Figure 1From: Fine scale structural variants distinguish the genomes of Drosophila melanogaster and D. pseudoobscuraSequence similarity between Drosophila melanogaster (D. mel) and D. pseudoobscura (D. pse) for the Sox21b (CG32139) gene. Top panel: sliding-window BLAST profile. We stepped through D. melanogaster Sox21b gene in 15 bp increments, and at each position BLASTed a 31 bp segment against the D. pseudoobscura ortholog. Each line represents a BLAST hit with a score above 45, the endpoints show the position of the hit in each genome, and the color of the line represents the orientation of the hit (black = same sequence orientation in each genome, red = different orientations in each genome). Central panel: structure of the Sox21b gene in D. melanogaster. Filled boxes represent exons, and open boxes represent untranslated regions (UTRs). Bottom panel: VISTA plot. The appropriate region of the D. melanogaster-D. pseudoobscura genome alignment was downloaded from the VISTA Browser [44]. We stepped through the alignment in 5 bp increments, and for each 501 bp window calculated the percentage of identical nucleotides between the sequences. The plot is shown relative to the D. melanogaster sequence, and represents a smoothed curve through the data using the ksmooth function in the statistical programming language R [49]. Areas under the curve are painted if they show >70% nucleotide conservation (dark blue = within an exon, light blue = within a UTR, pink = intronic and >100 bp in size).Back to article page