Figure 1

E-values of reverse genome alignments with six repeat-masking methods. In each column, the second-named genome was reversed and then aligned to the first-named genome twenty times, using twenty different scoring schemes. The red lines show the theoretically expected number of alignments at each E-value threshold, and the black lines show the observed number. Alignments in rows 1-5 and 7 were performed with LAST, and those in row 6 were done with BLASTZ, using BLASTZ's internal entropy-masking method. "TRFs": Tandem Repeats Finder with standard parameters; "TRF": Tandem Repeats Finder with non-standard parameters; "hard": hard-masking; "soft": soft-masking.