Simple Tandem Repeats by TRF (TTTTATTTATA)
 
Item: TTTTATTTATA
Position: NC_030851.1:13748457-13748491
Genomic Size: 35
View DNA for this feature (GCF_000208745.1/Criollo_cocoa_genome_V2 Jul. 2016)

Length of repeat unit11
Mean number of copies of repeat3.4
Length of consensus sequence11
Percentage Match92
Percentage Indel7
Alignment Score = 2*match-7*mismatch-7*indel; minscore=5056
Percent of A's in repeat unit22
Percent of C's in repeat unit0
Percent of G's in repeat unit0
Percent of T's in repeat unit77
Entropy0.78
Sequence of repeat unit elementTTTTATTTATA
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Description

This track displays simple tandem repeats (possibly imperfect repeats) on the 09 Jul 2016 Theobroma cacao/GCF_000208745.1_Criollo_cocoa_genome_V2/GCF_000208745.1 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 99,229 items in the track covering 8,649,988 bases, assembly size 324,879,930 bases, percent coverage % 2.66.

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This track was generated using a modification of a program developed by G. Miklem and L. Hillier (unpublished).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