One can realize that this transformation preserves all of the critical points [20]. Now, we will describe the construction of the gradient system and the Hessian in detail. In order to reduce the dominance of one variable over the other, the values of each of the nucleotides that belong to the consensus pattern at the position k will be represented in terms of the other three nucleotides in that particular column. Let Pikdenote the kth position in the segment Pi. This will also minimize the dominance of the eigenvector directions when the Hessian is obtained. The variables in the scoring function are transformed into new variables described in Table 2. Thus, Eq. (4) can be rewritten in terms of the 3l variables as follows: