Simple Tandem Repeats by TRF (CCGCCGATGGCACCAC)
 
Item: CCGCCGATGGCACCAC
Position: CM029767.1:13179512-13179588
Genomic Size: 77
View DNA for this feature (GCA_017562165.1/ASM1756216v1 Mar. 2021)

Length of repeat unit30
Mean number of copies of repeat2.6
Length of consensus sequence30
Percentage Match91
Percentage Indel0
Alignment Score = 2*match-7*mismatch-7*indel; minscore=50118
Percent of A's in repeat unit22
Percent of C's in repeat unit49
Percent of G's in repeat unit22
Percent of T's in repeat unit6
Entropy1.72
Sequence of repeat unit elementCCGCCGATGGCACCACCACCCAGAGCACCG
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Description

This track displays simple tandem repeats (possibly imperfect repeats) on the 24 Mar 2021 Ectropis grisescens/GCA_017562165.1_ASM1756216v1/GCA_017562165.1 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 203,253 items in the track covering 25,667,818 bases, assembly size 784,886,525 bases, percent coverage % 3.27.

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This track was generated using a modification of a program developed by G. Miklem and L. Hillier (unpublished).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