Figure 9

Occupancy probability increases sigmoidally with respect to z , is greater for stronger κB sites and depends upon the padding sequences in the case of self-overlapping binding motifs. Occupancy probability of the bcap and itm2b oligonucleotides used in the gel shift experiment, with either a C or a T at the beginning of the 3' padding sequence, was predicted using an HMM with different z's. The HMM's motif profile was the same in all instances. The predicted occupancy probability rises as a sigmoidal function of z. The occupancy probability of the stronger κB site (itm2b vs. bcap) saturates at lower z, and therefore the occupancy probability of the stronger site is greater at a particular z. Moreover, the occupancy probability of oligonucleotides is greater when the 3' padding sequence begins with a C (resulting in a stronger spurious site) than a T.