The annotation score for a cisRED motif is based on an edit distance calculated between the motif's sequence on the target genome and each site sequence for a known transcription factor in JASPAR or TRANSFAC. In calculating an edit distance, the distance value for each base is normalized by the information content of the JASPAR or TRANSFAC transciption factor at that position. A best match motif position and score is identified by translating the cisRED and known sequence past each other, and considering both forward and reverse complement sequences. A best score is converted into an annotation p-value via a distribution of scores from a large set of random sequences.

The strand information in the table below indicates whether the best score was based on the motif's forward sequence (+), or on its reverse complement (-).

(+)motif	(-)motif
ATTTATTT	AAATAAAT