The p53HMM Match and Insert Emissions. (a) The match-state sequence logo for the combined-palindromic p53 motif: 1 2 3 4 5 1 2 3 4 5 . (Motif position ã has the complement nucleotide-emission distribution of a.) The height of each letter is made proportional to its frequency at each position, and the letters are sorted in descending frequency order. The height of the entire stack at each position is then adjusted to signify the information content (in bits) of that position . The match-state nucleotide positions 4, 7, 14, and 17 (motif positions 4, 7, , and respectively) are the most conserved and are the main points of contact with the p53 protein. (b) The insert-state sequence logo for the same combined-palindromic p53-model. These nucleotide insertions occur in-between the nucleotide positions shown in part a. The specificity motif of the insert-state emissions is different from that of the match-state emissions. (c) The HMM logo that combines parts a and b and state transition information into one graph. The wide, white-background stacks correspond to the match states in part a, while the narrow, red-background stacks correspond to the insert states in part b. (A weakness of this HMM logo is that the insert-state stacks are so narrow that it is difficult to accurately see the stack specificity depicted in part b.) The y-axis is the same for all three graphs. However, the width of a stack in the HMM Logo is proportional to the expected contribution of that match or insert state to an emitted sequence of the model .