Figure 2

Hidden Markov model logos obtained using MEME/TOMTOM based on predicted soybean Hsp 20 promoter sequences. The motifs obtained via MEME analysis were plotted according to their position within the consensus sequences, and their locations are presented as graphs using HMM. The events are classified by p-value and aligned with motifs available at DB. The motif e-value is an estimate of the expected number of motifs with the same size and occurrence that would be present in a set of similarly sized random sequences. The heights of the symbols at each motif position indicate sequence conservation. The sequences were manually highlighted to indicate the perfect recognized HSE consensus (red box; nGAAnnTTCnnGAAn or nTTCnnGAAnnTTCn) and the imperfect HSE module (yellow box). Three motifs are found, with the elements being represented by the perfect HSE in alignments 1 (Matches to Query: 1) and 3 (Matches to Query: 3) in the figure. Only the upstream sequences of gene models with a predicted 5′UTR were analyzed.