# Tandem repeat

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Adjacent repeated pattern of nucleotides within DNA

Not to be confused with [Tandemly arrayed genes](/source/Tandemly_arrayed_genes).

In [genetics](/source/Genetics), **tandem repeats** occur in [DNA](/source/DNA) when a pattern of one or more [nucleotides](/source/Nucleotide) is repeated and the repetitions are directly adjacent to each other, e.g. ATTCG ATTCG ATTCG, in which the sequence ATTCG is repeated three times.[1]

Several [protein domains](/source/Protein_domain) also form [tandem repeats](/source/Protein_tandem_repeats) within their amino acid [primary structure](/source/Primary_structure), such as [armadillo repeats](/source/Armadillo_repeat). However, in proteins, perfect tandem repeats are rare in naturally occurring proteins, but they have been added to designed proteins.[2]

Tandem repeats constitute about 8% of the [human genome](/source/Human_genome).[3] They are implicated in more than 50 lethal human [diseases](/source/Disease), including [amyotrophic lateral sclerosis](/source/ALS), [Huntington's disease](/source/Huntington's_disease), and several [cancers](/source/Cancer).[4]

## Terminology

All tandem repeat arrays are classifiable as [satellite DNA](/source/Satellite_DNA), a name originating from the fact that tandem DNA repeats, by nature of repeating the same nucleotide sequences repeatedly, have a unique ratio of the two possible nucleotide base pair combinations, conferring them a specific mass density that allows them to be separated from the rest of the genome with density-based laboratory techniques, thus appearing as "satellite bands". Albeit, a tandem repeat array could not show up as a satellite band if it had a nucleotide composition close to the average of the genome.[5]

When exactly two nucleotides are repeated, it is called a *dinucleotide repeat* (for example: ACACACAC...). The [microsatellite instability](/source/Microsatellite_instability) in [hereditary nonpolyposis colon cancer](/source/Hereditary_nonpolyposis_colon_cancer) most commonly affects such regions.[6]

When three nucleotides are repeated, it is called a *trinucleotide repeat* (for example: CAGCAGCAGCAG...), and abnormalities in such regions can give rise to [trinucleotide repeat disorders](/source/Trinucleotide_repeat_disorders).

When between 10 and 60 nucleotides are repeated, it is called a [minisatellite](/source/Minisatellite). Those with fewer are known as [microsatellites](/source/Microsatellite_(genetics)) or [short tandem repeats](/source/Short_tandem_repeat).

When much larger lengths of nucleotides are repeated, on the order of 1,000 nucleotides, it is called a [macrosatellite](/source/Macrosatellite).

When the repeat unit copy number is variable in the population being considered, it is called a [variable number tandem repeat](/source/Variable_number_tandem_repeat) (VNTR). [MeSH](/source/Medical_Subject_Headings) classifies variable number tandem repeats under minisatellites.[7]

## Mechanism

Tandem repeats can occur through different mechanisms. For example, slipped strand mispairing, (also known as [replication slippage](/source/Replication_slippage)) [8], is a mutation process which occurs during DNA replication. It involves denaturation and displacement of the DNA strands, resulting in mispairing of the complementary bases. Slipped strand mispairing is one explanation for the origin and evolution of repetitive DNA sequences.

Other mechanisms include [unequal crossover](/source/Unequal_crossover) and [gene conversion](/source/Gene_conversion).

## Uses

### Inheritance signal

Tandem repeat describes a pattern that helps determine an individual's inherited traits.

Tandem repeats can be very useful in determining [parentage](/source/Parentage). [Short tandem repeats](/source/Short_tandem_repeat) are used for certain [genealogical DNA tests](/source/Genealogical_DNA_test). [DNA](/source/DNA) is examined from *[microsatellites](/source/Microsatellite_(genetics))* within the chromosomal DNA. Parentage can be determined through the similarity in these regions.

Polymorphic tandem repeats (alias VNTRs) are also present in microorganisms and can be used to trace the origin of an outbreak. The corresponding assay in which a collection of VNTRs is typed to characterize a strain is most often called [MLVA](/source/MLVA) (Multiple Loci VNTR Analysis). Using tandem repeat polymorphism, recombination has been reported in the natural transmission of [monkeypox](/source/Monkeypox) ([mpox](/source/Mpox)) virus genome during 2022 pandemic.[9]

### Domesticated living beings

Studies in 2004 linked the unusual genetic plasticity of [dogs](/source/Dog) to mutations in tandem repeats.[10]

## Detection and analysis

In the field of [computer science](/source/Computer_Science), tandem repeats in strings (e.g., DNA sequences) can be efficiently detected using [suffix trees](/source/Suffix_tree) or [suffix arrays](/source/Suffix_array).

Tandem repeats can themselves be divided into monomers and higher-order repeats. HORmon was developed for this purpose.[11]

The alignment of tandem repeats using a typical algorithm such as [Smith-Waterman](/source/Smith-Waterman_algorithm) tends to give biologically implausible results: these algorithms are unaware of the relatively high frequency of copy number changes at repeat sites and incorrectly penalize them as gaps. A more proper way to align tandem repeats from different individuals is to anchor the alignment on rare substrings.[12]

Nested tandem repeats are described as repeating unit lengths that are variable or unknown and frequently include an asymmetric hierarchy of smaller repeating units. These repeats are constructed from distinct groups of homologous-length monomers. An algorithm known as NTRprism was created by Oxford Nanopore Technologies researchers to enable for the annotation of repetitive structures in built satellite DNA arrays. The algorithm NTRprism is developed to find and display the satellite repeating periodicity.[13]

## Biotechnology

Kang. et al. successfully *in vitro* amplified up to 5kb of a sequence containing 36 identical 99bp tandem repeats and a 561bp sequence with 91% AT content using SHARP, which utilizes engineered superhelicases with enhanced processivity and speed.[14] SHARP combines single-stranded DNA binding protein (SSB) and superhelicases with standard PCR reagents to achieve isothermal amplification that mimics biological DNA replication. The method operates at a constant temperature, eliminating the need for thermal cycling, and has shown particular utility in cases where traditional PCR either fails to amplify target sequences or produces unwanted side products.

## See also

- [Microsatellite](/source/Microsatellite)

- [Minisatellite](/source/Minisatellite)

- [ProRepeat](/source/ProRepeat)

- [Satellite DNA](/source/Satellite_DNA)

- [Tandem Repeats Database](/source/Tandem_Repeats_Database)

- [Tandem repeat locus](/source/Tandem_repeat_locus)

- [Variable number tandem repeats](/source/Variable_number_tandem_repeat)

## References

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## External links

- Examples: - [VNTRs](http://www.rvc.ac.uk/review/DNA_1/4_VNTRs.cfm) [Archived](https://web.archive.org/web/20201109215619/http://www.rvc.ac.uk/review/DNA_1/4_VNTRs.cfm) 2020-11-09 at the [Wayback Machine](/source/Wayback_Machine) - info and animated example

- Databases: - [TRDB - The Tandem Repeats Database](http://tandem.bu.edu/cgi-bin/trdb/trdb.exe) [Archived](https://web.archive.org/web/20220401080814/https://tandem.bu.edu/cgi-bin/trdb/trdb.exe) 2022-04-01 at the [Wayback Machine](/source/Wayback_Machine) - [The Microorganisms Tandem Repeats Database](https://web.archive.org/web/20141225151444/http://tandemrepeat.u-psud.fr/) - [Short Tandem Repeats Database](http://www.cstl.nist.gov/div831/strbase/) - [Tandem Repeats in major genomes](http://victoria.biengi.ac.ru/cgi-bin/indelper/index.cgi/)

- Search tools: - [TAPO: A combined method for the identification of tandem repeats in protein structures](https://dali.crbm.cnrs.fr/index.php?route=tools&tool=2) - [Mreps](http://bioinfo.lifl.fr/mreps) [Archived](https://web.archive.org/web/20110929023604/http://bioinfo.lifl.fr/mreps/) 2011-09-29 at the [Wayback Machine](/source/Wayback_Machine) - [STAR](http://atgc.lirmm.fr/star) - [SERF](https://bioserf.org) De Novo Genome Analysis and Tandem Repeats Finder - [TRF](http://tandem.bu.edu/trf/trf.html) Tandem Repeats Finder - [Splinter](http://victoria.biengi.ac.ru/splinter/login.php) - [TRED - Tandem Repeats over the Edit Distance](https://web.archive.org/web/20080905145716/http://tandem.sci.brooklyn.cuny.edu/Tandem/) - [TandemSWAN](https://web.archive.org/web/20060712070732/http://strand.imb.ac.ru/swan/index.html) - [Microsatellite repeats finder](https://web.archive.org/web/20060709203109/http://www.biophp.org/minitools/microsatellite_repeats_finder/demo.php) - [JSTRING - Java Search for Tandem Repeats in genomes](https://web.archive.org/web/20060404015058/http://bioinf.dms.med.uniroma1.it/JSTRING/) - [Phobos - a tandem repeat search tool for perfect and imperfect repeats - the maximum pattern size depends only on computational power](http://www.rub.de/spezzoo/cm/cm_phobos.htm) - [UGENE](https://web.archive.org/web/20140606101328/http://ugene.unipro.ru/documentation/manual/plugins/repeat_finder.html#tandem-repeats) - an ultra fast and memory efficient open-source tandem repeats finder implementation. - [TRAL: Tandem Repeat Annotation Library - a meta-predictor tool with statistical filtering, with a range of functions for repeat annotation and analyses](https://www.vital-it.ch/software/tral) [Archived](https://web.archive.org/web/20200706164758/https://www.vital-it.ch/software/tral) 2020-07-06 at the [Wayback Machine](/source/Wayback_Machine)

v t e Genetics: repeated sequence, transposon, gene duplication Repeatome Repeated sequence Tandem repeats Satellite DNA Variable number tandem repeat/Minisatellite Short tandem repeat/Microsatellite (Trinucleotide repeat disorders) Macrosatellite Interspersed repeat Gene conversion Retrotransposon DNA transposon Polinton Helitron Other Inverted repeat Direct repeat Transposon Retrotransposon SINEs Alu sequence MIR LINEs LINE1 LINE2 LTRs HERV MER4 retroposon DNA transposon Academ Crypton Dada EnSpm/CACTA Ginger1 Ginger2 Harbinger hAT Helitron IS3EU ISL2EU Kolobok Tc1/mariner Merlin MuDR Novosib P element PiggyBac Polinton Sola Transib Zator Zisupton Gene duplication Gene amplification Tandemly arrayed genes Ribosomal DNA Gene family Gene cluster Pseudogene See also Genomic island Pathogenicity island Symbiosis island Low copy repeats CRISPR Telomere Protein tandem repeats

v t e Self-replicating organic structures Cellular life Bacteria Archaea Eukaryota Animalia Fungi Plantae Protista Incertae sedis Parakaryon Biological dark matter Virus dsDNA virus Giant virus ssDNA virus dsRNA virus (+)ssRNA virus (−)ssRNA virus ssRNA-RT virus dsDNA-RT virus Subviral agents Viroid Pospiviroidae Avsunviroidae Helper-virus dependent Satellite ssRNA satellite virus dsDNA satellite virus (Virophage) ssDNA satellite virus ssDNA satellite dsRNA satellite ssRNA satellite (Virusoid) Satellite-like nucleic acids RNA DNA Other Defective interfering particle RNA DNA Prion Mammalian prion Fungal prion Nucleic acid self-replication Mobile genetic elements Mobilome Horizontal gene transfer Genomic island Transposable element Class I or retrotransposon Class II or DNA transposon Plasmid Fertility Resistance Col Degradative Virulence/Ti Cryptic Cosmid Fosmid Phagemid Group I intron Group II intron Retrozyme Other aspects DNA replication RNA replication Chromosome Linear Circular Extrachromosomal DNA Secondary chromosome Genome Gene Gene duplication Non-coding DNA Origin of replication Replicon Endogenous viral element Provirus Prophage Endogenous retrovirus Transpoviron Repeated sequences in DNA Tandem repeat Interspersed repeat Endosymbiosis Mitochondria Mitosome Hydrogenosome Plastid Chloroplast Chromoplast Gerontoplast Leucoplast Apicoplast Kappa organism Organs Bacteriome Trophosome Nitroplast Abiogenesis Last universal common ancestor Earliest known life forms ?RNA life Ribozyme †Protocell Coacervate Proteinoid Sulphobe Research Model lipid bilayer Jeewanu See also Organism Cell Cell division Artificial cell Non-cellular life Synthetic virus Viral vector Helper dependent virus ?Nanobacterium ?Nanobe Cancer cell HeLa Clonally transmissible cancer Virome

v t e Life, non-cellular life, and comparable structures Cellular life "Prokaryota" Archaea Bacteria Synthia LUCA Eukaryota Animalia Vendobionta Fungi Plantae "Protista" Gabonionta Incertae sedis Parakaryon Microbes with highly unusual DNA (?) Non-cellular life Virus Viroid Satellite Viriform Realms Adnaviria Duplodnaviria Efunaviria Floreoviria Pleomoviria Riboviria Ribozyviria Singelaviria Varidnaviria Volvereviria Unassigned Classes Naldaviricetes Families Alphasatellitidae Ampullaviridae Avsunviroidae Bartogtaviriformidae Basaltiviridae Bicaudaviridae Brachygtaviriformidae Clavaviridae Eurekaviridae Fuselloviridae Globuloviridae Guttaviridae Halspiviridae Huangdiviridae Itzamnaviridae Lomiviridae Nipumfusiviridae Obscuriviridae Ovaliviridae Plasmaviridae Polydnaviriformidae Portogloboviridae Pospiviroidae Rhodogtaviriformidae Spiraviridae Thaspiviridae Tolecusatellitidae Xigoviridae Yamazakiviridae Genera Dinodnavirus Rhizidiovirus Other Nanobe (?) Obelisk Retroviroid Comparable structures Bio-like structure Cancer cell HeLa Clonally transmissible cancer "Cell body" Cosmid Defective interfering particle Endogenous viral element Endosymbiotic organelles Mitochondria Plastid Nitroplast Fosmid Integrative and conjugative element Jeewanu "Nanobacterium" Phagemid Plasmid Episome Prion Fungal prion Proteinoid microsphere Retroelements not elsewhere classified Retron Diversity-generating retroelement Telomerase reverse transcriptase Reverse transcriptase-related cellular gene Retrosequence Ribozyme Spiegelman's Monster shorter form Tandem repeat Transposable element Transpoviron Xenobot

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Adapted from the Wikipedia article [Tandem repeat](https://en.wikipedia.org/wiki/Tandem_repeat) by Wikipedia contributors ([contributor history](https://en.wikipedia.org/wiki/Tandem_repeat?action=history)). Available under [Creative Commons Attribution-ShareAlike 4.0 International](https://creativecommons.org/licenses/by-sa/4.0/). Changes may have been made.