You can use ChIPBase database to discovering transcription factor binding motifs, profiles and targets from ~10,200 curated peak datasets derived from ChIP-seq methods in 10 species(Human, Mouse, Fruitfly, Worm, A. Thaliana, Yeast, Rat, Zebrafish, X. tropicalis, Chicken).
Genomatix is a paid data-base that has this information. I believe there is a program called Match. The link provided points to a page that has the information about many programs. You need to register, and you can use the "free" version of the program on the website. If you need to do anything more you need subscription to Biobase or Genomatix.