I'm trying to understand profile plots for motifs. Homer has a function annotatePeaks.pl) to generate motif density profiles that looks like following (lifted from here)
While I understand what these profile plots convey for ChIP-seq data (e.g. those generated by deepTools plotProfile), but I'm not sure what exactly is the y-axis in above plot.
So the question is, is it just the probability of finding given motif at each position (as MEME does here) in a set of given sequences or is it the actual count normalized to something?
I didn't find any explanation on homer website. It would be great if anyone can explain what exactly is going on in above plot.