Figure 3
ZAS-N-selected sequence: MEME motif search and alignment, n = 25. Simplified position-specific probability matrix represents the probability of each possible letter appear a each possible position in an occurrence of the motif. Numbers are described as n/10 (eg 50 is represented as 5), with "0" described as ":". Information Content Diagram provides information of which positions in the motif are most (and least) highly conserved. Columns in the information content diagram are shaded according to the majority category of the letters occurring in that column of alignment. If no letter category has a frequency >0.5, the column is black. A = red, C = blue, G = orange, T = green. Summing of information content for each position gives the total information content of the motif, which is approximately equal to the log likelihood ratio divided by the number of occurrences times ln(2). Multilevel Consensus Sequence is calculated from the motif position-specific matrix where the most likely nucleotide is printed at the top of a column. Only letters with probabilities of 0.2 or higher are included. Summary Information is printed below the multilevel consensus sequence. "Width" describes the length of the motif. "Sites" describes the number of sequences in the dataset which contributed to the consensus sequence. The "log likelihood ratio" is the logarithm of the ratio of the probability of the occurrences of the motif given the motif model versus their probability given the null model. The "E-value" is an estimate of the expected number of motifs with the given log likelihood ratio (or higher), and with the same width and number of occurrences, that one would find in a similarly sized set of random sequences. Motif Alignment displays the occurrences of the motif in the dataset. Each site is identified by the name of the sequence where it occurs, the strand (+ or -), and the position in the sequence where the site begins. The p-value of a site is computed from the match score of the site with the position specific scoring matrix for the motif, and gives the probability of a random string having the same match score or higher. (Above is described in detail at MEME http://www.sdsc.edu/meme[30]).