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  }

=head1 PARAMETER FOR ALIGNMENT COMPUTATION

=head2 KTUPLE

 Title       : KTUPLE
 Description : (optional) set the word size to be used in the alignment
               This is the size of exactly matching fragment that is used.
               INCREASE for speed (max= 2 for proteins; 4 for DNA),
               DECREASE for sensitivity.
               For longer sequences (e.g. >1000 residues) you may
               need to increase the default

=head2 TOPDIAGS

 Title       : TOPDIAGS
 Description : (optional) number of best diagonals to use
               The number of k-tuple matches on each diagonal