MEME results in plain text format.

MEME results in XML format.

Help poup.

Click on the "+" or "-" buttons to the left of the motif to see the forward or reverse complement of the motif if available.

The statistical significance of the motif. MEME usually finds the most statistically significant (low E-value) motifs first. It is unusual to consider a motif with an E-value larger than 0.05 significant so, as an additional indicator, MEME displays these greyed out.

The E-value of a motif is based on its log likelihood ratio, width, sites, the background letter frequencies (given in the command line summary), and the size of the training set.

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 site count, that one would find in a similarly sized set of random sequences (sequences where each position is independent and letters are chosen according to the background letter frequencies).

The number of sites contributing to the construction of the motif.

The width of the motif. Each motif describes a pattern of a fixed width, as no gaps are allowed in MEME motifs.

The log likelihood ratio of the motif. The log likelihood ratio is the logarithm of the ratio of the probability of the occurrences of the motif given the motif model (likelihood given the motif) versus their probability given the background model (likelihood given the null model). (Normally the background model is a 0-order Markov model using the background letter frequencies, but higher order Markov models may be specified via the -bfile option to MEME.).

The information content of the motif in bits. It is equal to the sum of the uncorrected information content, R(), in the columns of the motif. This is equal relative entropy of the motif relative to a uniform background frequency model.

The relative entropy of the motif.

re = llr / (sites * ln(2))

The Bayes Threshold.

The strand used for the motif site.

+

The motif site was found in the sequence as it was supplied.

-

The motif site was found in the reverse complement of the supplied sequence.

The position in the sequence where the motif site starts. If a motif started right at the beginning of a sequence it would be described as starting at position 1.

The probability that an equal or better site would be found in a random sequence of the same length conforming to the background letter frequencies.

A motif site with the 10 flanking letters on either side.

When the site is not on the given strand then the site and both flanks are reverse complemented so they align.

The name of the sequences as given in the FASTA file.

The number to the left of the sequence name is the position of the sequence in the input sequence file.

These are the motif sites predicted by MEME and used to build the motif.

These sites are shown in solid color and hovering the cursor over a site will reveal details about the site. Only sequences that contain a motif site are shown.

These are the motif sites predicted by MEME plus any additional sites detected using a motif scanning algorithm.

These MEME sites are shown in solid color and additional scanned sites are shown greyed out. Hovering the cursor over a site will reveal details about the site. Only sequences containing a predicted or scanned motif site are shown.

The scanned sites are predicted using a log-odds scoring matrix constructed from the MEME sites. Only scanned sites with position p-values less than 0.0001 are shown.

These are the same sites as shown by selecting the "Motif Sites + Scanned Sites" button except that all sequences, including those with no sites, are included in the diagram.

This is the combined match p-value.

The combined match p-value is defined as the probability that a random sequence (with the same length and conforming to the background) would have position p-values such that the product is smaller or equal to the value calculated for the sequence under test.

The position p-value is defined as the probability that a random sequence (with the same length and conforming to the background) would have a match to the motif under test with a score greater or equal to the largest found in the sequence under test.

Hovering your mouse over a motif site in the motif location block diagram will show its position p-value and other information about the site.

Use this button to download the "Motif Locations" block diagrams as a PDF image suitable for publication.

Only the block diagrams currently visible in the inner scrolling window (below) will be included in the image, and the numbers to the left of each sequence name will not be included in the image. You can change the size of the inner scrolling by moving the bottom of the main document window up and down. You can display more diagrams by making your browser's font size smaller.

Use this button to download the "Motif Locations" block diagrams as a SVG image use in HTML documents.

Only the block diagrams currently visible in the inner scrolling window (below) will be included in the image, and the numbers to the left of each sequence name will not be included in the image. You can change the size of the inner scrolling by moving the bottom of the main document window up and down. You can display more diagrams by making your browser's font size smaller.

This button will only function if your browser was connected to the internet when you loaded this page.

To use this button, make sure your browser is connected to the internet and then reload this page. (You may need to do a "hard refresh" to clear the cache. On Mac, hold down the Shift key and click the Reload button. On Windows/Linux, hold down Ctrl and press F5.)

This diagram shows the location of motif sites.

Each block shows the position and strength of a motif site. The height of a block gives an indication of the significance of the site as taller blocks are more significant. The height is calculated to be proportional to the negative logarithm of the p-value of the site, truncated at the height for a p-value of 1e-10.

For complementable alphabets (like DNA), sites on the positive strand are shown above the line, sites on the negative strand are shown below.

Placing the cursor over a motif site will reveal more information about the site including its position p-value. (See the help for the p-value column for an explanation of position p-values.)

The name of the file(s) of sequences input to MEME.

The position specific priors file used by MEME to find the motifs.

The alphabet used by the sequences.

The number of FASTA sequences provided in this input file.

The number of characters in the sequences provided in this FASTA input file.

The name of the alphabet symbol.

The frequency of the alphabet symbol in the dataset.

The frequency of the alphabet symbol as defined by the background model.