Simple Tandem Repeats by TRF (TTCTCTTCTCTTCTTT)
 
Item: TTCTCTTCTCTTCTTT
Position: chr5:13785403-13785477
Genomic Size: 75
View DNA for this feature (GCF_001444195.1/X_couchianus-1.0 Sep. 2018)

Length of repeat unit22
Mean number of copies of repeat3.4
Length of consensus sequence22
Percentage Match78
Percentage Indel14
Alignment Score = 2*match-7*mismatch-7*indel; minscore=5075
Percent of A's in repeat unit2
Percent of C's in repeat unit34
Percent of G's in repeat unit1
Percent of T's in repeat unit61
Entropy1.18
Sequence of repeat unit elementTTCTCTTCTCTTCTTTCTCCTA
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Description

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.

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This track was generated using a modification of a program developed by G. Miklem and L. Hillier (unpublished).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