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all sequences should have the same length
Sequence(s) to scan

Escherichia coli K-12 (strain MG1655) sequence and annotations were taken from the sequencing project at the University of Wisconsin, Madison.

An upstream region was taken for a coding sequence if it is the first gene in the operon or follows an annotated promoter. Upstream regions contain between 50 and 600 nucleotides (uppercase) plus 20 nucleotides extending into the coding region (lowercase). Each upstream region is labeled with genes downstream in the same operon.
Negative examples (optional)

each sequence contributes a single negative example – its highest scoring site
Basic Method:


Use information content
Top:     report top n scoring sites
Cutoff: report sites with score >= cutoff
P-value: choose a cutoff so that P[score >= cutoff] = pvalue for a randomly generated sequence of the same length as the motif
Rank: report sites that score higher than the nth negative example
False-Positive Rate: choose a cutoff with an acceptable false-positve rate. specifically, a cutoff so that P[neg >= cutoff] = rate
rank and false-positive criteria require negative examples
use '$1','$2',... to read the value from the sequence description (at the specified position)

Please email questions or comments to msingh at

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