Simple Tandem Repeats by TRF (TG)
 
Item: TG
Position: NC_045152.1:11031943-11032078
Genomic Size: 136
View DNA for this feature (GCF_900700415.2/Ch_v2.0.2 Apr. 2019)

Length of repeat unit2
Mean number of copies of repeat68.0
Length of consensus sequence2
Percentage Match98
Percentage Indel0
Alignment Score = 2*match-7*mismatch-7*indel; minscore=50236
Percent of A's in repeat unit2
Percent of C's in repeat unit0
Percent of G's in repeat unit50
Percent of T's in repeat unit47
Entropy1.16
Sequence of repeat unit elementTG
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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This track was generated using a modification of a program developed by G. Miklem and L. Hillier (unpublished).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