Figure 1

Comparing window contents. Part (a) shows two pairs of non-overlapping windows. Here we have c(X 1, Y 1) = 3 - 2β - γ and c(X 2, Y 2) = 3 - 4β - γ. Observe that motif occurrences near the border between the windows show high similarity. In part (b) we show two extra pairs of windows which partly overlap the windows from (a). The cost of extra windows is c(Z 1, V 1) = 4 - β - γ and c(Z 2, V 2) = 2 - 3β - γ. In part (c) there is presented a similar situation, except the motifs near the border have changed. We obtain the cost for the new contents: c(Z 1', V 1') = 1 - 7β - γ and c(X 2', Y 2') = 3 - 6β - γ. The other contents in (c) remain the same as in (b). Hence, the total cost of alignment in (c) is smaller by 3 + 8β.