Convert the motif to a MEME representation, unless you have this already. Use this MEME matrix with FIMO to find hits or binding sites across the genome at a specified threshold. Use BEDOPS
bedmap to map these binding sites to gene annotations, converted to BED with BEDOPS
convert2bed, if necessary.
You can use GimmeMotifs (disclaimer: I am the author). You will have to use a motif representation (positional frequency matrix) that looks like this:
>motif_name 0 0 0 1 0.2 0 0 0.8
Then you can use
gimme scan to scan with this motif:
$ gimme scan sequences.fa -p motif.pwm -g hg19 -b
-b argument specifies BED output. See the full documentation of
gimme scan here.