About Position Frequency Matrix (PFM)

For degenerate consensus sequence representation of PFM we used IUPAC notations.

To define consensus sequence we followed following rules (adapted from Cavener, Nucleic Acids Res. 15, 1353-1361, 1987):

A single nucleotide is shown if its frequency is greater than 50% and at least twice as high as the second most frequent nucleotide.

A double-degenerate code indicates that the corresponding two nucleotides occur in more than 75% of the underlying sequences but each of them is present in less than 50%.

All other frequency distributions are represented by the letter "N".