Simple Tandem Repeats by TRF (AGTAGGCTAGGCCTCC)
 
Item: AGTAGGCTAGGCCTCC
Position: NKHJ01000001v1:21652812-21652860
Genomic Size: 49
View DNA for this feature (GCA_002209525.2_HG01352_prelim_2.1/Homo sapiens)

Length of repeat unit22
Mean number of copies of repeat2.3
Length of consensus sequence21
Percentage Match86
Percentage Indel10
Alignment Score = 2*match-7*mismatch-7*indel; minscore=5064
Percent of A's in repeat unit20
Percent of C's in repeat unit20
Percent of G's in repeat unit38
Percent of T's in repeat unit20
Entropy1.93
Sequence of repeat unit elementAGTAGGCTAGGCCTCCGGAGT
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Description

This track displays simple tandem repeats (possibly imperfect repeats) on the 02 Jul 2018 Homo sapiens/GCA_002209525.2_HG01352_prelim_2.1/GCA_002209525.2 genome assembly, located by Tandem Repeats Finder (TRF) which is specialized for this purpose. These repeats can occur within coding regions of genes and may be quite polymorphic. Repeat expansions are sometimes associated with specific diseases.

There are 1,011,770 items in the track covering 122,244,006 bases, assembly size 2,884,526,810 bases, percent coverage % 4.24.

Methods

For more information about the TRF program, see Benson (1999).

Credits

TRF was written by Gary Benson.

References

Benson G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 1999 Jan 15;27(2):573-80. PMID: 9862982; PMC: PMC148217

Credits

This track was generated using a modification of a program developed by G. Miklem and L. Hillier (unpublished).

References

Gardiner-Garden M, Frommer M. CpG islands in vertebrate genomes. J Mol Biol. 1987 Jul 20;196(2):261-82. PMID: 3656447