Simple Tandem Repeats by TRF (AGCCCTCTGAAGGTGA)
 
Item: AGCCCTCTGAAGGTGA
Position: NC_041019.1:19249614-19250062
Genomic Size: 449
View DNA for this feature (GCF_004193775.1/ASM419377v2 Feb. 2019)

Length of repeat unit24
Mean number of copies of repeat18.8
Length of consensus sequence24
Percentage Match82
Percentage Indel0
Alignment Score = 2*match-7*mismatch-7*indel; minscore=50371
Percent of A's in repeat unit21
Percent of C's in repeat unit21
Percent of G's in repeat unit36
Percent of T's in repeat unit21
Entropy1.95
Sequence of repeat unit elementAGCCCTCTGAAGGTGAGGGCGTGT
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Description

This track displays simple tandem repeats (possibly imperfect repeats) on the 21 Feb 2019 Glycine soja/GCF_004193775.1_ASM419377v2/GCF_004193775.1 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 450,287 items in the track covering 67,374,482 bases, assembly size 1,013,766,566 bases, percent coverage % 6.65.

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This track was generated using a modification of a program developed by G. Miklem and L. Hillier (unpublished).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