FIMO is a tool that searches for binding sites in sequences of interest (your DHS sites), for TFs of interest (your TF databases).

You might be interested to read my tutorial on how to use CENTIPEDE to determine if a transcription factor is bound to a genomic site by making use of DNase-Seq data.

With UGENE you can also find TFBSs in your sequences in a single-sequence or in streaming mode. Two methods are available: Weight matrix and SITECON.

You can try PlantRegMap for TFBS of Plants.