jbd2motifinputs.pl processes JBD output for use as input to motif discovery with the TAMO package.

cat sc_gcn4.1.1.jbd | jbd2motifinputs.pl --fasta chr1.fasta --basename sc_gcn4

Will append to two output files named sc_gcn4.bound.fasta and sc_gcn4.bound.score.

You can control how much sequence is pulled around each binding event with the --windowsize parameter. It specifies the number base pairs extracted for each binding event.

You can also use --posteriorbackground, --posteriorthresh, and --sizethresh (see jbd2bindingevents.pl).