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


DroEre_CAF1_left   TTTCAGGGTCGAACGT-CTTG--TTTCGCATTTGGCGGCGCTCAG-TCAACAGCTCCAGTGGCGCAATTGGTTAGCGCACGGTACTTATAATCAGTATTCTGTGTGTATGAGCTATGCCG
DroGri_CAF1_left   TCTCAACGTCGGCCAG-CTTTACATGCGCATTTGGCAGCCCTCGA-ACAACAGCTCCAGTGGCGCAATTGGTTAGCGCACGGTACTTATAATCAGTACTC--TGTGTATGAGCTATGCCG
DroMel_CAF1_left   TTTCAGGGTCGAGCGT-CTTG--TTTCGCATTTGGCGGCGCTCAG-TCAACAGCTCCAGTGGCGCAATTGGTTAGCGCACGGTACTTATAATCAGTATTCTGTGTGTATGAGCTATGCCG
DroMoj_CAF1_left   CTCAGTGGCTCTCCGCTTTAG--ATGCGCATTTGGCAGACATCGA-GCAACAGCTCCAGTGGCGCAATTGGTTAGCGCACGGTACTTATAATCAGTACTA-TTGTGTATGAGCTATGCCG
DroPer_CAF1_left   TCAGT-GGCCGGATCT-CTTG--CTGGGCATTTGGCAGCGCTCGATTCAACAGCTCCAGTGGCGCAATTGGTTAGCGCACGGTACTTATAATCAGTATTCTGTGTGTATGAGCAATGCCG
DroPse_CAF1_left   TCAGT-GGCCGGATCT-CTTG--CTGGGCATTTGGCAGCGCTCGATTCAACAGCTCCAGTGGCGCAATTGGTTAGCGCACGGTACTTATAATCAGTATTCTGTGTGTATGAGCAATGCCG
DroSec_CAF1_left   TTTCAGGGTCGAGCGT-CTTG--TTTCGCATTTGGCGGCGCTCAG-TCAACAGCTCCAGTGGCGCAATTGGTTAGCGCACGGTACTTATAATCAGTATTCTGTGTGTATGAGCTATGCCG
DroVir_CAF1_left   TCTCAGTGCCTCTCCG-CTTTACATGCGCATTTGGCAGACCTCGA-CCAACAGCTCCAGTGGCGCAATTGGTTAGCGCACGGTACTTATAATCAGTACACTG--TGTATGAGCAATGCCG
DroWil_CAF1_left   CTCATCGGCTGCTTCT-CTTA--TGGCTTATTTAGCAGCGAGCAC-ACAACAGCTCCAGTGGCGCAATTGGTTAGCGCACGGTACTTATAATCAGTATTCTGTGTGTATGAGCGATGCCG
DroYak_CAF1_left   TTTCAGGGTCGAGCGT-CTTG--TTTCGCATTTGGCGGCGCTCAG-TCAACAGCTCCAGTGGCGCAATTGGTTAGCGCACGGTACTTATAATCAGTATTCTGTGTGTATGAGCTATGCCG
DroAna_CAF1_left   TTTGAGGGTCGAATCT-CATA--CTGGGCATTTGGCGGCGCTGAA-CCAACAGCTCCAGTGGCGCAATTGGTTAGCGCACGGTACTTATAATCAGTATTCTGTGTGTATGAGCTATGCCG

DroEre_CAF1_left   GGGTTGTGAGTTCGAGCCTCACCTGGAGCAAGTCGC-TGGTGACTATATCTTTTTG-GTGCAGTTTTTTTTTTTTTCTTAAATAGTTTTGTATTTTAAAACTC-TTTAAATATT-ATTTC
DroGri_CAF1_left   GGGTTGTGAGTTCGAGCCTCACCTGGAGCAGGTCTT-TGTCGACAATTTTTTCATA-TTTTTTTTCAATTAATTTTCCATTGCTTTGCCTATTTCAGCAATTT-TCACGTTTCT-AGCTT
DroMel_CAF1_left   GGGTTGTGAGTTCGAGCCTCACCTGGAGCAAGTCGT-TGGTGACTATATATTTTTTG--GTCCAGTTTTTTTTTAATAAGTTTTTTTTTAGGACTGTTAAATA-TTACTTTAAATGTTTT
DroMoj_CAF1_left   GGGTTGTGAGTTCGAGCCTCACCTGGAGCAGGTCAC-TGTTGACTAATATTTTTAT-TTTTTTTTTTA---AATAATTTG-ACCAT-ATAAAAGTAACATAAA-A-GATGGTTTGAAGC-
DroPer_CAF1_left   GGGTTGTGAGTTCGAGCCTCACCTGGAGCAGGTCGG-TTGAGACTTAATTTTTTT-GCCCTCCTTTTCTTCATTTTCTTTCTTTTTCACGATTTCCTCATCAT-TCTCAGCTTTGGTTGG
DroPse_CAF1_left   GGGTTGTGAGTTCGAGCCTCACCTGGAGCAGGTCGG-TTGAGACTTAATTTTTTTTGCCCTCCTTTTCTTCATTTTCTTTCTTTTTCACAATTTCCTCATAAT-TCTCAGCTTTGGTTGG
DroSec_CAF1_left   GGGTTGTGAGTTCGAGCCTCACCTGGAGCAAGTCGC-TGGTGACTATGTATTTTTT-GATACAGTTTTTTTTTTTTCTTAATAAGACTTTATATTTAGGACTG-TTAAATATAA-CTTTA
DroVir_CAF1_left   GGGTTGTGAGTTCGAGCCTCACCTGGAGCAGGTCGT-TGTCGACTGTTCTTT-TTTATTTTTTTACGCTTTATTTTTATTTTCATGGTTTTTAAAAATAATTT-TTAAGCTTTA-TGTG-
DroWil_CAF1_left   GGGTTGTGAGTTCGAGCCTCACCTGGAGCAGGTCGT-TGT-GACTTTTTTTTTTATTTTTTTCTTTTCTCTTTTTTTTTTTTTTTTTTGCTGTTATATTTTCTTAG-CTTTCAA-TTTT-
DroYak_CAF1_left   GGGTTGTGAGTTCGAGCCTCACCTGGAGCAAGTCGC-TGGTGACTATATCTTTTTG-GTCCAG-TTTTT--TTTTTCTAA-TATTTTTTTTATTTTAAGGC---TTTAAATATT-ATTTC
DroAna_CAF1_left   GGGTTGTGAGTTCGAGCCTCACCTGGAGCAAGTCGCATGGTGACTTAATTTTTTAC-TAAACTTTTATAT--TTTATTTTAG-TTTTTCATTTT-TATTTTAT-TTTATTTATA-ATATA

DroEre_CAF1_left   AAGGGTTTTATTTGGT-TTTAGGGACTTTGAT---TCGCTTAGTATTTTAGTTTATCTTCT----AACGAA-GCCATTC---CCTCTT
DroGri_CAF1_left   GAAAATTGC---------GAT-CTGTAGA-AAGGTTTGAATAT---TGCAAGAAATAATTG----TT--TC-T-GCATT---TTTTTT
DroMel_CAF1_left   ATATGGCCT---------TCAGGGGCTTTAAA---TCGTTTAGTTGTGTATTTGAGTTTCT----TC--AG-GAATA-CAACCCTTTA
DroMoj_CAF1_left   -GT-ATTT--A-------TTATAAAAT-GCGTG-TGTTACAGGTTGTTTAAAA-TATTTTT----AC--TG-TGAGT-A---AAATGT
DroPer_CAF1_left   AGGTTTTTG---------GCT-CAAAATTCTAGGATCTAAAGCGGGTTTTGGTGTGAAATT-----T--AG-TTGTG-G---TTTGGT
DroPse_CAF1_left   AGGTTTTTG---------GAC-CAAAATTCTAGGAGCTAAAGCGGGTTTTGGTGTGAAATT-----C--AT-TTGTG-G---TTTGGT
DroSec_CAF1_left   AAATATTTTATATGGCCCTCAGTGGACTTAAG---TCGTTTATTTCTGTAGTTTAGTTTCT----TCAGAA-AACATTC---A-ATGC
DroVir_CAF1_left   -CT-ATTAT---------AGCGTTAATTGGTAGGATTTTTAAATACTT---TTTTGGACTA----AA--AATAAATA-T---TAATGT
DroWil_CAF1_left   -TT-TGTTT---------GACAAGTTTTAGAACTACTTCTTAGCAACA---AAATAACAAAAATTAA--TTAATGTA-A---AAGAAT
DroYak_CAF1_left   AGGGGTGGTTTGTGGT-TTTAGTGACTTTGTT---TCGTTAGGTATTTTAGCTTATTTTCT----TACGGA-GCCATTCAA-TACATC
DroAna_CAF1_left   AAGTAGTT---TTGGACTTTTTTTGAGCAGCT--TAAAGAAAGTTTTATAATATTGATTCG----AGGTAG-AACATTT---TTTGTT