CLUSTAL W --- LocARNA 1.4.8 - Local Alignment of RNA DroAna_CAF1_left A-ATTATT-TGAGGAAGGAGTGGCCTGGAAAGGA---GAAA-AC-TATTAA---CCACCATCACCAG-CAGACGCTTAC-----------------AGCTTAGCT--TAAAACC-AGATA DroEre_CAF1_left G-TTTG-T-TGTCAAAGCAATCACCTG-AAAGGT---GGGA-AG-GATTAG---GCACCATAACCAG-AGGACGCTCAC--A-AGT-TTGGCCTAAAATTAAGCACATCAATTCGAT--A DroGri_CAF1_left G-AAAC-T-TGAATTTCAAAACGTGAC-TTTTTT---TGTG-TT---TTCCATTTTACCTAGAGAAG--AAGCCAGCA------CC-AAAATTATTTGGGACAATCAACTAAAC-ATATA DroMel_CAF1_left G-TCTA-A-GT--AAAGTAAGCACCTG-AAAGGT---GGGA-AGGGATTAG---ACACCATAACCAGGGGGACGCTCAC--A-AGT-TTGGCTTAAAATTAAGCACTCCAATTCGATTCA DroSec_CAF1_left T-CT-A-A-GT--AAAGTAAGCACCTG-AAAGGT---GGGA-AGGGATTAG---ACACCATAACCAGGGGGACGCTCAC--AAAGT-TTGGCTTAAAATTAAGCACACCAATTCGATTAA DroVir_CAF1_left A-TTTC-A--A--AATGTGAACACTCG-TCTTTA---TTTT-G--TTGCCTAGAGTAGAAGAAGGAAACCAACGCCAAT--T--ATGTGGACAAACAA-ATATAAAGATAAGATATAT-G DroWil_CAF1_left GGGGAT-T-ATTATTTCAATATACAAC-CAAGAA---ATTT-GT---CGAAATGGAA--AACCAAAT--CGAAGTTTA------GT-AGTTTTTTCTTTTATTTTCCCAAAGCC-ATTCA DroYak_CAF1_left G-TTTG-T-TGTCTAAGTAATCACCTG-AAAGGT---GGAA-AG-GATTAG---GCACCATAACCAG-GGGACGCTCAC--A-AGT-TTGGCTTAAAATTAAGCACACCAGTTCGATCTA DroMoj_CAF1_left A-AATG-TGAAACCTTTTGTTTTTTAT-TTGGCCTGGGGAAGTG-GAAAAA---ACCCAACACCAAT-TAAAAGGACAAATA-AAC-AAGAACATATAGA-----TAATATATATATAGT DroAna_CAF1_left AGC-ACACCGATATCGTCGCCTTTCGAATGTTATACAAAGAGAGCAATTCCATGACAGTATTACAATCCG----TGTT-TTAACTTGACTGTCGACGGATAGCTCTCTTCATTTCACTAT DroEre_CAF1_left -----TAATCTAATCGTCGCCTTTCGAATGTTATACAAAGAGAGCAATTCCATGACAGTATTACAATCGG----T--A-TTAACTTGACTGTCGACGGATAGCTCTCTTCATTTCACAAT DroGri_CAF1_left TATATTATAAATATCGTCGCTTTTCGAATATTATACAAAGAGAGCAATTCCATGACAGTATTACAATCGG----T--ATATAACTTGACTGTCGACGGATAGCTCTCTTCATTTCGCTAT DroMel_CAF1_left TTCGATCTTATAATCGTCGCCTTTCGAATGTTATACAAAGAGAGCAATTCCATGACAGTATTACAATCGG----T--C-TTAACTTGACTGTCGACGGATAGCTCTCTTCATTTCACAAT DroSec_CAF1_left TTCGATCTTATAATCGTCGCCTTTCGAATGTTATACAAAGAGAGCAATTCCATGACAGTATTACAATCGG----T--C-TTAACTTGACTGTCGACGGATAGCTCTCTTCATTTCACAAT DroVir_CAF1_left TATATGTATAAAGTCGTCGCTTTTCGAATATTATACAAAGAGAGCAATTCCATGACAGTATTACAATCTG----T--A--TAGCTTGACTGTCGACGGATAGCTCTCTTCATTTCGCTAT DroWil_CAF1_left A-G-TTAGTAAAACCGTCGATTTTCGAATATTATACAAAGAGAGCAATTCCATGACAGTATTACAATTCGGATGT--ATTAAACTGGACTGTCGACGGATAGCTCTCTTCATTTCGCTAT DroYak_CAF1_left -----TAATCTAATCGTCGCCTTTCGAATATTATACAAAGAGAGCAATTCCATGACAGTATTACAATTGG----T--A-TTAACTTGACTGTCGACGGATAGCTCTCTTCATTTCACTAT DroMoj_CAF1_left TTATACATATATATCGTCGATTTTCGAATATTATACAAAGAGAGCAATTCCATGACAGTATTAAAATATG----T--ATATAACTTGACTGTCGACGGATAGCTCTCTTCATTTCGCTAT DroAna_CAF1_left TCGTGGAGT-ATCC-TT-GCGG--CCGGAGCCATAAC-AGACAGGACA--ACGGACAGATTAGATCG-AACAATACGATATTAGT-GGGTGTTAGT-GATCGGAGCGAAGCGT-CGAAT- DroEre_CAF1_left TCGTGGAGG-ATCT-GA-AAGCGAATAGCTGGAGCGC-TAGCACCACAGGACAGACAGGACAAAAGG-TTACGCCAGACGAACTG-GAAGTGGAAC-TGGGTTTAGTGGTTTGGTTAGT- DroGri_CAF1_left TCGTAATTTGTTGT-GA-AACTTAAAAGCCGCAAAGC-TTTGAAAGGACAACAGACAATTTATTTCA-GACAGAGGACAAGGTCA-ATTTGTTAGTTGTTCGGGCAACGTCGAATATC-- DroMel_CAF1_left TCGCGGAGG-ATCT-GA-AAGCGGAAATCTA---AGC-TAACACCTCA--ACGGACAGGACACAGTG-TTAGGCCAGACGAACTG-AATGTGGAACTTGGGTTTAGTCGTTTGGTTAGTC DroSec_CAF1_left TCGCGGAGG-ATCT-GA-AAGTGGAAAGCTG---GGC-TAGCACCTCA--ACGGACAGGACACAGGG-TTAGGCCAGACGAACTG-GAAGTGGAACT-GGGTTTAGTGGTTGGGTTAGTC DroVir_CAF1_left TCGCAAGTT-TGGT-TA-GCTTGAAA-AAGCCAAAGG-ACAATGGACA--T---TTTCCAGACAGAAAACAGGTTATATGGTGTT-AGATTCGGTTAGTTTGGGCAACGTCGAATATCAT DroWil_CAF1_left TCGGATGCAATTTT-GTGCAGGGGCAGGCCTAAAAAATAAGGCAAGTGAGGTTAGCTG-GGAGA-TT-AACTGGGGGTGGGGTTAGTTTTACTTTGGG------TCACGTCGAATATC-- DroYak_CAF1_left TCGTGGGGG-ATCT-GA-AAGCGGAAAGCTGAAGTGC-TAGCGCCTCAGGACAGACAGGACAAGAGG-TTAGGCCAGACAAGCTG-GGTTTAGTGGTTAGGTTAGTCAGCCTCATAGCG- DroMoj_CAF1_left TCGCAGAAC-TGAGGGA-CA-----A--------AGG-ACATAGGCAG--ACAGACAGTTATATCGG-TTAATCGGGGTTAGTT----TGGGCAAC-GTCGAATATCATACAAAGAGAG- DroAna_CAF1_left -AT--TATACA-AAG-A DroEre_CAF1_left -CA--GCCTCATAGT-G DroGri_CAF1_left --A--TACAAAGAGAGC DroMel_CAF1_left TCATTGCCTCACAGC-G DroSec_CAF1_left TCATTGCATCACAGCGC DroVir_CAF1_left ACAAAGAGAG-CAAT-T DroWil_CAF1_left --A--TACAAAGAGA-G DroYak_CAF1_left -CA--T-CGTCGAAT-A DroMoj_CAF1_left -CA--A-TTCCATGA-C