GBA uses forget rate (α) to compute the Repeat (R) and Non-Repeat (NR) matrices. These two matrices are used to filter the vertices
constructed for similar letter pairs when they are in the same window by chance (i.e. false positives).
*R* and *NR* are 20X20 matrices that show statistical information
on frequencies of pairs of letters in repeat and non-repeat regions respectively. The values *R(γ*_{i},γ_{j})
and *R(γ*_{i},γ_{j}) represent average probabilities that *γ*_{i} and *γ*_{j}
appear together in a repeat region and non-repeat region, respectively. Forget rate (α) is used as a parameter to calculate *R*
and *NR* ( 0 ≤ α ≤ 1). In general, it is used in various domains to capture the correlation between two objects
that are members of an ordered list of objects based on their spacial distance in that list. A default value of α is 0.95.
*t*_{1} is the length of the sliding window *w*. GBA uses *w* to construct the graph of vertices pair. The default
value of *t*_{1} is 15.
*t*_{2} and *t*_{3} are two distance threshold measure in GBA. Once, the graph of vericies pair is constructed,
GBA incerts edges btween vertices. An edge is added between two vertices *(i, j)* and *(k, m)* if *s(i)s(k)* and *s(j)s(m)*
do not conflict with each other. This property is enforced by introducing distance threshold *t*_{2} and *t*_{3}.
*t*_{2} specifies the maximum number of insertions and deletions between similar repeats. *t*_{3} specifies the
maximum distance between letters in cryptic repeats. The default values of *t*_{2} and *t*_{3} are 3 and 5 respectively.