RNAplot -o svg
change colours in inkscape if desired
transform inkscape svg to pgf/tikz code:
inkscape2tikz -o output.tex input.svg
change tikz code, e.g. add
\tikzstyle{every node} = [fill=white]
for better readability, and deleteline width = XXX
for standard line width
Remove background rectangle
\path[draw=white,fill=white,rounded corners=0.0000cm] (0.0000,0.0000) rectangle (452.0000,452.0000);
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