Genomes of plants and animals have many copies of simple DNA sequences. These range in size from a few base pairs to several megabases (MB-several million base pairs). The repeat unit may be as small as two base pairs (bp) or as large as 20,000 bp. There is a rough correlation between the size of the core repeat unit and the length of the repeated region of DNA.
At the upper end, are the satellites. DNA satellites were originally detected since such DNA formed a separate band in a density gradient centrifugation. The core repeat unit can be several hundred bp and the satellite might span several MB.
Next are the minisatellites. Minisatellites have repeat units in the range of 10 to 40 bp. They vary in length from a few hundred bp up to several thousand bp.
Microsatellites are the smallest and simplest repeated tandem repeat They have core repeat units of 1-4 bases and general span less than 100bp. There are no common definitions for microsatellites and minisatellites, however. The tandem repeated sequences show a large distribution of the size of the repeat unit and the over length of the repeated locus. Other researchers have proposed the terms midisatellites and macrosatellites to describe regions with increasing larger repeat units and overall lengths. Together, microsatellites and minisatelites make up the variable number of tandem repeats (VNTRs). Microsatellites have also been called other things.
| STR | Short Tandem Reprats |
| SSR | Simple Sequence Repeats |
| SSLP | Simple Sequence Length Polymorphisms |
The lengths of particular microsatellite sequences tend to be highly variable among individuals. These differences make up molecular "alleles".
Microsatellites tend to be flanked by unique sequences. These unique sequences can be used to make primers for PCR. DNA can be extracted from an organism and many different microsatellites can be amplified. The amplified DNA can be run on a gel and labeled to generate a unique genetic fingerprint. It is the relative length of a particular microsatellite that is scored. With modern computerized equipment, single base pair differences can be measured.