genes saved in sequence file look like this:
>hg18_refGene_NM_006511 range=chr1:15857951-15860804  
cctagtcacctgctaattaatctttttcctttcccctgtgttccatatagagaaaagtggtaaagaatctacctcactgggaATGTCATCATTACCAACTTCAGATGGGTTTAACCATCC
>hg18_refGene_NR_027268 range=chr1:28294033-28296656 
tttttttttttcttcttcttttttgtggagttgctttttttttttttcttcttttttgtgtcattgtttttttaccatgtcctcagagtctggaattttacaaagtagttgctgagtaaacaggTAGATACAAATCAAGATGAACTTTTCCGCAGGAGCTCTTATCATGAACAT

and the binding motifs:
>mot1
tttgtagatttt
>mot2
ggatcctttaag
>mot3
gtttaccccaa