PairwiseAlignment방법가운데 하나.

두서열중 하나 혹은 둘다가 길때, 많은 다른 LocalAlignment들이 존재 할 수 있으며, 생물학자역시 이것에 관심이 많다. 예를 들어, many copies of a repeated [Domain] or [Motif]. 이 방법은 asymmetric하며, 하나 혹은 그 이상의 non-overlapping copies of section 들을 찾는다. 

multiple matches를 찾는 접근은 Waterman & Eggert 에 의해 1987년 소개됨.

Threshold T. (T=20) --> there are always short LocalAlignment with small positive scores even between entirely unrelated sequences. Usually
 * y : containing the domain or motif
 * x : the sequence in which we are looking for multiple matches

{{{#!latex
$$ F(i,0) = \max \left\{ \begin{array}{ll} F(i-1,0) & \textrm{} \\ F(i-1,j)-T & \textrm{j=1,...,m;} \end{array} \right $$
}}}

{{{#!latex
$$ F(i,j) = \max \left\{ \begin{array}{ll} F(i-1,j-1)+s(x_i,y_j) & \textrm{} \\ F(i-1,j)-d & \textrm{} \\ F(i,j-1)-d & \textrm{} \\ F(i,0) & \textrm{} \end{array} \right $$
}}}

Traceback procedure is g global procedure.

Changing the value of T changes what the algorithm finds
 * Increasing T : exclude matches
 * Decreasing T : it may split them, as well as finding new weaker ones