CLUSTAL W --- LocARNA 1.4.8 - Local Alignment of RNA DroAna_CAF1_left TTGCTATTT--TTTAAACT---T---TTATGGG--AACATATTAAACGTTTATT---GC-ACTCTCGACGC----AA-AT-GTTGCCTCGT-TCTCATCCCAGC--CACCGCTTCTTAA- DroGri_CAF1_left ACTCAAACACGCAAGTACACTATG-------GA--CA-TCTCTGTCTGAC-ACGTGTTGCATGCACT--AC-------CC-AATATACACC-CAAAATACAATTGTCAGCAA-TGTGAA- DroMoj_CAF1_left GTGGCAGAC--TATGGTCG---T---CTCTTTCTAAC-ACGTGTTGCATG---CGCTGCCCAATA---TAT----AC-AA-AATTTGTAAT-AGTCAGCGCCGCCGCAGCAA-TGTGAA- DroVir_CAF1_left GAACCATAC--TATTGTCAT------CTCTGTC--TG-ACACGTGTTGCA-TGTGCTTCCAAATA---TAC----AC-AC-AATATGTAAC-ATTCAGCGCCGTCGCAGCAA-TGTGAA- DroWil_CAF1_left ATTTGCAAT--AACAGTCCTGTTTTACACCATG--GGTTTGTGTCCTGGCT------AACAATTCTG--TTGCTTAG-CATTGACAAGCAA-CCATGG-----C--CCGCAA--ATGAA- DroEre_CAF1_left CAGGCGTTC--GAACCACG---CGCAACCTATA--GT-TGTCTCTTTTCA-G-CTGCCCCGCAG----CTT----GAGCT-ACAGCGATGG-AGTGAGA-GGGC--CCGCACATTAAAA- DroMel_CAF1_left CAAGCGTTC--GAACCAAG---CGCACACTATA--GT-TGTCTCTTTTTA-G-CCTGCTCATAG----CAC----AAGGC-AGAGCGATGG-AGTGAGA-GGGC--TCGCACATTAAAA- DroPer_CAF1_left TAGAAA-AC-----CCCGG---TGCACACTATA--GT-CGTCTCGTTCAC-A-CCCGACTACAGA---CAT----ACGGA-CAAAAGCATGCCCCAGCA-GAGC--AAGCCCGTGCATTA DroPse_CAF1_left AATAGAAAC-----CCCGG---TGCACACTATA--GT-CGTCTCGTTCAC-A-CCCGACTACAGA---CAT----ACGGA-C-AAAGCATGCCCCAGCA-GAGC--AAGCCCGTGCATTA DroSec_CAF1_left CAAGTGTTC--GAACCACG---CGCACACTATA--GT-TGTCTCTTTTTA-G-CTTGCTTATAG----CAC----GAGCC-AGAGCGTTGG-AGTGAGA-GGTC--CCGCACATTAAAA- DroSim_CAF1_left CAAGTGTTC--GAACCACG---CGCACACTATA--GT-TGTCTCTTTTTA-G-CTTGCTTATAG----CAC----GAGCC-AGAGCGTTGG-AGTGAGA-GGGC--CCGCACATTAAAA- DroYak_CAF1_left CAGGTGTTC--GAACCACG---CGCACACTATA--GT-TGTCTCTTTTCA-G-CTTGCCCGTAG----CAA----GCGCT-AGAGCGATGG-AGTGAGA-GGGC--CCGCACATTAAAA- DroAna_CAF1_left GTGTAC-AATCCGGCGCTCCACCTTCAACTGGCTCGTTGGTCTAGAGGTATGATTCTCGCTTCGGGTGCGAGAGGTCCCGGGTTCAATTCCCGGACGAGCCCAAGC-TAATT------TG DroGri_CAF1_left ATATAC-AATATGGCGATCCACCTTCAACCGGCTCGTTGGTCTAGGGGTATGATTCTCGCTTCGGGTGCGAGAGGTCCCGGGTTCAATTCCCGGACGAGCCCAAGT-GGTAT-------- DroMoj_CAF1_left ATATAC-AATATGGCGGACCACCTTCAACCGGCTCGTTGGTCTAGGGGTATGATTCTCGCTTCGGGTGCGAGAGGTCCCGGGTTCAATTCCCGGACGAGCCCAAGT-TGTTC------AA DroVir_CAF1_left ATATAC-AATATGGCGATCCACCTTCAACTGGCTCGTTGGTCTAGGGGTATGATTCTCGCTTCGGGTGCGAGAGGTCCCGGGTTCAATTCCCGGACGAGCCCAAGT-GGTTAATGTAATT DroWil_CAF1_left ATAGAC-AATGCGGCGCTCAACCTTCAACCGGCTCGTTGGTCTAGAGGTATGATTCTCGCTTCGGGTGCGAGAGGTCCCGGGTTCAATTCCCGGACGAGCCCAAGT-GTTGA------AG DroEre_CAF1_left AGCGACATTCGGATCGCGTATGCTACCGCAGGCTCGTTGGTCTAGAGGTATGATTCTCGCTTCGGGTGCGAGAGGTCCCGGGTTCAATTCCCGGACGAGCCCAAGT-GATGT------CG DroMel_CAF1_left AGCGTCATTCTGATCGCTCCCAGTACCGCAGGCTCGTTGGTCTAGAGGTATGATTCTCGCTTCGGGTGCGAGAGGTCCCGGGTTCAATTCCCGGACGAGCCCAAGTTGACGT------CG DroPer_CAF1_left AATCCACAATAGGACTCTCCATGTTCAACTGGCTCGTTGGTCTAGAGGTATGATTCTCGCTTCGGGTGCGAGAGGTCCCGGGTTCAATTCCCGGACGAGCCCAAGG-TGGAA------GT DroPse_CAF1_left AATCCACAATAGGACTCTCCATGTTCAACTGGCTCGTTGGTCTAGAGGTATGATTCTCGCTTCGGGTGCGAGAGGTCCCGGGTTCAATTCCCGGACGAGCCCAAGG-TGGAA------GT DroSec_CAF1_left GCCATCATTCTGATCGATCCCAGTACCGCAGGCTCGTTGGTCTAGAGGTATGATTCTCGCTTCGGGTGCGAGAGGTCCCGGGTTCAATTCCCGGACGAGCCCAAGT-GATGT------CG DroSim_CAF1_left ACCATCATTCTGATCGCTCCCAGTACCGCAGGCTCGTTGGTCTAGAGGTATGATTCTCGCTTCGGGTGCGAGAGGTCCCGGGTTCAATTCCCGGACGAGCCCAAGT-GATGT------CG DroYak_CAF1_left AGCGACATTCTGATCGCTTATGCTACCGCAGGCTCGTTGGTCTAGAGGTATGATTCTCGCTTCGGGTGCGAGAGGTCCCGGGTTCAATTCCCGGACGAGCCCAAGT-GATGT------C- DroAna_CAF1_left A----AATTAATTTTTTTTCTATT-TTAA----AGTAG---T----TAT-TTTAAATTATTAAGTGTTACTTTAGTGGCTAT--TACTTTA-TCAGT-GTTTGATTTCA----------T DroGri_CAF1_left A----AATAAATTTTTTGTATTTT-TTTT----GACTG---TCTCATTT-TCTGTGTGTGCGAA----ATTGAT-----AAA--TAATAAT-AAAAA-GAATTCATGCCGCCGCTTTTTA DroMoj_CAF1_left A----ATAAA-T-TTTTTGTTGTGGTTTCTTCAATTTC---A----ATT-TCCTAAATAATACTATGAAAT------AAACA--AATAAAA-CAAAG-AAAAGTATTC------CG---C DroVir_CAF1_left A----TTTTGTACTTTCTTTTCTT-AATA----CAA----------AAA-ATCTGATTTCAATT-AATTGGCTGCAATTT-A--CAAAGAG-AACTA-ATAAAAAATAAA--T--T---G DroWil_CAF1_left T----ATGAAATTAATTTTTTTAC-GTTT----TAT----------AAA-TTTAGTTTTCTTTTTTTTTTTCTTCTTTCTCA--CAGTAAA-AAAGT-TTTTTCATGCTAAAATTA---T DroEre_CAF1_left GTTGTAATTTTTTTTTAAAAGCAAATATT----TTTAA--CAAGT-TTCTTTTTATATGTGCAA--TTGCAGTGTAAA-TAT--TTCAAAC-CCTGT-TTTTAAGA-C------CC---C DroMel_CAF1_left G----TTGTAATTTTTTTTTGTTT-TTTA----AATAA--TTGCA-ATG-TATCTTAATCCCA----GTTTCCTAAGC-CCC--CAAAAAT-GTAAG-TATTTAAATT------TA---C DroPer_CAF1_left G----AATTAAATTTTTTTTTC-C-GGTC----AACTT---TTTTTTTT-TGCCGATTTTGCAA--TACAATACTGTA-CTT--TCGCGAG-CCTTTAAAAAAACATA------AA---C DroPse_CAF1_left G----AATTAAATTTTT-TTTT-C-GGTC----AACTT---TTTTTTTT-TGCCGATTTTGCAA--TACAATACTGTA-CTT--TCGCGAG-CCTTA-AAAAAACATA------AA---C DroSec_CAF1_left G----TTGTTTTTTTTTTTTTTTT-T--A----AAAAAGTTTGTA-ACT-TTTTTGTTTTTGA------AATAACT---GCAATGTATAATGTATCC-TAATCCCAGT------TG---C DroSim_CAF1_left G----TTGTAATTTTTTTTTGTTT-TTTA----AATAAGTTTGTA-ACT-TTTTTGTTTTTT----TTAAATAAGT---GCA---ATGTGT-AATGT-ATCCTAATCC------CA---G DroYak_CAF1_left -----GGTTGTAATTTTTTTTC-T-TTTT----AATAT--GCGAT-TTT-TTTTAGATATGCAA--TTTTAGTGTAAA-TAT--TTAAATT-CCTGT-TTCCTGAGCC------CC---C DroAna_CAF1_left A-ATTTTTT-TG-GAAAAAGACTA--ATAAGTTATAA DroGri_CAF1_left T-AGGT---AAACAAAAC--AAAA--TAGCTGCTCTT DroMoj_CAF1_left T-CTAAAACAAAACAAGT-AGCTG--CTCTTAACTGC DroVir_CAF1_left C-CGCT-----T-TACAAACAAAA--CAAGTAGCTGC DroWil_CAF1_left A-CATTTGAAAAAAATAAAAAAAT--CAAAT-TAAAT DroEre_CAF1_left G-TAAATGTACC-TAGAAAATAAAGCATTTAATGGGC DroMel_CAF1_left A-ATTATTGCTC-TCCTTATTTAA--ATGAAGACGAA DroPer_CAF1_left C-ACTTTTTGGT-CGTTGTTTTTG--TCTT--TGATT DroPse_CAF1_left C-ATTTTTTGGT-CGTTGTTTTTG--TCTT-TGATTA DroSec_CAF1_left C-TCAGC-CCCC-AAAAATTGTAG--TTATTTAATTT DroSim_CAF1_left TTGCCCCCAAAA-AATGTAGTTAT--TTAATTTGTGC DroYak_CAF1_left G-AAAAAAATAC-CTAGAAAATCA--AGCA-TTACGT