Table 5 Comparison between (i) non-nested exact matches (nnem) and (ii) maximal matches from Lastz net alignment (net). Matches compared in this table exceed 30 nucleotide bases in length. Percentages show the conditional probabilities that a maximal match is in one set given that it is in the other. As a prerequisite for Lastz net alignment, the whole genomes were preprocessed by repeat-masker; NRM regions are those parts of the genome that repeat-masker did not mask
Genome Pairs | Conditional Probabilities | Forward Strand | Reverse Strand | ||
|---|---|---|---|---|---|
Whole Genome | NRM Regions | Whole Genome | NRM Regions | ||
Human vs. Chimpanzee | P(net | nnem) | 87.9% | 97.8% | 46.9% | 88.9% |
P(nnem | net) | 96.4% | 98.7% | 91.5% | 94.0% | |
Human vs. Mouse | P(net | nnem) | 12.9% | 92.0% | 11.2% | 90.5% |
P(nnem | net) | 97.1% | 97.7% | 96.6% | 97.2% | |