Figure 4

Trained z is inversely proportional to the length of the training promoter. HMMs were trained on TSS-n promoters keeping the initial motif profile fixed. The transition probability to the motif (z) is inversely proportional to the training promoters' length in the range between 500–3000 bp and hence z* is constant around 0.9. This quantity drops slightly between 500 to 200 bp and then substantially after 200 bp due to the lack of κBsites in the shorter training promoters.