### Column 1

If the first column contains a "-", then only known pairs of sites are involved in the clusters at this spacing. For other entries, predictions are numbered, ranked according to their probability.

### Spacing

For predictions based on individual separation distances, this is the most significant base-pair separation between sites.

### #known

This is the number of known pairs separated by the given spacing or spacing range.

### #seen

This is the number of pairs observed at the given spacing. If this number is equal to the number of known pairs (#known), then only the known pairs were observed at the given spacing (no new predicted sites involved).

### #expected

The number of pairs of sites expected by chance.

### ratio

The ratio of the number of pairs observed to the number of pairs of sites expected by chance.

### probability

The probability of seeing the observed number of sites at this separation or within this separation range.

**Abigail Manson McGuire
Genetics Department
Harvard Medical School/BCMP
200 Longwood Ave.
Boston, MA. 02115.
E-mail: amcguire@arep.med.harvard.edu
Telephone: (617) 432-4136
**