Figure 6.
The stacking effect. (A) The correct multiple alignment of seven sequences. (B) The multiple alignment of the same seven sequences, with the stacking effect. When only gap-open and gap-continue penalties are used, the stacked alignment (B) incurs one gap-open penalty less than the correct alignment (A), and therefore is optimal. When gap-end penalties are used, the correct alignment (A) is optimal because it incurs two gap-end penalties less than the stacked alignment (B).
