Figure 2.

A sequence logo representing the Hrp promoter HMM used for searching the P. s. tomato DC3000 genome (51). The vertical axis is information content in bits. The height of a nucleotide reflects its representation in the sequence at that position. Nucleotides are displayed upside-down in positions where they occur less frequently than 25%. The expected frequency of nucleotides is listed below each position. This figure represents only the expected nucleotide frequencies at each position, but not the underlying transition and insertion/deletion probabilities. Positions of relaxed insertion probabilities are indicated with an “i.”