The next step is to assess the significance of this score, which normally amounts to assessing the significance of finding a specific sequence given the PWM and the background DNA statistics.

The technique used in the bifa tool is to calculate the score and log likelyhood for every single possible nucleotide sequence using dynaic programming methods, ie calcalate the scores/likelyhoods for the four possible values of the first nucleotide, and then for each of these scores calculate what the new scores/likelyhoods will be for each possible value of the second nucleotide, and so on for each nucleotide. The number of scores increases exponentially, so similar scores are combined as necessary. This can then be used to create a map that shows how scores (which range between 0 and 1) map to likelyhoods, in 0.01 score increments.