGCAATGCCCATCAAAGCTGGCTGTGATACACTTCAAATGCAGAAATATCTC--TTCAGCCCTTTTTGATGACAT DroEre_CAF1_left C-CAGGTCACAGGTCACAGGTCACA--CTTGCCATCGATGCTCATTGCAATGCCCATCAAAGCTGGCTGTGATACGATTCAAATGCAGAAATATCTTTCTTCAGCCCTTTTTGATGACAT DroGri_CAF1_left G-TTG-----GC--GAAGTAATACTCTTTTTGCTACATTGCCCTTTGCAATGCCCATCAAAGCTGGCTGTGATACGATTCAATTGCAGATATATCATT-CTCAGCCCTTTTTGATGACAT DroMel_CAF1_left A-TAGGTCACGC--CACGGGTCACAT-TTTGCTATCGCTGCTCATTGCAATGCCCATCAAAGCTGGCTGTGATACGATTCAAATGCAGAAATATCTTTCTTCAGCCCTTTTTGATGACAT DroPer_CAF1_left A-CAT-----TT--TTTGTGACGCGAAACTGCAATCGATGCTCATTGCAATGCCCATCAAAGCTGGCTGTGATACGCTTCAAATGCAAATATATCTTTCTTCAGCCATTTTTGATGACAC DroPse_CAF1_left A-CAT-----TT--CTTGTGACGCGAAACTGCAATCGATGCTCATTGCAATGCCCATCAAAGCTGGCTGTGATACGCTTCAAATGCAAATATATCTTTCTTCAGCCATTTTTGATGACAC DroSec_CAF1_left A-TAG-----GT--CACGGGTCACAC-TTTGCTATCGCTGCTCATTGCAATGCCCATCAAAGCTGGCTGTGATACGATTCAAATGCAGAAATATCTTTCTTCAGCCCTTTTTGATGACAT DroSim_CAF1_left A-TAG-----GT--CACGGGTCACAC-TTTGCTATCGCTGCTCATTGCAATGCCCATCAAAGCTGGCTGTGATACGATTCAAATGCAGAAATATCTTTCTTCAGCCCTTTTTGATGACAT DroVir_CAF1_left T-GGC-----GT--TATTTGTTACTT-TTCTGCTACGTTGCCCTTTGCAATGCCCATCAAAGCTGGCTGTGATACGATTCAATTGCAGATATATCATT-CTCAGCCCTTTTTGATGACAT DroWil_CAF1_left G-GCG-----AAT-AATGAGGGGAAAAATGCAAAACGATGCTCATTGCAATGCCCATCAAAGCTGGCTGTGATACGCTTCAAATGCAAAAATATCTTTCTTCAGCCCTTTTTGATGACAT DroYak_CAF1_left GAGCGTTCACAGGTCACAGGTCGCA--CTTACTATCGATGCTCATTGCAATGCCCATCAAAGCTGGCTGTGATACGATTCAAATGCAGAAATATCTTTCTTCAGCCCTTTTTGATGACAT DroMoj_CAF1_left T-CTC-----TCT-TACTGTTAATGT-TACTGTTACTTCGCCCTTCGCAGTGCCCATCAAAGCTGGCTGTGATACAATTCAATTACAGAAATATCATTC-TCAGCCCTTTTTGATGACAC DroAna_CAF1_left TGAAAGTAAGAT-TCGTAGATACGTCGCTAAACGCAACTGC--ACA-CACACA-CA--CACAT-ATACACAC-ATATATACGCACACAAAT-AG-AAATTGACGTAACCGAGACTGCGAC DroEre_CAF1_left TGAAAGTAAGAT-ACGAGGTAACGTCGACACACACACACCG--TCA-CACACCGCA--CACAC-CCACAGGA-GGGTATTATTTCAAAGGA-AACCGAC-GTAATTCACGTAACCGG-CG DroGri_CAF1_left TGAAAGTAAGAC-ATGTACACACAAACACACACACACACAC--ACA-CACACA-CA--AAAAC-ACACACAC-ACAGAGAGAGAGAGAGAG-AG-AAGCACACTGATGTAAACGAACTCT DroMel_CAF1_left TGAAAGTAAGAT-ACGAGGTAACGTCGACGCACACACACCA--TCA-CACACATCG--CACAC-ACACACAC-ACACACAGCTGCAAAGGA-AACCGAT-GTAATTCACGTAACCGG-CG DroPer_CAF1_left TGAAAGTAAGGA-TACCAAGTGCCGATACGCACGCACACAC--ACA-CACGCA-CACGCACAC-GGACGCAATGCACCAACACCCACACCC-AC-ACGCGCCTCAATGCAAT--GTTCAC DroPse_CAF1_left TGAAAGTAAGGA-TACCAAGTGCCGATACGCAAGCACGCAC--GCA-CACACA-CG--CACAC-GCACGCAATACACCAACGCACACACCC-AC-ACGCGCCTCAATGCAAT--GTTCAC DroSec_CAF1_left TGAAAGTAAGAT-ACGAGGTAACGTCGACGCACACACACAC--AGCTGCA--GGAG--GGCAT-TATTTCAA-AGAAAACCGATGTAATTC-ACGTAACCGGCGACGACGTAAGGCG-TT DroSim_CAF1_left TGAAAGTAAGAT-ACGAGGTAACGTCGACGCACACACACCA--TCA-CAA--GTCG--CACAC-ACACACAC-ATCTGCAGGAGGGCATTA-TTTCAAAGGAAACCGATGTAATTCACGT DroVir_CAF1_left TGAAAGTAAGAC-ATGTACACACACACGCGCACACACACAC--ACA-CACACA-CA--GGCAC-GCACGCAC-TCGAACTCTTATAAATTC-AC-GTAACCAAGACGTTAACCGGCAATC DroWil_CAF1_left TGAAAGTAAGAC-G-CAATTCACACACACACACATGAACACAGACA-TAGACA-CA--CAG---GATGGGGATACACTGCACTGCTTATAA-AT-TATCCTGGTAAACGAACTCCAAATA DroYak_CAF1_left TGAAAGTAAGAT-ACGAGGTAACGTCGACGAACACGCACAC--ACA-CACACCCGT--CACATAACACACAC-ACCCGATGTAATTCACGT-AACCGGC-G-ACGACGTAAGGCGTT-TA DroMoj_CAF1_left TGAAAGTAAGACCAAGCATGTACACACAAACATACACACTC--ACA-CATACA-CT--GGCAC-ACCCGTGT-AAACGAACTCTAATACAATTC-ACGTAACCAAAGACGTTA-G-CCGG DroAna_CAF1_left CGG-- DroEre_CAF1_left ACG-- DroGri_CAF1_left AAT-- DroMel_CAF1_left ACG-- DroPer_CAF1_left GTA-- DroPse_CAF1_left GTAAC DroSec_CAF1_left TAG-- DroSim_CAF1_left AAC-- DroVir_CAF1_left TGG-- DroWil_CAF1_left TGT-- DroYak_CAF1_left GGG-- DroMoj_CAF1_left CAG--