Simple Tandem Repeats by TRF (TCTCACCTCT)
Position: chr5:13815672-13815703
Genomic Size: 32
View DNA for this feature (GCF_001444195.1/X_couchianus-1.0 Sep. 2018)

Length of repeat unit10
Mean number of copies of repeat3.3
Length of consensus sequence10
Percentage Match95
Percentage Indel4
Alignment Score = 2*match-7*mismatch-7*indel; minscore=5057
Percent of A's in repeat unit6
Percent of C's in repeat unit50
Percent of G's in repeat unit0
Percent of T's in repeat unit43
Sequence of repeat unit elementTCTCACCTCT
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This track displays simple tandem repeats (possibly imperfect repeats) on the 19 Sep 2018 Xiphophorus couchianus/GCF_001444195.1_X_couchianus-1.0/GCF_001444195.1 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 134,157 items in the track covering 14,719,442 bases, assembly size 688,541,509 bases, percent coverage % 2.14.


For more information about the TRF program, see Benson (1999).


TRF was written by Gary Benson.


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


This track was generated using a modification of a program developed by G. Miklem and L. Hillier (unpublished).


Gardiner-Garden M, Frommer M. CpG islands in vertebrate genomes. J Mol Biol. 1987 Jul 20;196(2):261-82. PMID: 3656447