Simple Tandem Repeats by TRF (TA)
 
Item: TA
Position: NW_019213155.1:435074-435101
Genomic Size: 28
View DNA for this feature (GCF_002532875.1/vjacob_1.0 Oct. 2017)

Length of repeat unit2
Mean number of copies of repeat14.0
Length of consensus sequence2
Percentage Match100
Percentage Indel0
Alignment Score = 2*match-7*mismatch-7*indel; minscore=5056
Percent of A's in repeat unit50
Percent of C's in repeat unit0
Percent of G's in repeat unit0
Percent of T's in repeat unit50
Entropy1.00
Sequence of repeat unit elementTA
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Description

This track displays simple tandem repeats (possibly imperfect repeats) on the 10 Oct 2017 Varroa jacobsoni/GCF_002532875.1_vjacob_1.0/GCF_002532875.1 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 39,880 items in the track covering 2,584,755 bases, assembly size 365,585,945 bases, percent coverage % 0.71.

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This track was generated using a modification of a program developed by G. Miklem and L. Hillier (unpublished).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