Simple Tandem Repeats by TRF (CACAGCAGTGAGAGGC)
 
Item: CACAGCAGTGAGAGGC
Position: RJWK010000001.1:82240-82271
Genomic Size: 32
View DNA for this feature (GCA_004363435.1/PlaMin_v1_BIUU Mar. 2019)

Length of repeat unit15
Mean number of copies of repeat2.1
Length of consensus sequence16
Percentage Match94
Percentage Indel5
Alignment Score = 2*match-7*mismatch-7*indel; minscore=5057
Percent of A's in repeat unit31
Percent of C's in repeat unit28
Percent of G's in repeat unit37
Percent of T's in repeat unit3
Entropy1.73
Sequence of repeat unit elementCACAGCAGTGAGAGGC
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Description

This track displays simple tandem repeats (possibly imperfect repeats) on the 22 Mar 2019 Platanista minor/GCA_004363435.1_PlaMin_v1_BIUU/GCA_004363435.1 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 845,860 items in the track covering 46,001,422 bases, assembly size 2,671,072,510 bases, percent coverage % 1.72.

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This track was generated using a modification of a program developed by G. Miklem and L. Hillier (unpublished).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