Weight matrices are kept in plain text file.
The number of weight matrices in a file is limited only by common sense.
Weight matrices are separated by line with double slash ("//").

Example:

NA  Motif-1
P0  A  C  G  T
01  0.5  0.1  0.1  0.3
02  0.1  0.1  0.7  0.1
03  0.2  0.3  0.3  0.2
04  0.7  0.0  0.2  0.1
//

"NA" field contains WM name.
"P0" field contains letters of sequence alphabet labeling corresponding columns.
Fields "01","02",.."XX" contain counts/frequencies of corresponding letter at this position.