The peaks of a particular Transcription factor CHIP-seq as identified by multiple peak calling algorithms e.g. MACS2 peakzilla e.t.c identify peaks of varying sizes or regions from 50 bp up to 1000 bp or more. In that case I was wondering that if the average size of transcription factor binding site is 10 bp based on available data in OReganno e.t.c (as indicated by [this post][1]) would it be safe to assume that for a particular peak the TFBS location is in its center or not. If not then what would be a good way to go about doing it and if such a method already exist or if someone has already done it.

 [1]: https://www.biostars.org/p/64854/
You could use <a href="http://meme-suite.org/doc/fimo.html?man_type=web">FIMO</a> in the MEME suite to scan for motif models (<a href="http://jaspar.genereg.net">JASPAR</a>, etc.) across your genome of interest, at a level of statistical significance that you deem acceptable (*e.g.*, 1e-4, 1e-5).

Take the search result from FIMO and convert it to a UCSC BED-formatted file. This file contains the putative binding sites of all motifs from the motif models across the whole genome.

Then do set operations with <a href="http://bedops.readthedocs.org">BEDOPS</a> tools (like *bedmap*) to precisely locate putative TF binding sites that overlap with - are contained entirely or partially within - your ChIP-seq peaks.

    $ bedmap --echo --echo-map peaks.bed wg-motifs.bed > answer.bed

If you repeat your experiments with other motifs, you can reuse your whole-genome search result to apply the same set operations.