Fig. 1

An example of local alignment. Two sequences s _a and s _b are aligned in this example. Alignment over sequence s _a is given by [x,y]=[ 1,8] while that over sequence s _b is given by [ z,w]=[ 3,10]. Notation “-” represents an empty symbol, which is skipped when computing x, y, z and w. In this example, the gap cost is o=−2 and the costs of a match and a mismatch are α=2 and β=−1, respectively