Figure 5.

Genome-wide comparison of repeat densities. A. Inverted repeats (IRs) associated with VCBP2/5 clusters represented by scaffold_295 (haplotype B) and scaffold_82 (haplotype A). The density of IRs in scaffold_295 (and scaffold_82, or the corresponding region of scaffold_82 only, shown as _82b) was compared to the distribution of IRs across the entire Branchiostoma floridae genome. Scaffold_295 (haplotype B) possesses a higher density of IRs than most other scaffolds of related size (and larger) in the amphioxus genome, including scaffold_82 (haplotype A). A large density of the IRs is clustered in the VCBP-associated regions of scaffold _82 (_82b). B. A similar analytical approach was used to compare the distribution and density of tandem repeats. Tandem repeat density in the VCBP locus is consistent with other areas of the genome and are not found to be elevated across these two haplotypes.