CLUSTAL W --- LocARNA 1.4.8 - Local Alignment of RNA


DroAna_CAF1_left   T--TCTCGTTGGCCGAAATATTTTGAAAAAAAAATTGAAATAAAATTTGTTTTTTGAAA--AATAA-TT------GAAATTT--G-GAAAAGGT-TTGTTTT------TTTTTTTTTTAA
DroEre_CAF1_left   T--CAAATTGTCAATTTTGAACTGATTCTCGTTGGCCGAA-AGGTTGTGACAAATTAAACAAATTG-AAAATTT-GGAAATA--A-GTATAAGT-TCT-TTG------TGCCATACCCAT
DroGri_CAF1_left   G--GTTGGTGTAGCTTGCCGAAATACTGAGTAAATTTAAA-AAAA--AAAAAAAAAAACAGAAAATACAAAATT-AGATTAG--A-CACTTC-A--CT-G--------CCTG-GTTTTTT
DroMel_CAF1_left   A--TTTTGAACTGATTCTCGTTGGCCGAAAGGTTGTAAAAATTAAACAAATTAAACAAATTGAAAA-ATTTAAA-ATAAATA--TAGGTTCTTT-TTT-GGA------ATC--GACCCAT
DroMoj_CAF1_left   AAAGCACTTTAATTTTTATTAATTTCAGTTTGTAATATAT-ATAC--ATATATATATGCATATATG-CATTATA-TGCATAC--A-TAGCTATA--AA-T--------ATAT-ATTTTGA
DroSec_CAF1_left   A-----ATTGTCAATTTTGAACTGATTCTCGTTGGCCGAA-AGGTTGTAA-AAATTAAACAAATTG-AAAATTT-TGAAATA--A-GTAAATGT-TTT-TTTTTTG--TAATCGACCCAT
DroSim_CAF1_left   T-----T--GTCAATTTTGAACTGATTCTCGTTGGCCGAA-AGGTTGTAA-AAATTAAACAAATTG-AAAATTT-TGAAATA--A-GTCAAGGT-TTT-TTTTTTTTATAATCGACCCAT
DroVir_CAF1_left   T--TCAATTCTGAACTGATTCTCGTCGGTTGGTTGCTTGC-CGAA--ATATTGGGTGAAAATTTGA--GAGAAA-ATAAAATTGA-TAAAAC-A--CT-T--------CACT-GAATTTT
DroYak_CAF1_left   T--CAAATTGTCAATTTTGAACTGATTCTCGTTGGCCGAA-AGGTTGTGAAAAATTAAACAAATTG-AAAATTT-GGGAATA--A-GTATACGT-TTT-TAG------TACCCAACCCAT
DroWil_CAF1_left   T--TAAAAATTAAATAAATAAACTATATATGTATAATATA-AAGAA-AACCATTTAAAATTCAATT-TTTCTGTTTTACACA--A-CTTCAC-AATTA-TTT------TTATTTACATA-

DroAna_CAF1_left   T-TATTCTCCCCTTGATGCGATTGGAGGATTCCC-GCTCTCAGCAAGAACTCAGACTGTGATGTGAGTTTCGAAA-----AAAA-GGACACAAGTCACAGAGAGAGTTCTTGGCAAGT-G
DroEre_CAF1_left   G-ATTTCGCTTTATGTTGC--TTCGAGGAT-TCC-GCGCTCAGCAAGAACTCAGACTGTGATGCGGCTTTT---------CAGT-ACACGCAGGTCACAGAGAAAGTTCTTGGCAAGT-G
DroGri_CAF1_left   TGATTT-TATGTATGCTGT--GGTGCGA-A-AGC-GCGCTCAGCAAGAACTCAGACTGTGATGCGATTTTCACATGA---AAGT-TCACGCAAGTCACAGAGAGAGTTCTTGACGAGT-G
DroMel_CAF1_left   G-ATTTCGCTTAATGTTGC--TTCGAGGAT-TTC-GCACTCAGCAAGAACTCAGACTGTGATGCGGCTTTT---------AAGT-ACACGCGGGTCACAGAGAAAGTTCTTGACAAGT-G
DroMoj_CAF1_left   TTTTGA-TTTTTATGTTGC--TGTGCGAAG-TGC-GCGCTAAGCAAGAACTCAGACTGTGATGCGGTTTGCATATAG---GAAT-TCACGCAGGTCACAGAAAAAGTTCTTGTTAAGT-G
DroSec_CAF1_left   G-ATTTCGCTTAATGTTGC--TTCGAGGAT-TTC-GCACTCAGCAAGAACTCAGACTGTGATGCGGCTTTT---------AAGT-ACACGCGGGTCACAGAGAAAGTTCTTGACAAGT-G
DroSim_CAF1_left   T-ATTTCGCTTAATGTTGC--TTCGAGGAT-TTC-GCACTCAGCAAGAACTCAGACTGTGATGCGGCTTTT---------AAGT-ACACGCGGGTCACAGAGAAAGTTCTTGACAAGT-G
DroVir_CAF1_left   CGTATA-TTCGTCTGTTGC--TGTGCGAAG-TGC-GCGCTAAGCAAGAACTCAGACTGTGATGCGGTTTGCATATAA---GAGT-TCACGCAAGTCACAGAAAAAGTTCTTGATAAGT-G
DroYak_CAF1_left   G-ATTTCGCTTTATGTTGC--TTTGAGGAT-TTC-GCGCTCAGCAAGAACTCAGACTGTGATGCGGCTTTT---------AAGT-ACACGCAGGTCACAGAGAAAGTTCTTGACAAGT-G
DroWil_CAF1_left   --TAAA-TCTTTAGGTTGT--CTTGCTTAG-CTCACCGCTCAGCAAGAACTCAGACTGTGATGCGGTTTTCATATATGATAAATCTCACGCAGGTCACAGAGAGAGATCTTGACAAGAAG

DroAna_CAF1_left   CGCCTCATAT------T--AGAGATGACA-G--CTTTTTTTTTG--CAGAAACTGGTAACACTTGAAATTATTTA-CAATATGCATGACATGGTCACAC---TTGGAAA
DroEre_CAF1_left   CGCCTCATGG------AGATCTAAATGCA-T--CGTAGGCTCCT--CAGCGAGCTGTGAGCTGC-GTATCTTTAA-CATAGTT-ACTACAAGTTACAAA---CGGATGC
DroGri_CAF1_left   GGCTTCATTT----CGAATTCGAACTGTTAA--CA--GTCGCTGTACAACTTGCTGC-TG-TTA-TTTACATAGG-CGATGTG-TG-GCGTATTTGATG---GGCGAAC
DroMel_CAF1_left   CGCCTCACAT------AGATCTAAATGCA-T--CGTAGGCACCT--CAGTTAGCTGCGTATCTT-TAAATATTTA-CTACAAA-A---AGAGTTACAGGCGGATGCAAA
DroMoj_CAF1_left   CGCTTCAAAT----CGAATGCGAACTGTTTA--CATAGGCACTGTAAAACTTGCGGC-TG-TTA-TTTACAT-GG-TGTCTAC-AG-ATGTATCGAATT----AAATGG
DroSec_CAF1_left   CGCCTCATGG------AGATCTAAATGCA-T--CGTAGGCACCT--CAGTGAGCTGCGTATCTT-TCAATATTTA-CTAAAGA-CAGATGCAAAGTGAT---CATGTAT
DroSim_CAF1_left   CGCCTCATGG------AGATCTAAATGCA-T--CGTAGGCACCT--CAGTGAGCTGCGTATCTT-TCAATATTTA-CTACGAA-AAGAGTTACAGACAG---ATGCAAT
DroVir_CAF1_left   CGCTTCAATAAAACCAAATTCGAACTGTTAAAGCA--GGCGCTGTAGAACTTGCTGC-TG-TTA-TTTACATAGA-CGAGATG-TA-GT-----GTATG----TTGTGA
DroYak_CAF1_left   CGCCTCATGG------AGAACTAATGGCA-T--CCAAGGCTTCT--CAGCGA-CAGCTACAGACGGATGCTGAAT-GGATGGA-TCATGAATGAATGAG---CGGCGAG
DroWil_CAF1_left   GGCTTCTCTT------TG-CTGTTTGGCC-A--CATTTGAATT--TGGTGCAACGCGGAGAGGA-GGATTTGCTTGCGGTTAG-AC-ATTTACATGCAA---ATTGATG