CLUSTAL W --- LocARNA 1.4.8 - Local Alignment of RNA DroAna_CAF1_left GCAAG-AGGG-TGAGGCTTAAAA--AATA-T-TTA-AA-TTTAAA-CAAAAATTA--A-CTGGTAAGAGTT--AAATACTTCCATCACT-CATTAATT-AA---T-GAA-A-TTAGTGTC DroEre_CAF1_left AAGC-----G-AATTCGGCTTTTGCACAAGATATTCAA-ACGTAA-CCGTTTCCAC-A-CAAGTATCTCAACCAAAAAGATGCCGAAAG-AATTCAAC-AA---A-TTA-G-TGAACTAA DroGri_CAF1_left CGCAGGAGGG-CGCCCGTTTTAA--AGGGGA--TTTCC--ATTTTTCATATTTAAA-G-TTTTAGTTAATTAC-ATAA-TCCCAAACAAAACAAAACA-AA---A-AAA-A-CGAAAAGA DroMel_CAF1_left GGTGA-AGCT-AAAGCGAATTTG--GCTTCT--GCACA-AGATAT-TCAAAAGTAA-C-CGTTACACACGACTATTCTCAATCAAGGAG-AATTAACC-AA---A-TTA-G-TGAATTAA DroMoj_CAF1_left TGATT-GGCG-CCCGTTTTCAAA--A-TGTTCAATCTA--TCAGT-CGCACACCC--T-CATCATATTATATTATTTTTAACTTCATAT-TTATCTTC-AT---T-TTA-T-CATACGAA DroPer_CAF1_left AGGAA-AGAG-ATGTGTTCGGTG--TTTATGTTTTGAA-TATA---CCTGCATATA-C-CCTGTCGTTCCACCAACCATCACAAATGAA-CGAAATTCGAAAATCAGTT-T-TGACCAAA DroPse_CAF1_left AGGAA-AGAG-ATGTGTTCGGTG--TTTATGTTTTGAA-TATA---CCTGCATATA-C-CCTGTCGTTCCACCAACCATCACAAATGAA-CGAAATTCGAAAATCAGTT-T-TGACCAAA DroSec_CAF1_left ACATC-CGCA-AGATGGTGAGCC--ACAAGCGAATTTG--GCTTT-TGCACAAGA--T-ATTCAAAAGTAACCGTTTTCAATCAAGGAG-AATTAACC-AA---A-TTA-G-TGAATTAA DroSim_CAF1_left ACATC-CGCA-AGATGGTGAGCC--AAAAGCGAATTTG--GCTTT-TGCACAAGA--T-ATTCAAAAGTAACCGTTGTCAATCAAGGAG-AATTAACC-AA---A-TTA-G-TGAATTAA DroWil_CAF1_left AAACA-AAAATCAACAACAAACA--AGGCAAATGGCAAGAGATTT-TTCCTCTGAGCATTCTAAATTGAAATTGATGAAAATTAATGTT-TAGTTTTG-TG---CGGTTTTCTACATGAA DroYak_CAF1_left GGCTAAAGCG-AATTCGACTTTT--GCACAA--AATAT--TTAAA-AAAACCGTTT-A-CATGAGTCGCAATCAAGAAGATGCCGAAAG-AACTAACC-AA---A-TTA-G-TGAATTAA DroVir_CAF1_left CGATT-GGCG-CCCCCTTTCAAA--G-TGTTTGTCGTG-TTCGTT-CATGATTTTGAT-TTAGA-ATACGTTTTTGTTG-TTTAAAAAG-CATTCTCC-AA---A-ACA-A-ACAAAAAA DroAna_CAF1_left TCATAATT-CAGTTACCTCAATTGGCTATGCGCTTTGGCAGTGTGGTTAGCTGGTTGTGTAGCTGGT-G--CTCGTTGG--CAATTAATTCACAGCCACTATCTTCACTGCCGCCGCGAC DroEre_CAF1_left --CCAATC-AAGTATTCTCAATTGGCTATGCGCTTTGGCAGTGTGGTTAGCTGGTTGTGTAGCCAAT-C--ATTGCTTG--T-GACAACTCACAGCCACTATCTTCACTGCCGCCGCGAC DroGri_CAF1_left -AAAAACCAAATTCCATTGAATTGGCTATGCGCTTTGGCAGTGTGGTTAGCTGGTTGTGTGGCCAAC--------------T-GACAAATCACAGCCACTATCTTCACTGCCGCCGCGAC DroMel_CAF1_left -TCCAAAC-AAGTATTCTTAATTGGCTATGCGCTTTGGCAGTGTGGTTAGCTGGTTGTGTAGCCAAT-T--ATTGCCGT--T-GACAATTCACAGCCACTATCTTCACTGCCGCCGCGAC DroMoj_CAF1_left -AAAATAC-CCTTTAATCCGATTGGCTATGCGCTTTGGCAGTGTGGTTAGCTGGTTGTGTGGCCACT--------------T-GAAAAATCACAGCCACTATCTTCACTGCCGCCGCGAC DroPer_CAF1_left -TCAAATC-CAGAAAATTCAATTGGCTATGCGCTTTGGCAGTGTGGTTAGCTGGTTGTGTAGCCAAAAT--ATTGCCTT--T-GACCATTCACAGCCACTATCTTCACTGCCGCCGCGAC DroPse_CAF1_left -TCAAATC-CAGAAAATTCAATTGGCTATGCGCTTTGGCAGTGTGGTTAGCTGGTTGTGTAGCCAAAAT--ATTGCCTT--T-GACCATTCACAGCCACTATCTTCACTGCCGCCGCGAC DroSec_CAF1_left -CCCAATCAAAGTATTCTCAATTGGCTATGCGCTTTGGCAGTGTGGTTAGCTGGTTGTGTAGCCAAT-T--ATTGCCGT--T-GACAATTCACAGCCACTATCTTCACTGCCGCCGCGAC DroSim_CAF1_left -CCCAATCAAAGTATTCTCAATTGGCTATGCGCTTTGGCAGTGTGGTTAGCTGGTTGTGTAGCCAAT-T--ATTGCCGT--T-GACAATTCACAGCCACTATCTTCACTGCCGCCGCGAC DroWil_CAF1_left -AGAATTCATTTAACATTCTATTGGCTATGCGCTTTGGCAGTGTGGTTAGCTGGTTGTGTAGCCAAT-TAAATTGCCAAAAC-AATAAACCACAGCCACTATCTTCACTGCCGCCGCGAC DroYak_CAF1_left -CCCAATC-AAGTATTCTCAATTGGCTATGCGCTTTGGCAGTGTGGTTAGCTGGTTGTGTAGCCAAT-T--ATTGCCGT--T-GACAATTCACAGCCACTATCTTCACTGCCGCCGCGAC DroVir_CAF1_left ---AAATTACCTTAAATCCGATTGGCTATGCGCTTTGGCAGTGTGGTTAGCTGGTTGTGTGGCCAAT--------------T-GACAAATCACAGCCACTATCTTCACTGCCGCCGCGAC DroAna_CAF1_left AAGCTAGAGCAACTTACCC-AGA-ATCCC-GATGGTTTTGTTAGGAT---TCTTAAGATCAAGG--AT-A-AGGAG----TTATTTCCCTATTTAAATTCGTTGTTTTCATCTCT-C-AG DroEre_CAF1_left AAGCTAAAGCAACGTACTC-AGG-ACATGGCGGAGGAACTTGCTCAGAA-CCACAA--CGGATT--GC-C-AGTAATCTGGAGCAGAACTGGAAGAG---ATTTCAT--ATCATA-TCAT DroGri_CAF1_left AAGCTATGACACCAATAAA-TAT-AAATA-ATTCACAAAAATAACTATA-TCAATT--TTGATA--TA-C-AGTATTGTAAACTATTATATTGTTTT---AAGCATT--TTATTA-ATGT DroMel_CAF1_left AAGCTAAAGCAACTTATAA-AGG-ACATGGCGGAGGAACTGGCTCATAA-TCACAT--CGGATT--GT-C-TGGAATCTCGTCTAGCACTAGGAAAG---ATTTTAG--AAAAT-GTAGG DroMoj_CAF1_left AAGCTATGACACCGAGAGA-AACTAGACA--AAAGGAACTAATTAATTAATAATTA--ATTAAC--AA-G-TATATAAATAACAACAATGTACAAGC--TAACAAAG--CA-AAC-TGCA DroPer_CAF1_left AAGCCATAACAACGATAAGCAAC-ATATAATCG-GGGACTTTCCCGGAAACCA--T--ACATGC--TTTA-TGTCACGGAGATTATTGCGGCGAATT--CAACGATG--TGTGGA-TGTG DroPse_CAF1_left AAGCCATAACAACGATAAGCAAC-ATATAATCG-GGGACTTTCCCGTAAACCA--A--TGGATT--TT-T-CGGAACTAAATACATACATGTTTTAT--GTCATGGA--GATTAT-TGCG DroSec_CAF1_left AAGCTAAAGCAACTTATAG-AGG-ACATGGCGGAGGAACTTGCTCATAGTTCACAT--CGGGTT--GC-C-CGGAATCTAGACCAGCACTTCCAAAG---ATTTTAG--AAAAT--ATAG DroSim_CAF1_left AAGCTAAAGCAACTTATGG-AGG-ACATGGCGGAGGAACTTGCTCATAGTTCATAT--CGGATT--GT-C-TGGAATCTGGGAAAGATTTTACACAA--TATAGAAC--CTGTG--TCAG DroWil_CAF1_left AGGCCATGACAACAATCGG-AAC-AAGCGAAAAAAAAACTAGGTCATAA-CTGGCC--TTCAAT--TC-A-AAAATTGAA-ATTGGGCTGT--AAAC---ACATAAT--AGACGT-CATA DroYak_CAF1_left AAGCTAAAGCAACGTACTC-AGG-ACCTGGCAGAGGAACTTGCTCATGA-GCACAA--CGGACT--GA-G-AGGAAGCTGGAGCAGAACTAGCAAAG---ATTTCAG--AAAATTGTTTG DroVir_CAF1_left AAGCTATGACAGCAAAAGAGACC-ACACGAAGAGCAGATTAAAACCCTT--AATAT--CTGCTCTAAACTACATTAAAAACCTATTTAAATGT-A-----TGTTAAC--ACAATT-TTTT DroAna_CAF1_left ATAAGGA-CCCAA-A-GTAA DroEre_CAF1_left TGT-GGC-AGCAT-C-GTAT DroGri_CAF1_left ATA-AAA-TCGAT-G-GTAG DroMel_CAF1_left ACC-TGT-ATCAG-A-TGGT DroMoj_CAF1_left ATA-TTTGCAGAT-T-ACTT DroPer_CAF1_left TCA-TGC-GGCAA-C-TAGC DroPse_CAF1_left GCA-AAT-TCAACGA-TGTG DroSec_CAF1_left ACC-TGT-ATCAG-A-TTGT DroSim_CAF1_left AT--TGT-TAGAG-C-AGCA DroWil_CAF1_left ACT-AATTCTAAT-T-AATA DroYak_CAF1_left GCA-GT--TATAT-GAACT- DroVir_CAF1_left AAA-TAC-AAAAT-A-TGTA