Cis-elements can be entered as TRANSFAC-style matrices, which look like this:
NA AML-1a
XX
DE runt-factor AML-1
XX
BF T02256; AML1a; Species: human, Homo sapiens.
XX
P0 A C G T
01 5 1 2 49 T
02 2 2 52 1 G
03 4 14 1 38 T
04 0 0 57 0 G
05 1 0 55 1 G
06 1 4 0 52 T
You can copy-and-paste these directly from the TRANSFAC website. All lines except the name line (beginning with 'NA') and the nucleotide frequency lines (beginning with digits) are ignored and not required. The name line is required, and should be above the base frequency lines. Alternatively, each cis-element can have a title line starting with ">" and then the name of the element, followed by 4 numbers per line describing nucleotide frequencies at each position in the cis-element. For example:
>element1
0 4 2 14
12 0 0 8
8 0 1 11
20 0 0 0
>element2
13 1 1 5
...
These numbers might come from a multiple alignment of experimentally determined cis-elements. The first column indicates the number of adenines observed in each position, the second column the number of cytosines, the third column the number of guanines, and the fourth column the number of thymines. The two formats can be mixed.
Finally, if you want to specify that some motifs are relatively more important than others in defining clusters, you can do so by placing a line like this within each motif definition (below the name/title line):
# WEIGHT 2.7
This line indicates that you expect this motif to occur 2.7-fold more densely than a motif with weight 1 (the default) within the type of cluster that you are looking for.