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Table 2 Correspondence among combinations of maxmer occurrences and non-nested/nested maximal matches. “Non-nested and nested occurrences” of local maxmers in [29, 37] differ from “non-nested and nested maximal matches” as we define in this table: an occurrence is a single sequence, whereas a maximal match consists of a pair of sequences. Maxmers are classified as “super” or “local.” Occurrences of super maxmers are subclassified as unique super, if they have exactly one occurrence in each of the corresponding genomes; or non-unique super, if occurrences appear multiply in at least one of those genomes. Occurrences of local maxmers are subclassified as non-nested or nested as in [29]. The designations super and local are exclusive of each other, therefore these four types of maxmer occurrences yield six different combinations, of which four are non-nested maximal matches and two are nested maximal matches

From: Primary orthologs from local sequence context

Occurrences of maxmerssuper maxmer(a) unique super or (b) non-unique super
local maxmer(c) non-nested local or (d) nested local
Non-nested maximal matchesMUMs(1) two unique supers
Non-nested maximal matches but not MUMs(2) a unique super + a non-unique super
(3) two non-unique supers
(4) two non-nested locals
Nested maximal matches(5) a non-nested local + a nested local
(6) two nested locals, if together they constitute a maximal match