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


DroGri_CAF1_left   A-AGTTATTAACCCTGT--T-TTCAATTTGTAGATTTAAGTTTGTTGACCATTAAAATAAAAACAATAAAAACAAAATTCGTTTTGCTTGTTGA----CACTTTGGTAACAC-ATCTCGT
DroMel_CAF1_left   T-GGTACCTCTAAAAGTATT-ATTTGATTTATAAGTTGTTGACATTGACCATTTAATTAAAATTCATGAAAAAAACAAGT-TCGGCATTTTATT----ATTTTCGGTG-ACC-GCTTGAT
DroMoj_CAF1_left   ACTATTTTGCC-ATGTTATTAATGTGTACATAGCTATAAGTTCGTTAACCATTAAAAATTGA-AT-ACAGAAATAC-CTAACTTTGTTCGTAAA----TGTATTCACAACGC-CCGTCTT
DroSec_CAF1_left   T-GGGACCTCCAAAAGTATT-ATTTGATTTATAAGTTGTTGACATTGACCATTAAATTAAAATTCATGAAAAAGACAAGT-CCGGGATTTTGTT----ATTTTCGGTG-ACC-ATTTGAC
DroWil_CAF1_left   G-TTTTAAGACTGTTGACTT-TGCAAATAAAATATTTAAATAAAACATATAAAATTACAAAATTTAATAT-TTTCCAAAG-GTCAAATCGGTTTGTTACAAATTG-CT-AGCTGAATACC
DroYak_CAF1_left   G-TACATTGC--AAAGTATT-ATTTAATATATAAGTTGTTGACATTGAATATTAAATTTAAATTCACGAAAAAAACACATGCCGGCCATGTTAA----TGTTTTGACTGCCT-ATTGAAC
DroSim_CAF1_left   T-GGGACCTCCAAAAGTATT-ATTTGATTTATAAGTTGTTGACATTGACCATTAAATTAAAATTCATGACAAAGACAA-GTCCGGCATTTTCTT----ATTTTCGGTG-ACC-ATTTGGC

DroGri_CAF1_left   ATATGGGGATGTAGCTCAGATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTACGGGGATCAATGCCCCGCATCTCCAGTTGTTCGAAATTATAT-TTTTGGC-TTTTGCTAATTTTCTAA
DroMel_CAF1_left   ATAAGGGGATGTAGCTCAGATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTACGGGGATCGATGCCCCGCATCTCCAGGA---ATAAGTCTTATATTTTCTT-TTTCCCAAACAAATGTT
DroMoj_CAF1_left   GCATGGGGATGTAGCTCAGATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTACGGGGATCGATGCCCCGCATCTCCAATG---GG---AATTAATCTTTTGC-TA-ATGTATTTAATAAA
DroSec_CAF1_left   ATAAGGGGATGTAGCTCAGATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTACGGGGATCGATGCCCCGCATCTCCAGAT--CTCAATAGTCTTATTTTTTC-TTTTTCAAACAAATGTT
DroWil_CAF1_left   ACAAGGGGATGTAGCTCAGATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTACGGGGATCGATGCCCCGCATCTCCAGGA---TTA--GATTT-CTTTTATTTTTATATTTATTT-----
DroYak_CAF1_left   ACAAGGGGATGTAGCTCAGATGGTAGAGCGCTCGCTTAGCATGTGAGAGGTACGGGGATCGATGCCCCGCATCTCCAGCT---CTT--TGT-TTATTTTTTC-GC----TATTGAATGGT
DroSim_CAF1_left   ATAAGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN--NNNNNNNNNNNNNNNNNNNN-NNNNNNNNNNNNNNNNN

DroGri_CAF1_left   ATTG-TGCAATA--AGATCAAGTTGTTGCTCTTATCTAATTAACTCAGAA-GCCCATGCCAAA-A---AAATACAGTTATATTGGGTATTTAAATATATGTGTG---TAAT
DroMel_CAF1_left   TATTTTTCGTTTTTCTT-AATTAAAGTGGT-TTTGCTTGTTTATTTACAGCAGTGTTTTTGTT-TGC-GTAGCCTGATAAAGTA-AAATGTGCAATTATCAGGCCA----A
DroMoj_CAF1_left   TTTA-GCT-A---GCTA-GTCTA---CAAA-TATATAA-TATATATGCGTAAGCTTATTTAAT-AGT-TTATTTGTTTACTGCA-CAACAAACAAAGCAT--ATATGCTTA
DroSec_CAF1_left   TATT-TCCGTTT--TTT-AATTAAAGCGGT-TTTGCTTGTTTAATTACAAAAGTGTTTTTGTT-TGC-GTAGCCACATAAGGTA-AAATGTGCAATTATCAGCCCA-GCGG
DroWil_CAF1_left   ---ATTGCTTGAATTTT-AGCCACATCTT---TTGA---TGGAGAAGAGCCAGTATTTTAAAGATAT-TTCCTTTTCTACGATA-AATAATATATAAGAA--TATTAGTCA
DroYak_CAF1_left   ATATTTTCTT-TTTCTA-AATTAATGTGGT-TTTGCTTGTTCATTTGCAATCGTATTTTTGTT-GTA-TTTA-CTCGTTTGC-C-CAGCGATATAAAGTAAAGTGCGTAGT
DroSim_CAF1_left   NNNN-NNNNNNN--NNN-NNNNNNNNNNNN-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-NNNNNNNNNNNNNNNNNNNN-NNNNN-NNNNNNNNNN-NNNNNNNNN