Yes, I did compared with the consensus of common motifs - it is recognized by a bunch of different TFs. This by itself is not surprising, since the genes I am looking at are co-regulated, and it is expected that they have some common TFs binding at the promoter. What I did not expect was to find such a large motif, which indeed looks like an assembly place for a larger TF complex. Still, my question remains: is it typical to find such a large common region in so many gene promoters?
PS. The motif was initially identified using MEME with standard parameters
It also depends on the target proteins. If the data is from histone modification study, you may find long motifs as histones spans a large part of DNA. Hence, reads generated from those regions gives you long motifs.
What is the target protein of your experiment/data?