CLUSTAL W --- LocARNA 1.4.8 - Local Alignment of RNA DroEre_CAF1_left AACC-GG---CAAA-AG-CA-ACAA--CCGG-TA--AAATCGAATGTTCACT-T--TGCACACAGACTCACAGATA-------CCC--AGTC-CC-AAATGGCTCACTC---CCACACAA DroMel_CAF1_left C-CG-GC---AAAA-AG-CA-ACAA--CCGG-TA--AAATCGAATGTTCACT-T--TGCACACAGACACACAGATA-------CCC--AGTC-CC-TAATGGCTCACTC---CCACACAA DroPse_CAF1_left A-CA-CA---AACA-CA-CAGGCGC--TCACCCA--CACCCACACCCACACCCACACACACATATATGTACTGGTC-------GCTCCGCCC-GC-ACAAGGGCCCTGC---ACACACAC DroSec_CAF1_left C-CG-GC---AAAA-AG-CA-ACAA--CCGG-TA--AAATCGAATGTTCACT-T--TGCACACAGACTCACAGATA-------CCC--AGTC-CC-TAATGGCTCACTC---CCACACAA DroSim_CAF1_left C-CG-GC---AAAA-AG-CA-ACAA--CCGG-TA--AAATCGAATGTTCACT-T--TGCACACAGACACACAGATA-------CCC--AGTC-CC-TAATGGCTCACTC---CCACACAA DroWil_CAF1_left C-TT-CT---CTCT-TT-TG-ATTT--TCTA-TC--TCACTCACAGTATATC-T--CTCTCACTCGCTCTCTTTCG-------TTC--TTTGATT-GTCTGTCTGTGTG---ATATACTC DroYak_CAF1_left C-CG-GC---AAAA-AG-CA-ACAA--CCGG-TA--AAATCGAATGTTCACT-T--TGCACACAGACACACAGATA-------CCC--ACTC-CC-TAATGGCTCACTC---CCACACAA DroAna_CAF1_left A-AAACCGGCAAAA-AG-CA-ACAA--CCGG-TA--AAATCGAATGTTCACT-T----GG---C-----TCACTCA-------TAC--ACTC-GTACGAGGGCTCCCTTACGGCCAACAC DroPer_CAF1_left A-CAAACACACAGGCGCTCA-CCCACACCCA-CACCCACCCACACACACACA-C----AT---A-----TATGTACTGGTCGCTCC--GCCC-GCACAAGGGCCCTGC----ACACACAC DroEre_CAF1_left T-GTATGT--GTA--TG-----------TG-TGGACG-CTG--GATGTAT-GGGTGTGTGGGCTCTGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACG DroMel_CAF1_left T-GTATGTATGTA--AGCCCAC--TCACAG-AGGACG-CCGGGGATGTAT-GGGTGTGTAGGGTCTGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACG DroPse_CAF1_left A-CATAAA--T-------ATA----T--TCACGGAGA-C-AGT-CTTATGTGTGAGTGTGGGGCCTGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACA DroSec_CAF1_left T-GTATGTATGTA--AGCTCAC--TCACAG-AGGACG-CCGTGGATGTAT-GGGTGTGTAGGGTCGGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACG DroSim_CAF1_left T-GTATGTATGTA--AGCTCAC--TCACAG-AGGACG-CCGTGGATGTAT-GGGTGTGTAGGGTCGGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACG DroWil_CAF1_left CCACATACATTGG--AAAGAGC---TT-CT-CC--GTAATATGTATATGT-ATTGCTGTAAAGTCTGAAATTTTGCACACATTTACAATTATTGTAAATGTGTTGAAAATCGTTTGCACA DroYak_CAF1_left T-GTATGTATGTACATATATAC--ACACAG-AGCAAG-CCGTGGATGTAT-GGGTGT---GGGTCTGAAATTTTGCACACATTTACAGTAATTGTAAATGTGTTGAAAATCGTTTGCATG DroAna_CAF1_left C-CACAC---------GGCGGG--ATATAT-AGG-------GC-TGTGTGTATTGGTAGTGGGTCTGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACA DroPer_CAF1_left A-CATAA---------ATATATTCACGGAG-ACC-------TG-CTTATGTGTGAGTGTGGGGCCTGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACA DroEre_CAF1_left -ACTGCGAGCAAAACA---CGTCGG-AGAAGAAATTACTCTCTCGCTGTGTATGTGTGTGTGGGTGAGT-GTG-TGCCTGTATTTGCTCATTTGTTAAGGGGAAATGGCC-TTTGTCTGT DroMel_CAF1_left -ACTGTGAGCAAAACA---CGTCGG-AGAAGAAATTACTCTCTCGCTGTGTACGTGTGTGTGGGTTAGT-GTA-TGCCTGTATTTGCTCATTTGTTAAGGGGAAATGGCC-TTTGTCTGT DroPse_CAF1_left -ACTGTGAGCAAAACA---CGTCGG-AGTAGAAATCACTCTCTCTCTCTCTCTGTGTGTGTGTGTGTGG-GTG-TGCATATACTTGCTCATTTGTTGAGGGGAAATGGCC-TTTGTCTGT DroSec_CAF1_left -ACTGTGAGCAAAACA---CGTCGG-AGAAGAAATTACTCTCTCGCTGTGTACGTGTGTGTGGGTGAGT-GTA-TGCCTGTATTTGCTCATTTGTTAAGGGGAAATGGCC-TTTGTCTGT DroSim_CAF1_left -ACTGTGAGCAAAACA---CGTCGG-AGAAGAAATTACTCTCTCGCTGTGTACGTGTGTGTGGGTGAGT-GTA-TGCCTGTATTTGCTCATTTGTTAAGGGGAAATGGCC-TTTGTCTGT DroWil_CAF1_left AACTGTGAGCAAAATCCTGTAGCTGGGAGTGAAAATATCTCCATGATAAGTGTGTGTGTTTGTGCGTGT-GTG-AGT-GTGTTTTGCTCATTTGTTAAGGGGAAATGACT-TTTGTCTGT DroYak_CAF1_left -ACTGTGAGCAAAACA---CTTCGG-AGAAGAAATTGCTCTCTCGCTGTGTACGTGTGTGTGGGTGAGT-GTG-TGCCTGTATTTGCTCATTTGTTAAGGGGAAATGGCC-TTTGTCTGT DroAna_CAF1_left -ACTGTGAGCAAAGCA---CGTCGG-AGTAGAAATCACTCTCTTTGTGTGTATGTACAAGTGTAGGGAGTGGG-TGGGTGAGTGCTGGTGTGCGGGTGTGCGGGTGTACG-GGTGAGTGT DroPer_CAF1_left -ACTGTGAGCAAAACA---CGTCGG-AGTAGAAATCACTCTCTCTCTCTGTGTGTGTGGGTGGGTGTACGTGTGTGTGTGTGTGTGTGGGTGTGCGTATACTTGCTCATTTGTTGAGGGG DroEre_CAF1_left CTTC--AGCTGGTGTGTGCGGGTGA-CGGGTGGGT DroMel_CAF1_left CTTC--AGCTGGTGTGTGCGGGTGT-GTGGGTGTG DroPse_CAF1_left CTCTCCAGCT--GCTGCGGGTGTGG-GTGCACGAG DroSec_CAF1_left CTTC--AGCTGGTGTGTGCGGGTGT-GCGGATGTG DroSim_CAF1_left CTTC--AGCTGGTGTGTGCGGGTGT-GCGGATGTG DroWil_CAF1_left CTCTC-AA-TGGTATGAGTGAGAATCTGTATGTGT DroYak_CAF1_left CTTC--AGCTGATGTGTGCGGGTGT-GTGTGTGGG DroAna_CAF1_left ATTT--GCTCA-TTTGTTAAGGGGA-AATGGTCTT DroPer_CAF1_left AAAT--GGC---CTTTGTCTGTCTC-TCCAGCTGC