Fig. 5

Schematic representation of the pairwise merging process. Dark color represents alignment blocks between the primary and secondary assemblies. Light color represents unaligned sequences. 1) For blocks of aligned sequence, the algorithm inserts the primary sequence to the new metassembly. 2) Insertion in the primary with respect to the secondary assembly: because the CE statistic is a large positive value (>3) for the primary sequence, the algorithm skips the primary insertion and chooses the secondary sequence instead. 3) Both assemblies have an unaligned insertion: because the primary insertion is shorter than the secondary insertion, and because the primary has a large negative CE statistic (< −3), the algorithm will choose the secondary insertion over the primary, thus correcting the CE statistic