Simple Tandem Repeats by TRF (CA)
 
Item: CA
Position: PJEM01000001.1:614793-614832
Genomic Size: 40
View DNA for this feature (GCA_004023845.1/HelPar_v1_BIUU Jan. 2019)

Length of repeat unit2
Mean number of copies of repeat20.0
Length of consensus sequence2
Percentage Match100
Percentage Indel0
Alignment Score = 2*match-7*mismatch-7*indel; minscore=5080
Percent of A's in repeat unit50
Percent of C's in repeat unit50
Percent of G's in repeat unit0
Percent of T's in repeat unit0
Entropy1.00
Sequence of repeat unit elementCA
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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This track was generated using a modification of a program developed by G. Miklem and L. Hillier (unpublished).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