Each "motif probability curve" shows the (estimated) probability of the best match to a given motif occurring at a given position in the input sequences. This estimated probability is based only on sequences that contain at least one match with score greater than the minimum score defined for this motif, and is the maximum likelihood estimate of the conditional probability shown below.

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

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.

If a negative dataset has been supplied then two lines are drawn for each motif representing both datasets. The normal dataset is plotted with a single unbroken line whereas the negative dataset is plotted with a dashed line.

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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.

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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.

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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.

Negative Sequences

Choose whet