The fields labelled "Motif A:" through "Motif J:" allow you to enter up to ten short nucleotide sequences (such as transcription factor binding sites or microRNA target sequences). The sequences may contain wildcards (M, R, W, S, Y, K, V, H, D, B, N) as shown in the table to the left of the form, as well as the letters A, C, G, or T. Each sequence must be at least four bases long. Genome Enhancer will search the genome for clusters of these sequences.

Entering a sequence will normally match both the forward sequence as entered and its reverse complement. Prefix a sequence with ">" to match the sequence only in the forward direction, or prefix with "<" to match only the reverse complement of the sequence.