## In the following example, we want to extract models composed of a single box,
## using a degenerate alphabet A,C,G,T,R,Y,N (see file 'alphabet_deg'),
## with at most 2 R.
## Length of the model is between 6 and 8. No subst. allowed. Quorum 90%.

FASTA file              fasta
Output file             1box_deg
Alphabet file           alphabet_deg
Quorum                  90
Total min length        6
Total max length        8
Total substitutions     0
Boxes                   1

Composition in *        1 
## No more than one N for each model (* represents the wild card).
## As the wild card is in the model alphabet ('alphabet_deg' file), it's necessary
## to limit the number of Ns per model. Else, a lot of NNN... models without
## interest will be generated.
Composition in AG       2
## At most 2 R.

Shufflings              10
Size k-mer              2
