check for binding sites of transcription factors

[antoza]

Hi all,
I would like to find putative binding sites of transcription factors for a batch of nucleotide sequences correspond to promoters regions (input file should be a fasta file). Is any suggestion for a tool /software that it could be make this job??
P.S. The promoter regions are from Arabidopsis.
Thanks in advance--

[SNPsaurus]

I've used RSAT (http://embnet.ccg.unam.mx/rsa-tools/) for identifying enriched TF sites in putative enhancer regions of 400 bp. The linked site warns about false positives when using promoter regions, so keep that in mind.