SeqPos motif tool output help

[Tyler Miller]

Hi,

Could someone point me to a resource that has an explaination for the output in the SeqPos motif tool on Cistrome? I've searched all over, and read both the 2011 Cistrome paper and the 2010 Nat. Genetics paper that SeqPos was based off of and it's still not clear to me.

Specifically, I'm wondering about the following questions:

1. What is the "mean_position"? Is this a percent away from the center of the peak? Like if I search 500 bp around the center of the peak, is this 8% away from center? 

2. What does the capitalization mean for the "collapsed_idfactor"? Does this mean some are human and some are mouse? If the motif is the same across both species, does it show up as one vs. the other? These were run on files derived from mm9. 

3. Something not specifically related to the output, but it's not entirely clear to me why making the "width of region to be scanned" larger seems to give better results. If someone has an explanation that would be great!

Thanks for your help!

Ty

clusters	collapsed_id	factor	DNA binding domain	hits	cutoff	zscore	-10*log(pval)	similarity to top	mean_position
1	MS00115	NFIX	Nuclear Factor I-CCAAT-binding Transcription Factor (NFI-CTF) Family	1769	6.228	-14.009	690.776		-0.08
	MC00475	Nfic	Nuclear Factor I-CCAAT-binding Transcription Factor (NFI-CTF) Family	2767	6.56	-11.91	690.776	0.943	-0.056
	MS00114	NFIB	Nuclear Factor I-CCAAT-binding Transcription Factor (NFI-CTF) Family	2408	3.978	-10.592	593.805	0.976	-0.054