http://www-bimas.cit.nih.gov/molbio/proscan/

http://www.ifti.org/cgi-bin/ifti/Tfsitescan.pl

These are the only sites I know. Just work good for mammalian sequences.

http://epd.vital-it.ch/

http://www.dna.affrc.go.jp/PLACE/

http://bioinformatics.psb.ugent.be/webtools/plantcare/html/

http://www.softberry.com/berry.phtml?topic=plantprom&group=data&subgroup=plantprom

https://www.wageningenur.nl/en/show/PRECISE-Prediction-of-REgulatory-CISacting-Elements.htm

http://meme.nbcr.net/meme/

Maybe some of these site could be to helpful for you,

regards,

http://www.rsat.eu/

It works with different organisms, and there are many tutorials and demos

:)

There are different tools, but MEME suite is the reference package to use. I have also used Dispom sometimes. Hope it help.