HMM hidden states for κB sites. OHMM consists of 21 states. The background state is colored red and designated by B. Each of the 20 motif states corresponds to each of the ten positions within the κB motif on the two DNA strands. The motif states are colored yellow and designated using M, the position within the motif and the strand. The emission probabilities of the motif states on the two strands are flipped from 5' to 3' so as to represent identical binding irrespective of the motif strand. Non-zero transition probabilities between states are represented by black arrows and their values are shown.