Simple Tandem Repeats by TRF (ACGGACAG)
 
Item: ACGGACAG
Position: NC_052499.1:30156409-30156447
Genomic Size: 39
View DNA for this feature (GCF_016617805.1/CSIRO_BtryS06_freeze2 Jan. 2021)

Length of repeat unit8
Mean number of copies of repeat4.9
Length of consensus sequence8
Percentage Match87
Percentage Indel0
Alignment Score = 2*match-7*mismatch-7*indel; minscore=5051
Percent of A's in repeat unit35
Percent of C's in repeat unit25
Percent of G's in repeat unit38
Percent of T's in repeat unit0
Entropy1.56
Sequence of repeat unit elementACGGACAG
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Description

This track displays simple tandem repeats (possibly imperfect repeats) on the 19 Jan 2021 Bactrocera tryoni/GCF_016617805.1_CSIRO_BtryS06_freeze2/GCF_016617805.1 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 156,903 items in the track covering 33,118,271 bases, assembly size 570,658,800 bases, percent coverage % 5.80.

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This track was generated using a modification of a program developed by G. Miklem and L. Hillier (unpublished).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