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Microsatellites, or Simple Sequence Repeats (SSRs), are short tandem repeats of 1–6 nt motifs present in all genomes. Emerging evidence points to their role in cellular processes and gene regulation. Despite the huge resource of genomic information currently available, SSRs have been studied in a limited context and compared across relatively few species.

We have identified ~ 685 million eukaryotic microsatellites and analyzed their genomic trends across 15 taxonomic subgroups from protists to mammals. The distribution of SSRs reveals taxon-specific variations in their exonic, intronic and intergenic densities. Our analysis reveals the differences among non-related species and novel patterns uniquely demarcating closely related species. We document several repeats common across subgroups as well as rare SSRs that are …