Let us consider the following example. sA = s1s2s3s4s5 and π(sA) = {s1, s2, s3, s4, s5}, where s1 = aaa, s2 = aat, s3 = att, s4 = ttt and s5 = tta. The self-alignment of this partition is show in Figure 1. The value of the self-alignment is , where |s1| and |s5| are the penalty scores for the two segments s1 and s5 aligned to spaces.