Fig. 1

MEMO index outline. A Numbers below the pattern (i.e. pivot genome) are matching statistic (MS) lengths with respect to the Text (i.e. other genome). Triangles represent MS positions and lengths. MS peak lengths are bolded; these correspond to maximal exact matches (MEMs). B Presence/absence of the Pattern’s k-mers depicted as green and red rectangles. Grey triangles represent overlaps between consecutive MEMs. C Order-MEM creation from a pangenome. Top left: Sequences of anchor genome (\(G_1\)) and genomes (\(G_2\)-\(G_5\)). Top right: MSs matrix of match lengths between \(G_1\) and \(G_2\)-\(G_5\). Bottom: Order-MEMs found from MSs. MEM and order triangles of \(G_2\)-\(G_5\) are colored distinctly. Retained match-lengths capturing the landscape are bolded; redundant match-lengths are translucent and discarded in the MEMO indexes. Peaks of a single order are composed of MEMs from varying genomes. K-mer presence/absence of an example query are depicted in green and red. The order-MEM k-mer query enables early stoppage, as depicted by the k-mer in the dotted outline