A motif is generated from the specified IUPAC sequence fragment by distributing the site counts equally over each possible residue. The pseudocount is added to each residue in proportion to the background. Thus the total count for a position is the site count plus the pseudocount. For example suppose one of the IUPAC codes entered is 'R'. The IUPAC code 'R' means that both Adenine and Guanine are possible, so with a site count of 10, pseudocount of 1 and a uniform background; the probability of Adenine and Guanine would be:
while the probility of Cytosine and Thymine would be:

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The background is used to determine how the pseudocount is distributed. While it is conventional to have the background sum to one these fields will be normalised so you don't have to be exact. You may even use counts instead. [close]

A matrix is column oriented if it has 4 rows and any number of columns. A matrix is row oriented if it has 4 columns and any number of rows. [close]

The site count is only used when a probability matrix is specified, otherwise it is derived from the matrix.
The pseudocount is added to each residue in proportion to the background. Thus the total count for a position is the site count plus the pseudocount. [close]

The filter supports selecting motifs from the file by their name and/or their order in the file. Any numbers are assumed to refer to the position of the motif in the file. Any other entry is assumed to be a motif name (or ID). Motif names can not start with a dash and can only contain alphanumeric characters plus : _ . and -. The motifs should be separated by spaces. [close]