Figure 1.

Genome-wide predicted high confident structure set and synonymous substitution rates. Pairs of vertical lines above the genome represent the stem regions of the high confidence structure set (HCSS; Additional file 2). The cyan and magenta vertical lines indicate the fifteen highest consensus ranked structures (as estimated using the highest average ranking across all consensus ranking tests performed, see Methods), with the cyan line representing the 5’-most stem of the structure – and the magenta the 3’ (single cyan lines represent structures to small to be displayed in their entirety at the current image scale). Nucleotide positions are shown on the x-axis. The vertical lines below the gene map indicate site-to-site variation in synonymous substitution rates (see colour key). Blue and green coloured lines represent codon sites having lower and higher than expected (elevated or reduced rate, relative to the mean) synonymous substitution, respectively.