The short arm of rye chromosome 1 (1RS) carries a variety of agronomically and genetically important genes. In summary, 76 microsatellite markers for 1RS were developed. From 724 designed primer pairs, 119 produced 1RS specific bands, and 74 showed polymorphism in a set of ten rye genotypes. The 76 microsatellite markers were physically mapped into three regions (bins) on 1RS; 29, 30 and 17 loci were assigned to the distal, intercalary and proximal regions of the 1RS arm, respectively. To identify microsatellites in genomic sequences a user-friendly software tool, SciRoKo, was developed. The combination of an extremely fast search algorithm with a built-in summary statistic tool makes SciRoKo highly suitable for whole genome analysis. Compound microsatellites are a special variation of microsatellites, in which two or more individual microsatellites are found directly adjacent to each other. An 'in silico' survey of microsatellite clustering in eight fully sequenced species was performed. Approximately 4-25% of all microsatellites may be compounded. It is shown that the majority of compound microsatellites originates by imperfections in the tracts of primary microsatellites, which are due to replication slippage duplicated in tandem. The findings suggest a more dynamic picture of microsatellite evolution than previously believed.