PWMScan
A Web-based genome-wide Position Weight Matrix (PWM) Scanner
... a PWM, the background probabilities for the letters of the DNA alphabet, and a threshold score or a p-value. The search is carried out across the entire genome sequence. It can accept PWMs, such as those available in the Transfac or Jaspar databases as well as plain-text PWMs. It computes all occurrences of the PWM in the genome sequence for a given p-value threshold or cut-off. The match list is provided in various genome annotation formats, including BEDdetail, FPS, and SGA.