CLUSTAL W --- LocARNA 1.4.8 - Local Alignment of RNA DroAna_CAF1_left A-CACA-C-ACTTA---TTAAATAATAATATATAT-AGGAGGCCATATAGATTGAGGGACCAATTGATTGATTGATAAGAGGGACA----CAATTTTGGGCAAAAAAAAA-ATGAATAAT DroEre_CAF1_left TATGTATGTATGTACATAAGCATTGAAAGCCATAT-AGATTGAGACCAATTGAGTGATTGATAAG--CGGGTCGAGGAAA---AAT------GAATATGGAGGA-AAACA-AGGTGATAA DroMel_CAF1_left T-GTACATATGTAT---ATATATGGGAAGCCATAT-AGATTGAGTCCAGTTGAGGGACTGATAAG--CGAGACGAGGATTATTAAT------TATTATGGAGGAAAAACA-AGGTGATCG DroMoj_CAF1_left C-TATAATAAAGGG---CAACGAG-ATATTATCAA-AGACAAAAGGAAATTTATAATATCAATTA--TCCAACTAGAAAGAAGGGGAAATTATCAATTCTAATACAAATA-ATGGATAAA DroSec_CAF1_left A-CAAACATACATA---CTATATGGGAAGCCATAT-AGATTGAGACCAATTGAGCAATTGATAAG--CGGAACGAGGATTATTAAT------TAATATGGCGAAAAAACA-AGGTGTTAG DroSim_CAF1_left A-CACACATACATA---CTATATGGGAAGCCATAT-AGATTGAGACCAATTGAGCAATTGATAAG--CGGAACGAGGATTATTAAT------TAATATGGCGAAAAAACA-AGGTGTTAG DroVir_CAF1_left T-ACATATATGTAC---ATCAGAT-CATGCAACAGGTCGCACCTTGAACCCCCTCGCCCGCCTAA--TGCAATTAATATTTAAATTTGT-TATCTATGGAAAAATAAATACATACACATA DroYak_CAF1_left A-CGAGTATAAAAATGTATGTATGCCAAGCCATAT-AGATTGAGACCAGTTGAGAGATTGATAAG--CGGGACGAGGAAA---AGT------AAATGTGGAGGAAAAACA-AGGTAATGG DroGri_CAF1_left C-AATTGTTACGCA-ACAATGATTAATA-TGATCA-ACAGCGACATCA-----GCA----ACAAG--CGGCACCTGAAATACCCTT------CTTCT--ATCTCATTCGG-TTTTTTTTT DroAna_CAF1_left TAAATTAGAAAGAAAATGTAACCATCCCAACTAGGAG---------CCAGTTGGATTGCAGGAGAAGT----------AC------AC----CCCCACTCAATTGG-------CTCAACT DroEre_CAF1_left GCGATAA-AAAGG--ATGTAACCTTCCCAACTAGGAA---------TTAGATGGTTGGCAGGAGGACG----------AG------TC---CTCC----CAGGTAA-------TTCAACT DroMel_CAF1_left GTGATAA-AAAGGAAATGTAACCTTCCCAACTAGGAA---------TTAGATGGTTTGCAGGGGGACAACAACAACA-AGTCGTCGTCCTCCCCCCACTCAGGTAA-------TTCAACT DroMoj_CAF1_left AACAAAA-AGATAATTTGTCAATTCTCCAACTAGGAC---------CCAGCGGTTTG-------TACAAGGGGAAAT-TAACGCCCACCTG------CTCCGCTGG-------CTCAACT DroSec_CAF1_left GTGATAA-AAAGGAAATGTAACCTTCTCAACTAGGAA---------TTAGATGGCTTGCAGGGGGAGAACAACAACA-AGTCGTTCTTCTCCGCCCACTCAGGTAA-------TTCAACT DroSim_CAF1_left GTGATAA-AAAGGAAATGTAACCTTCCCAACTAGGAA---------TTAGATGGCTTGCAGGGGGAGAACAACAACA-AGTCGTTCTTCTCCCCCCACTCAGGTAA-------TTCAACT DroVir_CAF1_left TACATAT-ATA-TATATGTCAATTCTCCAACTAGGAA---------TCAGCGGTACA-------TATTTCAGGACTT-TTA--CCTCCCTC------CTCCACTGA-------CTCAACT DroYak_CAF1_left GTGATAA-AAAAGAAATGTAACCTTCCCAACTAGGAA---------TTAGATGGTTGGCAGGAGGACG----------AG------TC---CTCCCGCTCAGGTAA-------TTCAACT DroGri_CAF1_left TTT---T-CAAAAAAATGTCAACTCTCCAACTAAGAGACAGCGGGGGATGTGGTGGTCCAAGGA---------ATAATAT-A-----C---TCCTCTTTCCACGTTCCACTGGCTCAACT DroAna_CAF1_left CTCTAGGGAGGGGCGCCCGGCCAAGTGCCA--CGCCCC---CGATTGCCCGGCGCGAACACTAGAACAGTGACCACAGGTGGGCGGGGGGT--GTGGCAC-AGCCGCATT--TAATGCTC DroEre_CAF1_left CTCTAGGGAAGGGCGCCCGACCAAGTGCCA--CGCCCC---GGATTGTCCGGCGTGATCACTAGAACAGTGACCACAGGTGGGCAGGGGGC--GTGGCAC-AGCCGCATT--TATTGCTC DroMel_CAF1_left CTCTAGGGAAGGGCGCCCGGCCAAGTGCCA--CGCCCC---GGATTGCCCGGCGTGGCCACTAGAACAGTGGCCACAGGTGGACAGGGGGA--ATGGCAC-AGCCGCATT--TATTGCTC DroMoj_CAF1_left CTCTAGGCGAA-TTACGCGACCAAGAACCA--CACATC---CATTGCCCGTGC---GCCACTAGAACAGTG-ACACA--ATGGGCGGAGGC--GTGGCAC-AGCCGCATA---TTTGCTC DroSec_CAF1_left CTCTAGGGAAGGGCGCCCGGCCAAGTGCCA--CGCCCC---GGATTGCCCGGCGTGGTCACTAGAACAGTGACCACAGGTGGACAGGGAGA--ATGGCAC-AGCCGCATT--TATTGCTC DroSim_CAF1_left CTCTAGGGAAGGGCGCCCGGCCAAGTGCCA--CGCCCC---GGATTGCCCGGCGTGGTCACTAGAACAGTGACCACAGGTGGACAGGGAGC--ATGGCAC-AGCCGCATT--TATTGCTC DroVir_CAF1_left CTCTAGGCGAA-TTACGCGACCAAGTGCCT--CGCACA---TCCGTTGCCCGCGC-GCCACTAGAACAGTGGACACAATGGGCGGA--GGC--GTGGCAC-AGCCGCATT--ATTTGCTC DroYak_CAF1_left CTCTAGGGAAGGGCGCCCGACCAAGTGCCA--CGCCCC---GAATTGTCCGGCGTGATCACTAGAACAGTGACCACAGGTGGGCAGGGGGC--GTGGCAC-AGCCGCATT--TATTGCTC DroGri_CAF1_left CTCTAGGCGAGTAAACGACTCAAAGTGACTAAAGCACATTCCATTGCCCCGTCGTTTCCACTAGAACAGTGAACACAGTTGAGCGGCCGGCTTTTGCCACAAGTCGCATTTTAATTGCTC DroAna_CAF1_left TATCACAAGTGTAACGCCTTTTGGTCGACGTGGCTTAAAAAACCCAAAACCAAACTGCTGACTGACTTGTGAAGAAAGG-TGC----AG-G-ATGTT-TACAA--T-TTTAAAGGATGTG DroEre_CAF1_left TATCACAGGTGTAACGCTATTCGGTTGACGTTT------AAAACCAGAACCGTACAGCTGACTGACCTGTGAAAACGTA-GACAGGATA-TCTCAAGGA-CCCT-TT-ATTCTGGACTAT DroMel_CAF1_left TATCACTGGTGTAACGCTATTCGGTTGACGTTT------AAAACCAGAACCGTACAGCTGACTGACCTGTGAAAACTCG-TGG----TT-AAAGGAT-ATCCTT-AA-GGACACTATATA DroMoj_CAF1_left TATCACAAGTGTAACGCTGTGGAGTTGAG--T---------TATTACAACTGAACAGCTGACTTACTTGTGAAAAACTCACAA----TCCATAACTA-TAGTGG-GAAATATATTTGAAG DroSec_CAF1_left TATCACAGGTGTAACGCTATTCGGTTGACGTGT------AAAACCAGAACCGTACAGCTGACTGACCTGTGAAAACACG-TGG----TTAAAAGGAT-ATCCTT-AA-GGACACTATTTA DroSim_CAF1_left TATCACTGGTGTAACGCTATTCGGTTGACGTGT------AAAACCAGAACCGTACAGCTGACTGACCTGTGAAAACACG-TGG----TT-AAAGGAT-ATCCTT-AAAGGACACTA--TA DroVir_CAF1_left TATCACAAGTGTAACGCTGTGGAGTTCAT--GT------A-AATTACAACTGAACAGCTGACTGACTTGTGAACAGATCCCAA----ATTGATAAAG-GGAAAT-TTATTAGAAAGAGAA DroYak_CAF1_left TATCACAGGTGTAACGCTATTCGGTTGACGTTT------AATACCAGAACCGTACAGCTGACTGACCTGTGAACCTGTG-AAAACGTAG-ACAGGAT-A-TCTG-AA-GGACACTATATA DroGri_CAF1_left TATCACAAGTGTAACGCTGTAGAGTTAA-ATTC------A-AGTAACAACTAAACAGCTGACTGACTTGTGAAAACCCA-AGCG--AAA-AAGAGAT-ATCTCCTCT-TTTTATTATAAA DroAna_CAF1_left GGGGGTG--TGCTAGGTATTTTATTATT------TTT-TTAT-----------GTATAATTTTTTT-TTAT-ATTTTTTT-T--TTTTGGTG---TGGAAA DroEre_CAF1_left A----------TAAAATTCCGCCCACAC------ATACCACAG-ATATAAGGGAAAAGAGAGGATC-GGGT-TGAT------------TT-G--TGGTTCG DroMel_CAF1_left AGTTTAATAAGAAACATTCCGCGCACGC------AAT-AACA-----------GTACTCTGTGGGA-GGGG-AAATGAGA-G--GATCTTGGAT---GAGA DroMoj_CAF1_left --GGAAG--AGAATTGATCCTCAAAAAAGCTTCATTC-TAAA-----------TAAAAATTCCGCTCATTCAACAGTCGAGCGTCACCGA-G--CGAGCTC DroSec_CAF1_left TAGTTAATGAGGAAAATTCCGCCCACGC------AAT-AACA-----------GT---ACTCTGGG--GGG-AAATGAGA-G--GATCTCGATGAGAGAGG DroSim_CAF1_left TAGTTAATGAGGAAAATTCCGCCCACGC------AAT-AACA-----------GTAGTACTCTGGG-GGGG-AAATGAGA-G--GATCTCGATG--AGAAA DroVir_CAF1_left --ATGAT--CCTTAAAAACCCTCAACGCGCTCTTATC-TTTT-----------TCTTTCCTATCTC-TCTC-TCATTCTT-C--TTTCAT-T--GCTGCCG DroYak_CAF1_left A----------GTAGTACGTATGGAAA-------ATTCCACTACTACCAGGGAAAAGGAGAGGATC-GGAT-TGATTTCA-G--GCTCGA-A--CTCGCGA DroGri_CAF1_left TAACCAACTC-AACATTTTTCCCCACAC----CCAAC-T--T-----------ACATTCGAACACG-CGAC-TTAT-TTA-T--ACTCCA-A--GCTTCTG