Sample Motif FormatMotifs and their raw scores are represented in the format depicted to the left.

(a)  The scoring matrix is represented according to the log2(Pi/Qi) at each position, in which Pi is the probability of observing the letter at a particular position, and Qi is the background probability. In the final set of motifs, the scoring matrix is followed by the probability matrix of Pi's (but not in the example to the right.)

(b) A text-based logo of the motif in which the height of letters is proportional to the sum of the relative information content of all the letters at that position.

(c) A single line repeating the one-letter summary of the motif, along with several scores and metrics. For example the following line,

(Bits: 14.82  MAP: 42.51   D: 0.000  -1) E: 16.860  ch: 18.34  f:  1.00  Ra: 0.9945

summarizes this information:

Bits

Total number of bits

MAP

For AlignACE and MDscan, this is the MAP score.  For MEME and MEME_c, this is -log10(E-value)

D

Not Used

-1

Not Used

E

Enrichment Score, as described in Methods

ch

Specificity Score, as described in Hughes, et al. (Not Used)

f

Fraction of probes containing motif (1.00 means all probes)

Ra

ROC area under the curve, as described in Methods


(d) A set of 20 generated sequences that, when taken together, approximate the probability values at each position of the matrix.  Used mainly for convenience with other programs that take sets of sequences instead of numerical values.

CACGTGACCA 4 17.996

The "4" value is not used.  The trailing number (e.g. 17.996) is the score the matrix assigns to each sequence.