## In the following parameter file, we show how to use the "against" method
## of evaluation.

FASTA file              fasta
Output file             against
Alphabet file           alphabet
Quorum                  50
Total min length        8
Total max length        8
Total substitutions     1
Boxes                   2

## We want models with at most 4 As in the 2 boxes...
Composition in A        4
## You can write here several lines of composition.

BOX 1
Min length              4
Max length              4
Substitutions           1
Min spacer length       4
Max spacer length       8
## ...and at most 2 As in the first box.
Composition in A        2

BOX 2
Min length              4
Max length              4
Substitutions           1

## Now we use the second method for evaluation: we want to evaluate the
## models found during the first step by looking for them in a "wrong" file
## of sequences (where we do not expect to find them). These sequences are
## in the file 'fastawrong'.
Against wrong sequences    fastawrong

## The results file is the same than after a shuffling, except that 
## statistics for sequences and for total number of occurrences are on
## the same line ('T' means 'statistics on total number of occurrences').
## The only statistical measure we can apply is the Chi2. With this measure,
## we cannot know if the model is over or under-represented (no sign).
## So, a sign is written beside the Chi2 to indicate it.
