Dotplots of sequence similarity in an allelic bin before and after ordering into hypercontigs by DDA. The x-axis and y-axis in both plots represent sequence from sub-bins A and B, respectively, and cover approximately 550 kilobases (kb). In both plots green dots record a region of sequence similarity on the positive strand and red dots sequence similarity on the negative strand. (a) Before the Double Draft Aligner (DDA) is run on this bin, supercontigs from each sub-bin are unordered and not oriented with respect to one another; their locations are denoted by alternating light and dark blue lines along the appropriate axis. (b) After the DDA is run, contigs from both sub-bins have been ordered and oriented to produce a pair of linearly consistent hypercontigs.