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


DroAna_CAF1_left   TATTTAA-AGATGAAG--CCA-ATTCAAAT-T-ATCAGTGA-AAGTTTGCC---AAAGGGAAAAGGTAGAAACTTTTAAAAT-AAAAATCACTAAATATTTCTTTTAAAAATATCAAAAA
DroEre_CAF1_left   CGATATG-GTATTAAT--GCAGATGCATAA-A-ATGTTATA-CTTAACAGT---CATTTCCCCACAGAGAAATCATGTAAAA-TACGTCTTCAAAGAATGTTTAAAAAAAGGAGAAATAA
DroMel_CAF1_left   TCGTATT-GATACAGATGAATAATACATTC-T-GCCTGACA-CTTCTTTCC---TAGCAGAGAAATACATT-ATTTC--AAA-TACTATCACAAAATGTAAACTTGG--AAAAGGAAAAA
DroPer_CAF1_left   TAATAGC-AAAGCCAA--GGGTCTTCTCTATAGTT-----T-TCTATAAAG---GATAT----TGCGGGAGACCATTTTCAA-AGTTTGTGTTATTCTATATCCCTCGTGATACAAAA-A
DroPse_CAF1_left   TAATAGC-AAAGCCAA--GGGTATTCTCTATAGTT-----T-TCTATAAAG---GATGT----TGCGGGAGACCATTTTCAA-AGTTTGTGTTATTCTATATCCGTCGTGATACAAAAAA
DroSim_CAF1_left   AATAAAT-TTCAACAA--TCAAA--CTCTT-T-AAAATAAT-GGATTCGAT---ATGGTATTAATGCAGAT-TATTA--ATA-AATTGCCTGACATTTCTTTCCTAG--CAGAGAAAAAA
DroWil_CAF1_left   TTGGTCC-TGCTCCTAT-ACTTTATCATTATTTACCTAAAA-CAAATGCTG---ATGAA----ATATTTAGTTTAAATTCTGAAAAATTTGACTTAAATAAAGAATCGTA-GAAAAAA-A
DroYak_CAF1_left   ATGAATACAAAGCTCA--TTAACTC-ATAG-A-GACATACAACATGTAAAATACGAGTT--CAAATTAAAA-ATTCTAACTTGTAGAGGCAAGAATCATTATTAAATAGAAGAAATAAAA

DroAna_CAF1_left   AATCCAAATCCGATTGAAT----TTAC--ATTCTTAGCAGAACAAGGTTTCGATCCTCGGACCTCTGGGTTATGGGCCCAGCACGCTTCCACTGCGCCACTCTGCTTGTTGAATTCGCCG
DroEre_CAF1_left   AAAATTCACCGCGCGGAAT----TTAC--AA-ATTAGCAGAGCAAGGTTTCGATCCTCGGACCTCTGGGTTATGGGCCCAGCACGCTTCCACTGCGCCACTCTGCTTGCAGAAAACGGAG
DroMel_CAF1_left   TAATTCTTGCAC-CAGAAT----CTACCTAT-TTTAGCAGAGCAAGGTTTCGATCCTCGGACCTCTGGGTTATGGGCCCAGCACGCTTCCACTGCGCCACTCTGCTTGTAAAATGATGAG
DroPer_CAF1_left   AAAGAGCCGAAA-ACGAACA---AGTT-TCA-TTTAGCAGAGCAAGGTTTCGATCCTCGGACCTCTGGGTTATGGGCCCAGCACGCTTCCACTGCGCCACTCTGCTAGCTGATGTCGCAG
DroPse_CAF1_left   AAAGAGCCGAAA-ACGAAC----AGTT-TCA-TTTAGCAGAGCAAGGTTTCGATCCTCGGACCTCTGGGTTATGGGCCCAGCACGCTTCCACTGCGCCACTCTGCTAGCTGATGTCGCAG
DroSim_CAF1_left   AAATTCA--A-A-CAGAAT----CTAC--TA-TTTAGCAGAGCAAGGTTTCGATCCTCGGACCTCTGGGTTATGGGCCCAGCACGCTTCCACTGCGCCACTCTGCTTGTAAAACGTTGAG
DroWil_CAF1_left   AAAAAAGAAACA-CAGAAGTTTCCATA-CTC-CATAGCAGAGCAAGGTTTCGATCCTCGGACCTCTGGGTTATGGGCCCAGCACGCTTCCACTGCGCCACTCTGCTTGTTGTGTCAACCG
DroYak_CAF1_left   AAGATTCACCGC-GCGAAT----TTAC--AA-TTTAGCAGAGCAAGGTTTCGATCCTCGGACCTCTGGGTTATGGGCCCAGCACGCTTCCACTGCGCCACTCTGCTTACGATTCACCGAC

DroAna_CAF1_left   CGTTTCAAAGGCTCTCATGAAATTAAGGGATCGGGTTCTAACCC--GATCTATTATAACGA-AAAACT-AACGCTTCTTT-TCACTCTGCTAAT--GTGTATAGTAGATT
DroEre_CAF1_left   CACAATGTTCATTATGAGTTAACG--TGCAACGTTTAACCACAA--CCTCAGGAGAGCCTT-TTTAGG-ATTGTGTTAAG-TAATCTGAGTTTTACGCTTAAACTTGTTT
DroMel_CAF1_left   CAGAATGTTCAATATGAGTTAACG--TACAACATTTAAGCACCAC-TGAAATTCGTATATG-AATTTAGATTAGTTATCT-GAGTTTTA-AGAC-AATTACTTAGCTAAG
DroPer_CAF1_left   CGCGAAAAAGTCTCTGTTGTATGA--AACATAATGTATGTATAA--CGAAAATTATTCTTA-AATCTAGAAAATAAAACA-GATTTGATTCAAT-TTAATCAAATTAAAA
DroPse_CAF1_left   CGCGAAAAAGTCTCTGTTATATGA--AACATAATGTATGTATAA--CGAAAATTATTCTTA-AATCTAGAAAATAAAACA-GATTTGATTCAAT-TTAATCAAGTTAAAA
DroSim_CAF1_left   CACAATGTTCAATATGAGATAACG--TGCAACAATTAAGCACCCT-TGAATTTCTTCTATG-AATTTAGATTATTGATCT-NNNNNNNN-NNNN-NNNNNNNNNNNNNNN
DroWil_CAF1_left   TGTCAGAAACTTCCCATGTCA-AA--AGCACCGTTCACAGTCAC--TTTTATTTAACCATTCAAGTTCCTTTTGCAAATA-TTATTGCCGAATT-GACAATACACAAAAT
DroYak_CAF1_left   CGCTATGTTGAATATGAGTACGCG--AGGTTGATTGGATGAGATGACGGCAATAGTTACTG-TA-TT-GTGAAATTCATTATATTAGTT-ATAT-GACAAATATTTGCAA