Highlight CpG sites with Texshade
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.