Knowledge (XXG)

Tandem repeat

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107:, 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. 263:
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
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Altemose, Nicolas; Logsdon, Glennis A.; Bzikadze, Andrey V.; Sidhwani, Pragya; Langley, Sasha A.; Caldas, Gina V.; Hoyt, Savannah J.; Uralsky, Lev; Ryabov, Fedor D.; Shew, Colin J.; Sauria, Michael E. G.; Borchers, Matthew; Gershman, Ariel; Mikheenko, Alla; Shepelev, Valery A. (April 2022).
178:), 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. 225:
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
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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.
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Yeh, Ting-Yu; Hsieh, Zih-Yu; Feehley, Michael C.; Feehley, Patrick J.; Contreras, Gregory P.; Su, Ying-Chieh; Hsieh, Shang-Lin; Lewis, Dylan A. (9 December 2022).
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TRAL: Tandem Repeat Annotation Library - a meta-predictor tool with statistical filtering, with a range of functions for repeat annotation and analyses
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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.
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Phobos - a tandem repeat search tool for perfect and imperfect repeats - the maximum pattern size depends only on computational power
2783: 2713: 1032: 2718: 230:(Multiple Loci VNTR Analysis). Using tandem repeat polymorphism, recombination has been reported in the natural transmission of 829: 72:. However, in proteins, perfect tandem repeats are rare in naturally proteins, but they have been added to designed proteins. 2641: 1991: 1586: 130: 2629: 2127: 1063: 909: 896: 303: 159: 776: 1775: 791: 1695: 1451: 781: 1180: 822: 115: 1996: 1068: 218: 141: 2646: 1843: 1744: 1661: 522: 326: 163: 174:
Tandem repeats can occur through different mechanisms. For example, slipped strand mispairing, (also known as
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Cui, Ya; Ye, Wenbin; Li, Jason Sheng; Li, Jingyi Jessica; Vilain, Eric; Sallam, Tamer; Li, Wei (April 2024).
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Duitama J, Zablotskaya A, Gemayel R, Jansen A, Belet S, Vermeesch JR, Verstrepen KJ, Froyen G (May 2014).
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When much larger lengths of nucleotides are repeated, on the order of 1,000 nucleotides, it is called a
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within the chromosomal DNA. Parentage can be determined through the similarity in these regions.
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When the repeat unit copy number is variable in the population being considered, it is called a
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Tandem repeat describes a pattern that helps determine an individual's inherited traits.
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TAPO: A combined method for the identification of tandem repeats in protein structures
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classifies variable number tandem repeats under minisatellites.
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When between 10 and 60 nucleotides are repeated, it is called a
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When exactly two nucleotides are repeated, it is called a
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Studies in 2004 linked the unusual genetic plasticity of
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When three nucleotides are repeated, it is called a
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JSTRING - Java Search for Tandem Repeats in genomes
478:Oki E, Oda S, Maehara Y, Sugimachi K (March 1999). 339:Jorda J, Xue B, Uversky VN, Kajava AV (June 2010). 79:. They are implicated in more than 50 lethal human 27:
Adjacent repeated pattern of nucleotides within DNA
762:De Novo Genome Analysis and Tandem Repeats Finder 200:Tandem repeats can be very useful in determining 2161: 1331: 830: 103:All tandem repeat arrays are classifiable as 8: 777:TRED - Tandem Repeats over the Edit Distance 2724:Reverse transcriptase-related cellular gene 2385: 2325: 2308: 2192: 2168: 2154: 2146: 1642: 1526: 1488: 1338: 1324: 1316: 1005: 996: 879: 837: 823: 815: 725:The Microorganisms Tandem Repeats Database 75:Tandem repeats constitute about 8% of the 678: 612: 568: 521:at the U.S. National Library of Medicine 495: 454: 413: 364: 325:at the U.S. National Library of Medicine 2705:Retroelements not elsewhere classified 315: 238:) virus genome during 2022 pandemic. 7: 122:most commonly affects such regions. 120:hereditary nonpolyposis colon cancer 2657:Integrative and conjugative element 720:TRDB - The Tandem Repeats Database 906:Short tandem repeat/Microsatellite 25: 2714:Diversity-generating retroelement 519:Variable+Number+of+Tandem+Repeats 2719:Telomerase reverse transcriptase 2291:Microbes with highly unusual DNA 735:Tandem Repeats in major genomes 357:10.1111/j.1742-4658.2010.07684.x 260:to mutations in tandem repeats. 140:. Those with fewer are known as 114:(for example: ACACACAC...). The 2642:Defective interfering particle 1992:Last universal common ancestor 1587:Defective interfering particle 910:Trinucleotide repeat disorders 304:Variable number tandem repeats 131:trinucleotide repeat disorders 49:when a pattern of one or more 1: 2630:Clonally transmissible cancer 2128:Clonally transmissible cancer 1564:Satellite-like nucleic acids 897:Variable number tandem repeat 787:Microsatellite repeats finder 730:Short Tandem Repeats Database 614:10.1126/science.306.5705.2172 160:variable number tandem repeat 85:amyotrophic lateral sclerosis 2183:, and comparable structures 711:- info and animated example 2800: 1684:Class II or DNA transposon 1679:Class I or retrotransposon 553:10.1016/j.medj.2022.11.003 456:10.1016/j.cell.2024.03.004 116:microsatellite instability 29: 1997:Earliest known life forms 1871:Repeated sequences in DNA 864: 181:Other mechanisms include 2784:Repetitive DNA sequences 2647:Endogenous viral element 1844:Endogenous viral element 1662:Horizontal gene transfer 523:Medical Subject Headings 327:Medical Subject Headings 64:within their amino acid 30:Not to be confused with 1541:dsDNA satellite virus ( 663:10.1126/science.abl4178 294:Tandem Repeats Database 2099:Helper dependent virus 1415:Biological dark matter 1305:Protein tandem repeats 1233:Tandemly arrayed genes 497:10.1038/sj.onc.1202583 394:Nucleic Acids Research 210:genealogical DNA tests 32:Tandemly arrayed genes 1859:Endogenous retrovirus 1832:Origin of replication 1548:ssDNA satellite virus 1538:ssRNA satellite virus 768:Tandem Repeats Finder 208:are used for certain 2746:Transposable element 2736:Spiegelman's Monster 1803:Secondary chromosome 1798:Extrachromosomal DNA 1674:Transposable element 1278:Pathogenicity island 206:Short tandem repeats 176:replication slippage 146:short tandem repeats 127:trinucleotide repeat 89:Huntington's disease 2039:Model lipid bilayer 1881:Interspersed repeat 449:(9): 2336–2341.e5. 299:Tandem repeat locus 112:dinucleotide repeat 2615:Bio-like structure 2537:Tolecusatellitidae 1349:organic structures 1228:Gene amplification 657:(6588): eabl4178. 406:10.1093/nar/gku212 2771: 2770: 2601: 2600: 2575: 2574: 2571: 2570: 2509:Portogloboviridae 2411:Alphasatellitidae 2305:Non-cellular life 2300: 2299: 2181:non-cellular life 2143: 2142: 2084:Non-cellular life 1891: 1890: 1630: 1629: 1603: 1602: 1557:ssRNA satellite ( 1313: 1312: 1214: 1213: 1082: 1081: 986: 985: 875:Repeated sequence 850:repeated sequence 595:(December 2004). 216:is examined from 183:unequal crossover 70:armadillo repeats 66:primary structure 16:(Redirected from 2791: 2386: 2326: 2309: 2193: 2170: 2163: 2156: 2147: 1820:Gene duplication 1643: 1639:self-replication 1527: 1489: 1347:Self-replicating 1340: 1333: 1326: 1317: 1290:Low copy repeats 1283:Symbiosis island 1220:Gene duplication 1006: 997: 880: 858:gene duplication 839: 832: 825: 816: 693: 692: 682: 641: 635: 634: 616: 589: 583: 582: 572: 532: 526: 516: 510: 509: 499: 475: 469: 468: 458: 434: 428: 427: 417: 400:(9): 5728–5741. 385: 379: 378: 368: 345:The FEBS Journal 336: 330: 320: 243:computer science 241:In the field of 21: 2799: 2798: 2794: 2793: 2792: 2790: 2789: 2788: 2774: 2773: 2772: 2767: 2607: 2597: 2567: 2542: 2453:Finnlakeviridae 2398: 2377: 2319: 2315: 2296: 2268: 2233: 2184: 2174: 2144: 2139: 2089:Synthetic virus 2077:Artificial cell 2050: 1978: 1887: 1776:RNA replication 1771:DNA replication 1759: 1750:Group II intron 1648: 1638: 1626: 1617:Mammalian prion 1599: 1575: 1554:dsRNA satellite 1551:ssDNA satellite 1521: 1514: 1483: 1476: 1421: 1350: 1344: 1314: 1309: 1261: 1210: 1078: 1050: 1027: 1001:Retrotransposon 982: 973:Inverted repeat 961: 946:DNA transposon 942:Retrotransposon 937:Gene conversion 928: 921: 918: 869: 860: 843: 702: 697: 696: 643: 642: 638: 591: 590: 586: 547:(12): 824–826. 534: 533: 529: 517: 513: 477: 476: 472: 436: 435: 431: 387: 386: 382: 351:(12): 2673–82. 338: 337: 333: 321: 317: 312: 270: 219:microsatellites 195: 187:gene conversion 172: 142:microsatellites 101: 58:protein domains 35: 28: 23: 22: 15: 12: 11: 5: 2797: 2795: 2787: 2786: 2776: 2775: 2769: 2768: 2766: 2765: 2760: 2755: 2754: 2753: 2743: 2738: 2733: 2728: 2727: 2726: 2721: 2716: 2711: 2703: 2695: 2694: 2693: 2683: 2678: 2673: 2664: 2659: 2654: 2649: 2644: 2639: 2634: 2633: 2632: 2627: 2617: 2611: 2609: 2603: 2602: 2599: 2598: 2596: 2595: 2590: 2583: 2581: 2577: 2576: 2573: 2572: 2569: 2568: 2566: 2565: 2558: 2550: 2548: 2544: 2543: 2541: 2540: 2533: 2526: 2519: 2512: 2505: 2502:Polydnaviridae 2498: 2491: 2484: 2477: 2470: 2467:Globuloviridae 2463: 2460:Fuselloviridae 2456: 2449: 2442: 2439:Bicaudaviridae 2435: 2428: 2421: 2418:Ampullaviridae 2414: 2406: 2404: 2400: 2399: 2395:Naldaviricetes 2392: 2390: 2383: 2379: 2378: 2376: 2375: 2368: 2361: 2354: 2347: 2340: 2332: 2330: 2323: 2306: 2302: 2301: 2298: 2297: 2295: 2294: 2288: 2280: 2278: 2275:Incertae sedis 2270: 2269: 2267: 2266: 2259: 2254: 2249: 2243: 2241: 2235: 2234: 2232: 2231: 2226: 2225: 2224: 2219: 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1905:Mitochondrion 1903: 1902: 1900: 1898: 1897:Endosymbiosis 1894: 1882: 1879: 1877: 1876:Tandem repeat 1874: 1873: 1872: 1869: 1865: 1862: 1860: 1857: 1855: 1852: 1850: 1847: 1846: 1845: 1842: 1838: 1835: 1834: 1833: 1830: 1826: 1823: 1821: 1818: 1816: 1813: 1812: 1811: 1808: 1804: 1801: 1799: 1796: 1794: 1791: 1789: 1786: 1785: 1784: 1781: 1777: 1774: 1773: 1772: 1769: 1768: 1766: 1764:Other aspects 1762: 1756: 1753: 1751: 1748: 1746: 1743: 1741: 1738: 1734: 1731: 1730: 1729: 1726: 1721: 1719: 1715: 1712: 1709: 1707: 1704: 1702: 1699: 1697: 1694: 1693: 1692: 1689: 1685: 1682: 1680: 1677: 1676: 1675: 1672: 1668: 1665: 1663: 1660: 1659: 1658: 1655: 1654: 1652: 1650: 1644: 1641: 1637: 1633: 1623: 1620: 1618: 1615: 1614: 1612: 1610: 1606: 1593: 1590: 1589: 1588: 1585: 1584: 1582: 1578: 1569: 1566: 1565: 1563: 1560: 1556: 1553: 1550: 1547: 1544: 1540: 1537: 1536: 1534: 1532: 1528: 1525: 1523: 1517: 1511: 1510: 1509:Avsunviroidae 1506: 1504: 1503: 1502:Pospiviroidae 1499: 1498: 1496: 1494: 1490: 1487: 1485: 1479: 1473: 1470: 1468: 1465: 1463: 1460: 1458: 1455: 1453: 1450: 1448: 1445: 1441: 1438: 1437: 1436: 1433: 1432: 1430: 1428: 1424: 1416: 1413: 1411: 1410: 1406: 1405: 1404: 1403: 1399: 1395: 1392: 1390: 1387: 1385: 1382: 1380: 1377: 1376: 1375: 1372: 1370: 1367: 1365: 1362: 1361: 1359: 1357: 1356:Cellular life 1353: 1348: 1341: 1336: 1334: 1329: 1327: 1322: 1321: 1318: 1306: 1303: 1301: 1298: 1296: 1293: 1291: 1288: 1284: 1281: 1279: 1276: 1275: 1274: 1271: 1270: 1268: 1264: 1258: 1255: 1251: 1248: 1247: 1246: 1243: 1239: 1238:Ribosomal DNA 1236: 1235: 1234: 1231: 1229: 1226: 1225: 1223: 1221: 1217: 1207: 1204: 1202: 1199: 1197: 1194: 1192: 1189: 1187: 1184: 1182: 1179: 1177: 1174: 1172: 1169: 1167: 1164: 1162: 1159: 1157: 1154: 1152: 1149: 1147: 1144: 1142: 1139: 1137: 1134: 1132: 1129: 1127: 1124: 1122: 1119: 1117: 1114: 1112: 1109: 1107: 1104: 1102: 1099: 1097: 1094: 1093: 1091: 1089: 1085: 1075: 1072: 1070: 1067: 1065: 1062: 1061: 1059: 1057: 1053: 1047: 1044: 1042: 1039: 1038: 1036: 1034: 1030: 1024: 1021: 1019: 1016: 1015: 1013: 1011: 1007: 1004: 1002: 998: 995: 993: 989: 979: 978:Direct repeat 976: 974: 971: 970: 968: 964: 956: 953: 951: 948: 947: 945: 943: 940: 938: 935: 934: 932: 930: 924: 917: 914: 911: 907: 904: 902: 901:Minisatellite 898: 895: 893: 892:Satellite DNA 890: 889: 887: 885: 881: 878: 876: 872: 868: 863: 859: 855: 851: 847: 840: 835: 833: 828: 826: 821: 820: 817: 809: 806: 803: 800: 798: 795: 793: 790: 788: 785: 783: 780: 778: 775: 773: 770: 767: 764: 761: 758: 756: 753: 751: 748: 746: 743: 742: 740: 736: 733: 731: 728: 726: 723: 721: 718: 717: 715: 710: 707: 706: 704: 703: 699: 690: 686: 681: 676: 672: 668: 664: 660: 656: 652: 648: 640: 637: 632: 628: 624: 620: 615: 610: 606: 602: 598: 594: 588: 585: 580: 576: 571: 566: 562: 558: 554: 550: 546: 542: 538: 531: 528: 524: 520: 515: 512: 507: 503: 498: 493: 489: 485: 481: 474: 471: 466: 462: 457: 452: 448: 444: 440: 433: 430: 425: 421: 416: 411: 407: 403: 399: 395: 391: 384: 381: 376: 372: 367: 362: 358: 354: 350: 346: 342: 335: 332: 328: 324: 323:Tandem+Repeat 319: 316: 309: 305: 302: 300: 297: 295: 292: 290: 289:Satellite DNA 287: 285: 282: 280: 279:Minisatellite 277: 275: 272: 271: 267: 265: 261: 259: 254: 252: 251:suffix arrays 248: 244: 239: 237: 233: 229: 223: 221: 220: 215: 211: 207: 203: 198: 192: 190: 188: 184: 179: 177: 169: 167: 165: 161: 156: 154: 149: 147: 143: 139: 138:minisatellite 134: 132: 128: 123: 121: 117: 113: 108: 106: 105:satellite DNA 98: 96: 94: 90: 86: 82: 78: 73: 71: 67: 63: 59: 54: 52: 48: 44: 40: 33: 19: 2758:Transpoviron 2740: 2691:Fungal prion 2667: 2560: 2555:Dinodnavirus 2553: 2535: 2528: 2523:Spiraviridae 2521: 2514: 2507: 2500: 2493: 2488:Ovaliviridae 2486: 2479: 2474:Guttaviridae 2472: 2465: 2458: 2451: 2446:Clavaviridae 2444: 2437: 2430: 2423: 2416: 2409: 2393: 2372:Varidnaviria 2370: 2363: 2356: 2351:Monodnaviria 2349: 2342: 2335: 2283: 2273: 2094:Viral vector 1937:Gerontoplast 1875: 1864:Transpoviron 1636:Nucleic acid 1622:Fungal prion 1520:Helper-virus 1507: 1500: 1407: 1400: 1250:Gene cluster 1018:Alu sequence 927:Interspersed 883: 654: 650: 639: 604: 600: 587: 544: 540: 530: 514: 487: 483: 473: 446: 442: 432: 397: 393: 383: 348: 344: 334: 318: 262: 255: 247:suffix trees 240: 224: 217: 199: 196: 180: 173: 157: 150: 135: 126: 124: 111: 109: 102: 83:, including 77:human genome 74: 55: 42: 36: 2701:microsphere 2620:Cancer cell 2365:Ribozyviria 2118:Cancer cell 1984:Abiogenesis 1932:Chromoplast 1927:Chloroplast 1710:Degradative 1452:dsRNA virus 1447:ssDNA virus 1440:Giant virus 1435:dsDNA virus 1245:Gene family 1156:Tc1/mariner 1111:EnSpm/CACTA 716:Databases: 99:Terminology 51:nucleotides 2751:Retroposon 2698:Proteinoid 2608:structures 2606:Comparable 2382:Unassigned 2285:Parakaryon 2198:Prokaryota 2026:Proteinoid 2021:Coacervate 1974:Nitroplast 1967:Trophosome 1962:Bacteriome 1947:Apicoplast 1942:Leucoplast 1783:Chromosome 1701:Resistance 1409:Parakaryon 1257:Pseudogene 1074:retroposon 992:Transposon 854:transposon 782:TandemSWAN 705:Examples: 310:References 68:, such as 60:also form 2358:Riboviria 2337:Adnaviria 2321:Satellite 2239:Eukaryota 2035:Research 2016:Protocell 1755:Retrozyme 1714:Virulence 1696:Fertility 1543:Virophage 1531:Satellite 1522:dependent 1374:Eukaryota 1176:P element 1126:Harbinger 867:Repeatome 671:0036-8075 593:Pennisi E 561:2666-6359 465:0092-8674 284:ProRepeat 232:monkeypox 202:parentage 170:Mechanism 45:occur in 2778:Category 2731:Ribozyme 2676:Phagemid 2403:Families 2263:Protista 2247:Animalia 2212:Bacteria 2062:Organism 2055:See also 2031:Sulphobe 2008:Ribozyme 2003:RNA life 1910:Mitosome 1854:Prophage 1849:Provirus 1837:Replicon 1793:Circular 1740:Phagemid 1657:Mobilome 1649:elements 1559:Virusoid 1482:Subviral 1394:Protista 1379:Animalia 1364:Bacteria 1300:Telomere 1266:See also 1206:Zisupton 1186:Polinton 1181:PiggyBac 1136:Helitron 955:Helitron 950:Polinton 846:Genetics 772:Splinter 689:35357911 631:10680162 623:15618495 579:36495863 506:10321739 484:Oncogene 424:24682812 375:20553501 268:See also 162:(VNTR). 81:diseases 56:Several 39:genetics 2763:Xenobot 2681:Plasmid 2662:Jeewanu 2593:Obelisk 2389:Classes 2257:Plantae 2222:Plastid 2207:Archaea 2044:Jeewanu 1958:Organs 1922:Plastid 1722:Cryptic 1691:Plasmid 1389:Plantae 1369:Archaea 1196:Transib 1171:Novosib 1151:Kolobok 1121:Ginger2 1116:Ginger1 1101:Crypton 680:9233505 651:Science 601:Science 570:9733179 415:4027155 366:2928880 93:cancers 2709:Retron 2652:Fosmid 2637:Cosmid 2587:Nanobe 2547:Genera 2329:Realms 2317:Viroid 2135:Virome 2113:Nanobe 1810:Genome 1788:Linear 1733:Fosmid 1728:Cosmid 1493:Viroid 1484:agents 1295:CRISPR 1161:Merlin 1146:ISL2EU 1096:Academ 929:repeat 687:  677:  669:  629:  621:  577:  567:  559:  525:(MeSH) 504:  463:  422:  412:  373:  363:  329:(MeSH) 2686:Prion 2580:Other 2313:Virus 2252:Fungi 1609:Prion 1580:Other 1427:Virus 1384:Fungi 1201:Zator 1141:IS3EU 1046:LINE2 1041:LINE1 1033:LINEs 1010:SINEs 966:Other 802:UGENE 750:Mreps 709:VNTRs 627:S2CID 2625:HeLa 2229:LUCA 2177:Life 2123:HeLa 2067:Cell 1815:Gene 1191:Sola 1166:MuDR 1106:Dada 1069:MER4 1064:HERV 1056:LTRs 760:SERF 755:STAR 685:PMID 667:ISSN 619:PMID 575:PMID 557:ISSN 502:PMID 461:ISSN 443:Cell 420:PMID 371:PMID 258:dogs 236:mpox 228:MLVA 193:Uses 185:and 164:MeSH 2589:(?) 2293:(?) 1706:Col 1594:DNA 1591:RNA 1570:DNA 1567:RNA 1131:hAT 1023:MIR 766:TRF 675:PMC 659:doi 655:376 609:doi 605:306 565:PMC 549:doi 541:Med 492:doi 451:doi 447:187 410:PMC 402:doi 361:PMC 353:doi 349:277 249:or 214:DNA 144:or 118:in 47:DNA 37:In 2780:: 2179:, 1718:Ti 856:, 852:, 848:: 683:. 673:. 665:. 653:. 649:. 625:. 617:. 603:. 599:. 573:. 563:. 555:. 543:. 539:. 500:. 488:18 486:. 482:. 459:. 445:. 441:. 418:. 408:. 398:42 396:. 392:. 369:. 359:. 347:. 343:. 253:. 212:. 204:. 189:. 155:. 148:. 133:. 95:. 87:, 41:, 2672:" 2666:" 2265:' 2261:' 2200:" 2196:" 2169:e 2162:t 2155:v 2111:? 2105:? 2014:† 2001:? 1716:/ 1561:) 1545:) 1339:e 1332:t 1325:v 912:) 908:( 899:/ 838:e 831:t 824:v 691:. 661:: 633:. 611:: 581:. 551:: 545:3 508:. 494:: 467:. 453:: 426:. 404:: 377:. 355:: 234:( 34:. 20:)

Index

Tandem repeats
Tandemly arrayed genes
genetics
DNA
nucleotides
protein domains
tandem repeats
primary structure
armadillo repeats
human genome
diseases
amyotrophic lateral sclerosis
Huntington's disease
cancers
satellite DNA
microsatellite instability
hereditary nonpolyposis colon cancer
trinucleotide repeat disorders
minisatellite
microsatellites
short tandem repeats
macrosatellite
variable number tandem repeat
MeSH
replication slippage
unequal crossover
gene conversion
parentage
Short tandem repeats
genealogical DNA tests

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