In homer, when using the findMotifGenome.pl tool, there is a parameter, which plays an imprtant role in searching for enriched motifs, the size of the region to search for.

In the description of the tool, they mention this sentence:

... However, for Transcription Factor peaks, most of the motifs are found +/- 50-75 bp from the peak center, making it better to use a fixed size rather than depend on your peak size.

Why is that?

Would this apply to all organisms (we're working on bacteria)?

What would be the differences between findMotifsGenome.pl and findMotifs.pl?

thanks