Figure 8.
Partial alignments in the alignment module. Three partial alignments of length k = 6 between a pair of reads coalesce to yield a single full alignment of length k = 19. Vertical bars denote matching bases, whereas x's denote mismatches. This illustrates the commonly occurring situation where an extended k-mer hit is a full alignment between two reads (k = 6 is used in the figure for simplicity).
