VNTR remodeling at the DNA level. (A) Comparison of the repeat unit schemata of orthologous SVA_D elements in human and chimpanzee. D11 to D20 are generic identifiers. The genomic positions of the elements are provided in Additional file 1. Repeat unit arrays detailed in B, C and D are highlighted in grey. A likely duplication in the human D15 ortholog is marked with an arrow. HSA – Homo sapiens; PTR – Pan troglodytes. (B) and (C) represent examples of indels resulting from a microhomology-driven mechanism. Repeat units are separated by dashes; microhomologies are highlighted in grey. Note that in (C) identity within the microhomology is not 100% - likely due to divergent sequence evolution in the two species. BP – breakpoint (D) shows an example of repeat unit conversion resulting from small scale insertion/deletion. The complete pairwise alignments for all ten elements analyzed are provided in Additional file 1: Figure S5.