Simple Tandem Repeats by TRF (TTTTTTATGTCTTTAT)
 
Item: TTTTTTATGTCTTTAT
Position: PJEM01000001.1:608655-608697
Genomic Size: 43
View DNA for this feature (GCA_004023845.1/HelPar_v1_BIUU Jan. 2019)

Length of repeat unit21
Mean number of copies of repeat1.9
Length of consensus sequence24
Percentage Match86
Percentage Indel13
Alignment Score = 2*match-7*mismatch-7*indel; minscore=5065
Percent of A's in repeat unit13
Percent of C's in repeat unit2
Percent of G's in repeat unit2
Percent of T's in repeat unit81
Entropy0.89
Sequence of repeat unit elementTTTTTTATGTCTTTATTTTATTAT
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Description

This track displays simple tandem repeats (possibly imperfect repeats) on the 15 Jan 2019 Helogale parvula/GCA_004023845.1_HelPar_v1_BIUU/GCA_004023845.1 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 595,520 items in the track covering 26,650,093 bases, assembly size 2,392,471,390 bases, percent coverage % 1.11.

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This track was generated using a modification of a program developed by G. Miklem and L. Hillier (unpublished).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