Figure 2

The two classes of local alignment. Each example shows how the nodal guide tree best aligns to the target sequence. At the bottom is the RSEARCH output for the alignment. On the left is an example of begin locality, while on the right is an example of end locality. The numbers next to the query sequence represent positions relative to the entire query; the numbers next to the target sequence represent positions relative to the subsequence defined in the "Target =" line.