Figure 3

Spurious alignment quantities compared to total alignment quantities, with soft repeat-masking. The horizontal axis of each graph represents an E-value threshold and the vertical axis represents the number of alignments (first row) exceeding that threshold, and the number of aligned bases contained in those alignments (second row). In each column, the second-named genome was reversed (black lines) or not (blue lines), and then aligned to the first-named genome using twenty different scoring schemes. The red lines show the theoretically expected number of alignments at each E-value threshold. Repeat-masking was done with WindowMasker, including its DustMasker component.