Figure 6

A problem with large X-drop values. This sketch represents two similar regions with positive alignment scores (red) separated by a dissimilar region with a negative alignment score. For low X-drop values, the two similar regions are found as separate alignments. For high X-drop values, the X-drop algorithm crosses the dissimilar region: so the alignment seeded from the right-hand similarity has sub-optimal score. In this case, LAST would only report the one alignment with score = 500.