Sequence-tagged sites (STSs) are short stretches of DNA sequence, usually a few hundred bases long, which can be amplified by the polymerase chain reaction, and are regarded as landmarks in a genome. Presence of a specific STS in a genomic clone or DNA from a specific chromosome can be tested by PCR. STSs are most useful when they have been mapped to a specific chromosome using somatic cell hybrids and to a specific region by screening cell hybrids containing fragments of human chromosomes. An STS map is a collection of STSs ordered along a chromosome with their physical position known. They are used to orientate and order genomic clones such as BACs and YACs in order to generate physical maps. STS maps have been generated for the human genome as part of the human genome project. They have also been generated for other organisms such as the mouse and the zebrafish, usually as a precursor for full genomic sequencing.

STSs can be generated in different ways. Many STSs were generated for the human genome by sequencing a few hundred bases of both ends of BACs. Other STSs were generated by randomly cloning and sequencing small fragments of the human genome. STSs were also generated for the human genome when simple tandem repeat sequence markers (microsatellites) were isolated for genetic mapping. These STSs are therefore used as physical markers and as genetic markers, providing a link between physical and genetic maps.

Clones containing a certain STS can be isolated by screening genomic libraries by PCR. This is an alternative to screening genomic libraries by hybridisation with the STS used as a radioactively labeled probe. The PCR-based screening method is labor-intensive and false negatives are more common in PCR compared to hybridization, so the hybridization method is more commonly used.