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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

From: Primary orthologs from local sequence context

Genome PairsConditional ProbabilitiesForward StrandReverse Strand
Whole GenomeNRM RegionsWhole GenomeNRM Regions
Human vs. ChimpanzeeP(net | nnem)87.9%97.8%46.9%88.9%
P(nnem | net)96.4%98.7%91.5%94.0%
Human vs. MouseP(net | nnem)12.9%92.0%11.2%90.5%
P(nnem | net)97.1%97.7%96.6%97.2%