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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!

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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. enter image description here

enter image description here

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