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We describe the first haploid minisatellite, the human Y chromosome-specific locus, MSY1. It consists of an array of 48–114 AT-rich 25 bp repeats of at least five different variant types. A minisatellite variant repeat PCR (MVR-PCR) system gives Y-specific DNA codes, with a virtual heterozygosity of 99.9%, making MSY1 by far the single most variable locus on the Y. African populations contain the most diverged MSY1 structures. MSY1 is the only Y-chromosomal system where the characteristics of large numbers of mutations can be studied in detail: it provides a uniquely powerful tool both for the investigation of mutation in a haploid system, and for the dating of paternal lineages.

Hypervariable Digital DNA Codes for Human Paternal Lineages: MVR-PCR at the Y-specific Minisatellite, MSY1 ( DYF155S1 )