Alignment of the T. cacao cv. Matina 1-6 physical map to the T. cacao cv. Criollo draft genome sequence. A. A SyMAP dot plot alignment of the anchored contigs of the T. cacao cv. Matina 1-6 physical map and the T. cacao cv. Criollo genome assembly . Purple boxes highlight synteny blocks. The red shaded box is a dot plot view of alignments detailed in 5B. B. A 2D view of T. cacao cv. Matina 1-6 chromosome 5 aligned to T. cacao cv. Criollo chromosome 5. Purple lines represent BES matches to respective locations. Markers from the T. cacao cv. Matina 1-6 chromosome 5 linkage group are designated on the left. C. A SyMAP 3D view illustrating duplications of regions of T. cacao cvv. Matina 1-6 pseudomolecule ten and matches for those regions on various T. cacao cv. Criollo chromosomes. Green shade indicates direct orientation and red shade is inverted orientation.