Sanger-sequenced sub-region aligned to pooled BAC 454 assembly. A. The Sanger-sequenced (reference) and 454 35L-20PP pseudomolecules are compared on this percent identity plot produced using the LAGAN algorithm  implemented using the VISTA browser . Regions of assembly discrepancy are indicated with arrows. Inset shows MUMMER dot plot of this alignment. B. Left panel shows alignment of Matina 1-6 454 35L-20PP pseudomolecule with the first 3.5 Mbp of Tc05 contig derived from the T. cacao cv. Criollo genome assembly. Region between the black open circles indicate approximate location of Sanger-sequenced interval. The right panel shows alignment of Matina 1-6 Sanger-sequenced pseudomolecule against the same segment of the Criollo genome assembly.