Simple Tandem Repeats by TRF (GTCTTCTATTATCGAG)
 
Item: GTCTTCTATTATCGAG
Position: NW_006256909.1:7253827-7253906
Genomic Size: 80
View DNA for this feature (GCF_000478725.1/Eutsalg1_0 Nov. 2013)

Length of repeat unit40
Mean number of copies of repeat2.0
Length of consensus sequence40
Percentage Match100
Percentage Indel0
Alignment Score = 2*match-7*mismatch-7*indel; minscore=50160
Percent of A's in repeat unit42
Percent of C's in repeat unit12
Percent of G's in repeat unit12
Percent of T's in repeat unit32
Entropy1.80
Sequence of repeat unit elementGTCTTCTATTATCGAGTAATGAAAGTAAAAACATAATCAT
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Description

This track displays simple tandem repeats (possibly imperfect repeats) on the 05 Nov 2013 Eutrema salsugineum/GCF_000478725.1_Eutsalg1_0/GCF_000478725.1 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 70,755 items in the track covering 7,898,278 bases, assembly size 243,110,105 bases, percent coverage % 3.25.

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This track was generated using a modification of a program developed by G. Miklem and L. Hillier (unpublished).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