Motifs and their raw scores
are represented in the format depicted to the left.
(a) The scoring matrix is represented according to the log_{2}(P_{i}/Q_{i})
at each position, in which P_{i} is the probability of observing the
letter at a particular position, and Q_{i}
is the background probability. In the final set of motifs, the scoring matrix
is followed by the probability matrix of P_{i}'s (but not in the
example to the right.)
(b) A textbased 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 oneletter 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(Evalue)

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