For individual motifs, I prefer fimo from the MEME suite. It accepts fasta format. Bedtools getfasta can convert coordinates to fasta. Motif PFMs can be downloaded from JASPAR.

You could make your own database with FIMO and query it as needed:

https://bioinformatics.stackexchange.com/questions/2467/where-to-download-jaspar-tfbs-motif-bed-file/2491#2491

Once you have such a resource, it is easy to query on an ad-hoc basis:

$ echo -e "chrN\t1234\t5678" | bedmap --echo --echo-map --delim '\t' - fimoResults.bed > answer.bed

Or:

$ bedmap --echo --echo-map --delim '\t' myRegions.bed fimoResults.bed > answer.bed

FIMO results generally include the sequence of the TF model, but you can export to samtools faidx for getting back specific sequence over the wider region.