Fig. 6

Tandem segmental duplications are bounded by GAT STRs. a Segmental duplications that include D1 genes are present in all three clusters (dark gray rectangles), are bounded by GAT STRs (black triangles denote GAT STRs of 35 or more repeats; gray triangles denote 4–17 repeats), and are indicated by the Cluster number and order of appearance (1–1, 1–2, etc.). 3* indicates a partial segmental duplication in Cluster 3, which is flanked by a GAT STR on the left and GA STR on to the right. The locations of putatively deleted genes in Cluster 3 are marked as “Gene?” in light gray that correlate with the positions of long GA repeats (see Fig. 5). b An alignment of the full length segmental duplications was employed for phylogenetic analysis by maximum parsimony using MEGA. Bootstrap numbers are indicated and based on 500 iterations. The regions surrounding B8 and B8a are defined as the outgroup (OG-1, OG-2). The sequences of the segmental duplications used for the alignment and phylogenetic tree are from BAC 10B1 (GenBank accession number KU668451) duplication 1–1 is nt 110752–115376; duplication 1–2 is nt 115460–120091; duplication 1–3 is nt 120177–124609; outgroup OG-1 is nt 106160–110660. BAC 10K9 (GenBank accession number KU668453) duplication 2–1 is nt 121690–126221; duplication 2–2 is nt 126365–130976; outgroup OG-2 is nt 117100–121600. BAC 3104P4 (GenBank accession number KU668454) duplication 3–1 is nt 91585–93433 and the partial duplication 3* is nt 96723–98626