Simple Tandem Repeats by TRF (TATATGTTAGTATTAT)
 
Item: TATATGTTAGTATTAT
Position: NC_045152.1:11033322-11033391
Genomic Size: 70
View DNA for this feature (GCF_900700415.2/Ch_v2.0.2 Apr. 2019)

Length of repeat unit34
Mean number of copies of repeat2.0
Length of consensus sequence35
Percentage Match91
Percentage Indel2
Alignment Score = 2*match-7*mismatch-7*indel; minscore=50115
Percent of A's in repeat unit28
Percent of C's in repeat unit2
Percent of G's in repeat unit20
Percent of T's in repeat unit48
Entropy1.63
Sequence of repeat unit elementTATATGTTAGTATTATATGTATAGGCTGCTATATG
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Description

This track displays simple tandem repeats (possibly imperfect repeats) on the 16 Apr 2019 Clupea harengus/GCF_900700415.2_Ch_v2.0.2/GCF_900700415.2 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 1,318,661 items in the track covering 105,596,896 bases, assembly size 786,325,606 bases, percent coverage % 13.43.

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This track was generated using a modification of a program developed by G. Miklem and L. Hillier (unpublished).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