CLUSTAL W --- LocARNA 1.4.8 - Local Alignment of RNA DroEre_CAF1_left ATTTTCATGCTCATGT------AATGATATAAACAAAATCAGACGCTTGTTACCGTTTATACTT--GTGGAGTT-CAATTATGCAT-TG-TTTT-AATTTTTTT--GGAA-A------T- DroMel_CAF1_left TTTT-CATGCTCATGT------AATGATATAAACAAAATCAGACACTTGTTACCGTTTTTATACTTTTTGTGTT-CAATTATGCTT-TTTTTTT-GGAATTTTC--AAAT-TGTT-TTTT DroMoj_CAF1_left AGAA-T--TTTTTTTATTT-TATTATTATTATTTTTTTTTTTTAATATTAAATTTACT-TTAACAATTTTTAGG-CTATCTTAGTT-TT-TTGT----TTTTTT--ATTAATTTT-TTTT DroSec_CAF1_left TCA--T--GATTATGT------AATGATATAAACAAAATCAGACACTTGTTACCGTTTTAATACTTCTTGTGTT-CAATTATGCAT-TT-TTGT----TTGTGG--AATT-TTAA-AAT- DroSim_CAF1_left TTCA-T--GCTCATGT------AATGATATAAACAAAATCAGACACTTGTTACCGTTTTAATACTTCTTGTGTT-CAATTATGCGT-TT-TTGT----TTGTGC--AATT-TAAA-ATTG DroYak_CAF1_left TGAT-T--TTCATGCTCAT-GTAATGATATAAACAAAATCAGAGGCTTTTTACCGTTT-TATACTTGTTG-AGTTCCATT-ATGC-------------CTTTTT--TTTCATTTT-TA-- DroAna_CAF1_left CTTT-G--ATTTCTTCATT--TTTTTATTATTTTTTTTTTTTTTGCTGTAATTT--G---CT-GAAAAATCACT-AATTAATATT------ATAAT--TTTATT--TGTAATTTTTTGAT DroGri_CAF1_left TTAA-T--GGTATGAGGAA-ACACTTAAATGAATAAACACGTGCGCTGTGGTGCAAAA--ATATGTATTGATTT-CAATTTAAAGT-----TGA-T--TTGTTTTTTTG--TGATATTTT DroPer_CAF1_left AACG-A--AATAAACACTT-GCAACGTTACAATAAGCACTGTTTTGTCATTTTT------CCATGTTTGATGTT-TCATCTTTCTT-----CGA-T--TATTTTATTCG--CCTTGGATG DroPse_CAF1_left AACG-A--AATAAACACTT-GCAACGTTACAATAAGCACTGTTTTGTCATTTTT------CCATGTTTGATGTT-TCATCTTTTTT-----CGA-T--TATTTTATTCG--CCTTGGATG DroVir_CAF1_left TGTT-A--ATTTTGTTCAA-TGATAAATGTAATGAAAATTGCGCCGTGCTTATTATTA--ATATGTAAATGTTA-TTAGTTTTAAT-----CAA-T--TTATTTTTGAT--GAATGTTTT DroWil_CAF1_left TATT-A--AAATTTATCTTCTGTCTTAGCCATTTCGTAGTTTGTAGCAATTAATA-----TTAAAATTTAAGCA-CAAATT-TGTTTA---ACACT-ATTTTCC--TGTTAATTTGTCAA DroEre_CAF1_left --TGTGCTTTTTTTTTGTCTTGAG-CATCGCGTCGCTCCTCAAAGCTGGCTGTGATATGAATAGGCATAAAAAGGCAAACATTTCACAACCACTTTGAAGAATGACACAATTCTCCTACT DroMel_CAF1_left GATTGATTTTTTTTTTGCCTTGAG-CATCGCGTCGCTCCTCAAAGCTGGCTGTGATATGAATAGGCATAAAAAGGCAAACATTTCACAACCACTTTGAAGAATGACACAATTCTCCTGTT DroMoj_CAF1_left TCATGTTTTGAATTTTGTACTGAG-CATCGTGTCGCTCCTCAAAGCTGGCTGTGATATGAGTAGGCAGAAAAA-GCAAACATTTCACAACCACTTTGAAGAATGACACAATTCTCTCTCT DroSec_CAF1_left --TGTGATTTTTTTTTGCCTTGAG-CATCGCGTCGCTCCTCAAAGCTGGCTGTGATATGAATAGGCATAAAAAGGCAAACATTTCACAACCACTTTGAAGAATGACACAATTCTCCTGTT DroSim_CAF1_left TGATTTTTTTTTTTTTGCCTTGAG-CATCGCGTCGCTCCTCAAAGCTGGCTGTGATATGAATAGGCATAAAAAGGCAAACATTTCACAACCACTTTGAAGAATGACACAATTCTCCTGTT DroYak_CAF1_left AATTGCGATTTTTTTTGTCTTGAG-CATCGCGTCGCTCCTCAAAGCTGGCTGTGATATGAATAGGCAGAAAAAGGCAAACATTTCACAACCACTTTGAAGAATGACACAATTCTCTTGCT DroAna_CAF1_left TT--TTTTTTTTTTTTGTCTTGAG-CATTGCGTCGCTCCTCAAAGCTGGCTGTGATATGAATAGGCATAAAAAGGCAAACATTTCACAACCACTTTGAAGAATGACACAATTCTCCTGTG DroGri_CAF1_left CAATCTTTTTTTTTTTGTGTTGAG-CATCGTGTCGCTCCTCAAAGCTGGCTGTGATATGAGTAGGCATAAAAAGGCAAACATTTCACAACCACTTTGAAGAAGGACACAATTCTCTCTCT DroPer_CAF1_left GT---TTATTTCTTTTGTCTTGAG-CATCGTGTCGCTCCTCAAAGCTGGCTGTGATATGAATAGGCATAAAAAGGCAAACATTTCACAACCACTTTGAAGAATGACACAATTCTCCTTGG DroPse_CAF1_left GT---TTATTTCTTTTGTCTTGAG-CATCGTGTCGCTCCTCAAAGCTGGCTGTGATATGAATAGGCATAAAAAGGCAAACATTTCACAACCACTTTGAAGAATGACACAATTCTCCTTGG DroVir_CAF1_left TG---TTTTTGTTTTTGTGCTGAG-CATCGTGTCGCTCCTCAAAGCTGGCTGTGATATGAGTAGGCATAAAAAGGCAAACATTTCACAACCACTTTGAAGAATGACACAATTCTCTTTCT DroWil_CAF1_left TTTTTTTTTTAAATGTAACTTGAGCCATTGCGTCGCTCCTCAAAGCTGGCTGTGATATGAATAGGCATAAAAAGGCAAACATTTCACAACCACTTTGAAGAATGACACAATTCTCCTGCC DroEre_CAF1_left TCG-ATTCGA--TGAGAGC---CGAGGTTCAGATT-C-----A-GATGGAGACCCGTC-TTCT--CCTAGAGTCTTTTAGCAACGTTCT-CACGGCCA-TGG-GCTTGGAGCCTT----- DroMel_CAF1_left TCG-ATTCGA--TGAGAGC---CGAGGTGCAGATT-C-----A-GATTCAGATTCTTC-TAGG-------GGTCTTTTTGCAACGTTCT-CACGGCCG-TCG-GCTTTGAGCCTTGTAC- DroMoj_CAF1_left TGG-TCTCTC--ACTCGGC---CGCGCTCCCGCTC-CCGCTCT-CGCTCTCTCCCTTGCTGTT--CGT--------TGAGTGGAGA-CT-CTCTCCCC-CGA-CCTTTT--TGTTAACC- DroSec_CAF1_left TCG-GTTCGA--CGAGAGC---CGAGGTTCAGATTCAGATTCA-GATTGAGACCCGT-CTTCT--TCT--------AGAGTCTTTTTGC-AACGTTCT-C-A-C---GG--CCGTCTGCT DroSim_CAF1_left TCG-ATTCGA--CGAGAGCCGCCGAGGTTCAGATTCAGATTCA-GATTGAGACCCGT-CTTCT--TCT--------AGAGTCTTTTTGC-AACGTTCT-C-A-C---GG--CCGTCGGC- DroYak_CAF1_left TCG-ATTTGA--TGAGAGC---CGAGGTTCAGATT-CAGATTG-AGATTCTTCCTTT-AGAAT--CTT--------TTAGCGACGTTCT-CACGGCCA-TGG-ACTAGG--AGCCTTGT- DroAna_CAF1_left GGA-TGGCGC--CGAGGTC---AAGGTTCAGATTC-AAAATTG-A-GACGACTCTTCTTCGAG--T----------TCTATTGCGTTCT-CACGGCCA-CGGACGCCAGA-GATCTTTG- DroGri_CAF1_left CTC-TCTCAC--TCTCTCA---CTCACTCACTCTC-TCTCGCT-C-GCTCTCTCTCTCTCGCT--C----------GCTCTCTCTCTCTTGTCTCCTTGCC--CCACTTC-TCTCCTCT- DroPer_CAF1_left CCC-GGACAC--GGGGGCC---CCGAGACCCGAGG-CTTTGGG-T-TCTTTGGGTTCGATGAT--G----------TCTTCCGAGTGCCAGAGAGCCC-CC--TGATCGT-GCGCTTGG- DroPse_CAF1_left CCC-GGACAC--GGGGGCC---CCGAGACCCGAGG-CTTTGGA-T-TCTTTGGGTTCGATGAT--G----------TCTTCCGAGTGCCAGAGAGCCC-CC--TGATCGT-GCGCTTGG- DroVir_CAF1_left CTC-TCTCTC--GCTCGCT---CGCTCGCTCTTCC-TCACTCAGC-GCTGTGCAATGCACATG--C----------GCACACACTCTCTGT-CCTCTCGCT--CTTTCAC-ACATACTG- DroWil_CAF1_left TCCTCC-GCCACCATCCT-----GCGCGACGGCGA-CCACTTG-A-AATGCACTTTACCATTGGGT----------GGACGCGACTTTTGTACTGGGA-TG--GGAGG-A-GGACGATG- DroEre_CAF1_left ----GTA DroMel_CAF1_left --T-TTT DroMoj_CAF1_left --T-GCT DroSec_CAF1_left TTG-AGC DroSim_CAF1_left --T-TTG DroYak_CAF1_left --A-CTT DroAna_CAF1_left --C-TTT DroGri_CAF1_left --C-ACA DroPer_CAF1_left --CTGAG DroPse_CAF1_left --CTGAG DroVir_CAF1_left --C-TGC DroWil_CAF1_left --A-TGA