Trained HMM Parameters. A. Sequence logo of the motif profile of the HMM trained on 50 bp sequences each consisting of a known κB site and surrounding region (surround-50 HMM) with initial transition probability to the motif (z) equal to 0.02. B. The estimated transition probability to the motif (z) for upstream 800 bp and downstream 100 bp regions with respect to the transcription start site (TSS) as the number of randomly selected training genes increases. The estimated z stabilizes after the addition of a few thousand genes. Each training set contains all sequences with known κB sites in the relevant region (20 and 4 known sites for the upstream 800 bp and downstream 100 bp regions, respectively).