Some background, I am looking for E-Boxes around genes that showed increased expression after a certain treatment involving a E-Box binding protein. Right now I am looking for a tool that could tell me how many times the E-Box pattern comes up in and around these genes in order to better decide on who to focus on and who are more likely to be influenced directly by my E-Box binding protein.

I managed to show through ucsc’s genome browser where they are but I cant find an option there to tell me how many there are (there are dozens to hundreds) so I am looking for an alternative…

Any ideas?