This tool takes as input a set of "sites" (genomic coordinates), and reports cis-regulatory enriched regions (CRER), i.e. genomic intervals containing a higher number of sites than expected by chance.

The tool can be used to predict cis-regulatory modules (CRM) from collections of transcription factor binding sites obatined by various methods.

1. Predictions obtained by scanning sequences with position-specific scoring matrices (for example the output of matrix-scan
2. Peaks from ChIP-seq experiments.
3. Annotated binding sites imported from a transcription factor database.
4. Any other data source that produces a set of genomic features.