Density of predicted TFBS and binding TF in different DNA sequences. Transcription factor binding sites (TFBS) were predicted with MATCH, using the nucleotide matricial description of each site as compiled in TRANSFAC. Predictions were run on three DNA sequences: the URR of HPV16, the HPV16 full-genome except the URR, and a random DNA sequence with the same base composition than HPV16. Results were normalised with respect to the actual predictions in the randomised sequence. Values are shown for the total number of predicted TFBS (a) and for the total number of predicted binding TF (b) since some TF were predicted to have more than one binding site.