Fig. 3.

Left figure is a toy example to illustrate line segments corresponding to multiple local alignments obtained between a query and reference sequence. Each alignment segment is labeled with an alignment score. Suppose we want to filter best mappings for the query sequence. These segments are laid out as weighted intervals over the query sequence (right figure). In the above case, two intervals marked with a cross are completely subsumed by higher scoring intervals, and therefore, will be labeled as redundant by our filtering heuristic