#Here is an example of an extraction using the new palindrom functionality.
#We aim to extract 3 boxes models, of 4 to 6 bp length each, with one global
#substitution allowed. The quorum is fixed to 50%. Each box is separated
#by 2 to 8 bp.
#We want the first and last boxes of each model to be palindroms.


EXTRACTION (Step 1) =======================================================
FASTA file			fasta
Output file			fasta.out

GLOBAL PARAMETERS =============
Alphabet file			alphabet
Quorum				    5
Total min length		12
Total max length		18
Total substitutions		0
Boxes				    3


BOX 1 ================
Min length			    4
Max length			    6
Substitutions			0
Min spacer length		2
Max spacer length		8

BOX 2 ================
Min length			    4
Max length			    6
Substitutions			0
Min spacer length		2
Max spacer length		8

BOX 3 ================
Min length			    4
Max length			    6
Substitutions			0
Palindrom of box 1            #This line tells that the 3rd box should be
                              #a palindrom of the first one.
