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Scoring the match to the consensus sequence

The simplistic picture of transcription factor binding is that it will bind to a specific sequence or consensus sequence (e.g. AATCGTTA) within the DNA. In reality there will be a range of different, but similar sequences that it may bind to, with some sequences being a better match, and so associated with a higher binding probability than others.

There are two ways of calculating the probability of binding: p values and using a Baysian scores.