Simple Tandem Repeats by TRF (AGAGAG)
 
Item: AGAGAG
Position: NW_021604565v1:10825451-10825562
Genomic Size: 112
View DNA for this feature (GCF_004785775.1/NIH_TR_1.0 Apr. 2019)

Length of repeat unit6
Mean number of copies of repeat20.0
Length of consensus sequence6
Percentage Match75
Percentage Indel12
Alignment Score = 2*match-7*mismatch-7*indel; minscore=50105
Percent of A's in repeat unit42
Percent of C's in repeat unit0
Percent of G's in repeat unit57
Percent of T's in repeat unit0
Entropy0.99
Sequence of repeat unit elementAGAGAG
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Description

This track displays simple tandem repeats (possibly imperfect repeats) on the 12 Apr 2019 Grammomys surdaster/GCF_004785775.1_NIH_TR_1.0/GCF_004785775.1 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 1,424,025 items in the track covering 77,913,452 bases, assembly size 2,412,664,998 bases, percent coverage % 3.23.

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This track was generated using a modification of a program developed by G. Miklem and L. Hillier (unpublished).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