I'm currently learning how to use MEME-Suite (web tool) to find a specific known transcriptor binding site in the promoter region of 5 putative bacterial genes of interest, but the results obtained with just the five promtoer sequences have an E-value too high. What can I do to improve these results? Can I use as input some other reported sequences that have the motif I'm looking for without introducing any bias?
I used the option ZOOPS, with a background model of first order, and I limited the search to palindromes only, since I'm looking specifically for a 20 bp sequence with dyad symmetry. The input sequences are the promoter regions of each gene (200 pb upstream of the start codon).