Each "site-probability" graph shows the probability of the best site of a given motif occuring at a given position in the input sequences. This probability is based only on sequences that contain at least one site with score greater than the score threshold ( bits).

Points (X,Y) on the plot are:
  Y = Pr(best site occurs at position X | sequence contains a site)

Note: The plots are smoothed according to the function selected from the "Smoothing" menu on the right. Setting the smoothing window size to 1 turns off smoothing.

This shows a listing of all motifs currently plotted on the graph.

The color used to plot a motif can be changed by clicking on the color swatch next to the motif you want to change, followed by clicking on the color swatch you wish to swap it with.

These are extra colors you may use for plotting motifs.

Click on the color swatch next to one of the above motifs, then click on one of these "unused color" swatches to change the color of the motif's plot.

These options change the display of the graph.

Smoothing:

Allows selection of the smoothing function applied to the graph.

The weighted moving average option uses weights shaped as an isosceles triangle where the central point (or points in an even sized window) get the maximum weight.

The moving average simply weights all points in the smoothing window equally.

Note: Setting the smoothing window size to 1 turns off smoothing.

Window

The window size used to smooth the graph. The larger the smoothing window size, the smoother the graph, at the cost of hiding detail.

Below a smoothing window size of 10, thinner lines are used on the graph to allow more detail to be visible.

Note: Remember to press "return" or "enter" after changing the number in the input box in order to see the effect of the new smoothing window size.

Legend

Choose to display/disable the on-graph legend. The legend can be moved by clicking on the graph.

Download EPS

Download the graph that you are currently viewing as an encapsulated postscript (EPS) image. EPS images are scalable making them suitable for publication.

List only centrally enriched motifs that meet the selected filter criteria below.

Selected motifs are always listed; deselect all motifs first by clicking on the "X" above the color swatches if you wish to filter all motifs.

To filter on "ID" or "Name", you can enter any Javascript regular expression pattern. See here for documentation on Javascript regular expression patterns.

The name of the database (file name) that contains the motif.

A name for the motif that is unique in the motif database file.

An alternate name of the motif that may be provided in the motif database file.

The probability that a single random motif would have any central bin as enriched for best matches as this combination of motif and bin width does.

The p-value is calculated by using the one-tailed binomial test on each possible centered bin width. The test computes the probability of "bin sites" or more best sites falling in the central bin, given that "total sites" best sites fall somewhere, assuming a uniform null probability. In other words, the probability that a given best site falls in the central bin is assumed to be the central bin width divided by the number of places a motif can align in the sequence (sequence length minus motif width plus 1). The smallest p-value is then corrected to account for the number of bin widths tested.

The expected number of random motifs that would have a central bin as enriched for best matches or better. The E-value is the p-value multiplied by the number of motifs in the input database(s).

The width (in sequence positions) of the central region where the motif may match. This is the width of the most enriched central bin (the one with the smallest p-value).

The number of sequences where the best match to the motif falls in the central bin.

Note: This number may be less than the number of sequences that actually have a match to the motif within the central bin because there may be a match outside of the central bin with a larger score. When there are ties for best match between sites inside and outside the central bin, one is selected at random. This will also cause "bin sites" to be less than the actual number of sequences with a match within the central bin.

The number of sequences containing a match to the motif above the given score threshold ( bits).

The maximum probability observed for the best match occuring at any given position. If the window size on the graph is set to 1, then this is the height of the highest peak.