Length of peaks

[laij...@gmail.com]

Hello, 

I used MACS2 to obtain .narrowPeak files for 2 biological replicates to use as input to IDR. I then converted my IDR bed file into a FASTA file for downstream motif analysis, but noticed that the lengths of the sequences is very long (average length 13,000 bp). This seems strange as I am profiling a transcription factor so I thought the peaks called should be much shorter width. I would greatly appreciate any input on if others have seen something similar and how I can troubleshoot/limit the length of the peaks. 

Thank you,

Jenny