Can someone explain how the nsites parameter in a meme motif file is used, specifically with fimo? I have a non-standard motif position weight matrix I need to convert to meme format to use with fimo, and since it has no such parameter I must choose one.

Here is what the meme format documentation says about nsites:

The "nsites= source sites" will default to 20 if it is not provided...source sites is used to apply pseudocounts to the motif

I haven't seen any elaboration on other meme website pages or in the 2015 MEME Suite paper, but I haven't combed through any of the other MEME-related publications.

Thanks!