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Background  Compound microsatellites are a special variation of microsatellites in which two or more individual microsatellites are found directly adjacent to each other. Until now, such composite microsatellites have not been investigated in a comprehensive manner.    Results  Our  in silico  survey of microsatellite clustering in genomes of  Homo sapiens ,  Maccaca mulatta ,  Mus musculus ,  Rattus norvegicus ,  Ornithorhynchus anatinus ,  Gallus gallus ,  Danio rerio  and  Drosophila melanogaster  revealed an unexpected high abundance of compound microsatellites. About 4 – 25% of all microsatellites could be categorized as compound microsatellites. Compound microsatellites are approximately 15 times more frequent than expected under the assumption of a random distribution of microsatellites. Interestingly, microsatellites do not only tend to cluster but the adjacent repeat types of compound microsatellites have very similar motifs: in most cases (>90%) these motifs differ only by a single mutation (base substitution or indel). We propose that the majority of the compound microsatellites originates by duplication of imperfections in a microsatellite tract. This process occurs mostly at the end of a microsatellite, leading to a new repeat type and a potential microsatellite repeat track.    Conclusion  Our findings suggest a more dynamic picture of microsatellite evolution than previously believed. Imperfections within microsatellites might not only cause the "death" of microsatellites they might also result in their "birth".

Survey of microsatellite clustering in eight fully sequenced species sheds light on the origin of compound microsatellites