Highlight CpG sites with Texshade I am using Texshade to produce figures for MSA. Upon reading the documentation I could not find anyway to highlight how conserved CpG sites within the alignment. Does anyone know if this is possible? If not is there another MSA visualizer I can use that can produce a figure like this. Thanks!
The best solution I could find was to use the \shaderegion function on all the sequences so it ended up looking something like this:

\shaderegion{1}{CG}{Red}{OrangeRed}

\shaderegion{2}{CG}{Red}{OrangeRed}

...


Then I cast the rest of shading similarity to grey so the CG pairs were more easily distinguishable.

\shadingcolors{grays}


Two examples one with \fingerprints and one regular.