CLUSTAL W --- LocARNA 1.4.8 - Local Alignment of RNA DroAna_CAF1_left T-CT-----CGC-TCGCACACGACGCCATTCTAACGGTACCTCATTTTC-C-GAGAA-AATAA--A----TTCTGAGCTTCTCA-AAAATGAAGTTTTTCCTTAGAAGTTTTACCT-GT- DroEre_CAF1_left AACCGTATCAGC-TGTCATCTCGCTCGCACATAACGGAATGTGCATTTC-C-AAGAA-AAGTC--C--A-AATT-GATTATATA-ATTTTATGATT---TCACAGATATTCA---A-GT- DroMel_CAF1_left A-CCGCAACAGC-TGTCATCTCGCTCACACCTAACGGATTGCGGATTTC-C-GAGAA-AAGCG--C--A-ACTGGATTTTTATA-ATTTTACGATT---TCACAGATTTAAA---T-GT- DroMoj_CAF1_left GGACTCTACTTT-TATGCATACATATTCGTGCACAAAAACGCCGCGGTA-C-AATTT-CTATT--TACA-TACA-GACATACCATAGAATTATGAA---TTATGTACATAGT---T-GA- DroPer_CAF1_left C-TTTGTGCGCTGCTACACGGCTGTTCCGTATAACGGATTTTATTCCTCAC-GAAAG-GAATT--T--T-AAAGAGAAAAATGA-AAAACAC--TC---TGGTGCTATT-TT---TAGA- DroPse_CAF1_left C-TTTGTGCACTGCTACACGGCTGTTCCGTATAACGGATTTTATTCTTCAC-GAAAG-GAATT--T--A-AAAAGAAAAAGGGA-AAAACAC--TC---TGGTGCTATT-TT---TAGA- DroSec_CAF1_left A-CCGCAACAGC-TGTCATCTCGCTCACACCTAACGGAATGCGGATTTC-C-GAGAA-AAGCG--C--A-ACTTGCGTTATATA-ATTTTATGATT---TCACAGATATTAA---A-GT- DroSim_CAF1_left A-CCGCAACAGC-TGTCATCTCGCTCACACCTAACGGAATGCGGATTTC-C-GAGAA-AAGCG--C--A-ACTTGCGTTATATA-ATTTTATGATT---TCACAGATATTAA---A-GT- DroVir_CAF1_left T-CGCTCGCACTTGCTGCCATTAAAGCCGATCGTCGTCCTAACGGGACTAT-GCTCTTCAACA--C--ATACATACATACACGC-AGTACAT--TT---ATATTTATATTTG---ATGAA DroYak_CAF1_left A-CCGTAACAGC-AGTCATCTCGCTCGCACCTAACGGAATGTTCATTTC-C-AAGAA-AAGCC--C--A-AATTGAATTATATA-ATTTTATGATT---TCACAGATATCCA---A-GT- DroWil_CAF1_left C-AATTGTTGAA-TTTTAT-A--TCCAAACATATTTGACAAGTCC-GTC-CAAAGAA-TGTTTGAA--A-ATTTGTGGTCATTG-ACTCCTTCTTT---TTCCCCACCCGGG---A-TG- DroAna_CAF1_left AGGAACATT-TA-CACTTATAGGCCGGGAGGTGTGCAATATA---TGTTTATAA-----AATATA-TATATTGTCA-CGCTCCCCGT--CCTGCAAGTG-TTT-ATGTT--TTGCTATTT DroEre_CAF1_left TGAAACACTGGA-CATTTAAAGGGCGGGAAGTGTGCAATATA---GC-T-AAGA-----GATCAA-TACATTGACA-CACGACCCGT--CCTGCAAATA-TTT-GTGTA--TTTGCAAG- DroMel_CAF1_left TGAAACATTGGA-CATTTAAAGGCCGGGAAGTGTGCAATATA---GC-T-AAGA-----TATAAA-TACACTGACA-CACGACCCGC--CCTGCAAATG-TTT-ATGTT--TTCGCAAAC DroMoj_CAF1_left ATTGTGCATTTA-CACTTGTAGGCCGGGAGATGTGCAATATG---AT-A-AATACAATTTAAATA-CATATTGTCA-CATAGCACGG--CCTAAAAATG-GAT-ACATT--TAAACGATA DroPer_CAF1_left CG-AGGCAATCAAAT-TTAGAGGCAAGAAAAAGTGCAATATT---AATT--AA-------AGAGA-AATATTGAAA-CTGATTTTTG--CCTATAA-ATGTTT-TGC-AGCTTATCACA- DroPse_CAF1_left CG-AGGCAATCAAAT-TTAGAGGCAAGAAAAAGTGCAATATT---AATT--AA-------AGAGA-AATATTGAAA-CTGATTTTTG--CCTATAA-ATGT-T-TGTCAGCTTATCACA- DroSec_CAF1_left TGAAACATTGGA-CATTTAAAGGCCGGGAAGTGTGCAATATA---GT-T-AAGA-----AGTAAA-TACACTGACA-CACGACCCGT--CCTGCAAATG-TTT-ATGTT--TTTGCAAGC DroSim_CAF1_left TGAAACATTGGA-CATTTAAAGGCCGGGAAGTGTGCAATATA---GC-T-AAGA-----AGTAAA-TATACTGACA-CACGACCCGT--CCTGCAAATG-TTT-ATGTT--TTTGCAAGC DroVir_CAF1_left TT-ATGCATCTA-CACTTATAGGCCGGGAGATGTGCAATATG---ATTA-TAGT-----TAAAAA-CATATTCACA-CAGAGCACGG--CCTAAAAATG-ATT--ACATAAGGCGCAAG- DroYak_CAF1_left CGAAACACTGGA-CATTTAAAGGGCGGGAAGTGTGCAATATA---GC-T-AAGA-----AATCAA-TACACTGCCA-CACGACCCGT--CCTGCAAATG-TTT-GTGTA--TTTGCAAGC DroWil_CAF1_left TTCAAAAG-TTA-ATTTAGAGGCCGGAAAAGGTGCAATATGGGGAGT-T-ATTA-----GAATAAACCATTTT-GCAAC-AACCCCGAAGCCTATAAAT-TACACTTTT--TACCATTTC DroAna_CAF1_left TCGC--ACTT-TT--AGTCACAGATGACGAGCG-CCGGAGATCATCAGG--CCGGTATAAGTGCAATATG-TTTGAA-ATA-TC-CATATT--------------GACACAAATACCG DroEre_CAF1_left ACTT--TTTG-AT--GTAAGTCCTTGATATTTT-CAGGCCGGTGAATGT--GC-----------AATATA-TTCTAACAAG-GA-AATATTGAC-GCAGATA-CCGTCCGAA-AAACT DroMel_CAF1_left ACTT--TTTT-TT--CACTTTTCGATGTTAATT-CTTGATATTTTCAGG--CC-----------GGTGAA-TGTGCA-ATA-TA-TTCGACAAA-TGAAATA-TTAACCCAT-ATACC DroMoj_CAF1_left TTTA--TGGT-GA--AAATTTATTTTAAATACA-CAAATCATTTAAATCGACG------------GGCTCACAACTG-TTT-TATAGGCC-GGGAGATG--T-GCAATATGC--TGAA DroPer_CAF1_left GCACTTTCAC-TT--TTGATTCTAACACAAGTGTGCGAAATCACTTTGC--AG-----------ATATTA---TCTATAGACGA-CACATTGAA-ATTTATA-GGCACA-AA-AATGT DroPse_CAF1_left GCACTTTCAC-TT--TTGATTCTAACACAAGTGTGCGAAATCACTTTGC--AG-----------ATATTA---TCTATAGACGA-GACATTGAA-ATTTATA-GGCACG-AA-AATGT DroSec_CAF1_left ACTT--TTATTTT--TCTTTTTCGATGCTAATT-CTTGATATTTTCAGG--CC-----------GGTGAA-TGTGCA-ATA-TA-TTCGAAAAA-GAAAACA-TTGACTCAT--ATAC DroSim_CAF1_left ACTT--TTTT-TT--TCTTTTTCGATGCTAATT-CTTGATATTTTCAGG--CC-----------GGTGAA-TGTGCA-ATA-TA-TTCGAAAAA-AAAAAAA-TATTGACTC-ATATA DroVir_CAF1_left GCTA-TGCGC-AG--TA-TTTACCAAATTGTTTTAATGTTCCATATATC--GA-----------AGAG-A---GCACGGTTCAT-TTTTAGGCC-GGGAGATGTGCAAT-AT-GCTAA DroYak_CAF1_left ACTT--TTCG-AT--GCAAGTCCTTGATATTTT-CAGGCCGGTGAATGT--GC-----------AATATA-TTCTAACAAG-GA-AATATTGAC-GCAGATA-CCGTCCGC--AAAAC DroWil_CAF1_left TGGT--CACA-TTTAGTACATTTT---TTGAGG-AAATTTCTGCGGTTT--AA-----------CTTGAA-CTTTTC-CGG-CC-GTGAAGTGT-GCAATTA-TTTTCGTAT-ATTAC