DWE has output in the following format:
{MOTIF} {Frgrnd succs} {Frgrnd trials} {Bg succs} {Bg trials} {Log Freq Ratio} {Z test} {p-val}

Please specify whether you would like the output sorted by LFR, Z or p-val (when sorting by p-val lower p-val corresponds to a stronger signal, and when sorting by LFR or Z higher values correspond to stronger signals).

Select "Yes" for "Remove dependent words" to supress the output of dependent lower scoring motifs.

For example:
Selecting "number of motif to report" as 10 and widow size as 7 will report 10 motifs, where none has a window of width 7 that is more similar than 5% to any other reported motif.

DWE reports all motif tuples instead of single motifs. It expects to get a list of single motifs as input, and it reports all motif tuples in the same format as DWE. There are no thresholds. Currently, DWET only supports 2-tuples (pairs).

Reference:
Sumazin, P., Chen, G., Hata, N., Smith, A.D., Zhang, T. and Zhang, M.Q. DWE: Discriminating Word Enumerator, Bioinfomatics, 2004.