The query motifs section lists the motifs that were searched for in the target databases as well as links to matches found.

Name

The motif name.

Alt. Name

The alternative motif name. This column may be hidden if no query motifs have an alternate name.

Website

A link to a website which has more information on the motif. This column may be hidden if no query motifs have website information.

Preview

The motif preview. On supporting browsers this will display as a motif logo, otherwise the consensus sequence will be displayed.

Matches

The number of significant matches.

List

Links to the first 20 matches

The target motifs section lists details on the motif databases that were specifed to search.

Database

The database name.

Number of Motifs

The number of motifs read from the motif database minus the number that had to be discarded due to conflicting ids.

Motifs Matched

The number of motifs that had a match with at least one of the query motifs.

The summary gives the important statistics about the motif match.

Name

The name of the matched motif.

Alt. Name

The alternative name of the matched motif.

p-value

The probability that the match occurred by random chance according to the null model.

E-value

The expected number of false positives in the matches up to this point.

q-value

The minimum False Discovery Rate required to include the match.

Overlap

The number of letters that overlaped in the optimal alignment.

Offset

The offset of the query motif to the matched motif in the optimal alignment.

Orientation

The orientation of the matched motif that gave the optimal alignment. A value of "normal" means that the matched motif is as it appears in the database otherwise the matched motif has been reverse complemented.

The image shows the alignment of the two motifs. The matched motif is shown on the top and the query motif is shown on the bottom.

By clicking the link "Create custom LOGO ↧" a form to make custom logos will be displayed. The download button can then be clicked to generate a motif matching the selected specifications.

Image Type

Two image formats, png and eps, are avaliable. The pixel based portable network graphic (png) format is commonly used on the Internet and the Encapsulated PostScript (eps) format is more suitable for publications that might require scaling.

Error bars

Toggle error bars indicating the confidence of a motif based on the number of sites used in its creation.

SSC

Toggle adding pseudocounts for Small Sample Correction.

Flip

Toggle a full reverse complement of the alignment.

Width

Specify the width of the generated motif.

Height

Specify the height of the generated motif.