Overlapping motif occurrences

[mparida]

Hi I am using FIMO to find all the significant+non-significant occurrences of a motif in a set of input sequences.
Sometimes I am getting an isolated motif occurrence and other times I am getting overlapping motif occurrences. Meaning motif #1 and motif #3 occur at the same position in the sequence and with same exact start and end. I am resolving this using the most significant occurrence. Another scenario is motif #1 and motif #3 occurrences overlap with each other but not entirely, sometimes the overlap can be 1 base pair or 3 base pair or 4 base pair. It varies. My question is if this is a problem when I consider there are 2 motifs at this location with overlapping occurrences or is this wrong to say that. Please comment.
Thanks in advance.

[mparida]

FIMO motif co-occurrences

For anyone who is interested I found a valid answer from Charles E Grant.
Biologically, a single site may bind to multiple transcription factors. In fact, the competition between TF for attachment to the binding site may be a key element of the regulatory system.

https://groups.google.com/forum/#!topic/meme-suite/7dAsV-NwuYo