[Webmail CCG] Understanding output bed file

[romane....@epfl.ch]

Dear all

I am using your tool to evaluate the quality of the motifs of specific transcription factors in a subset of regions (obtained from ChIP-sequencing). For example, in my Nanog regions, I want to estimate the quality of the Oct4 motif compare to random regions.
I am having issues interpreting the score (5ht column) of the output Bed file. I understand it is a score to evaluate how different the sequence is from a random sequence, so the higher the score and the more likely this sequence is a binding site (for Oct4). However, what is a "good" score. Where can I put the threshold after which I consider the sequence not a motif, or a ver degenerate motif ? If I have a score of 135 what does it mean ?

Thank you for your help

Best Regards
Romane Mizeret