Simple Tandem Repeats by TRF (CACGGCTCCCGCGAGT)
 
Item: CACGGCTCCCGCGAGT
Position: NC_047505.1:17815788-17815833
Genomic Size: 46
View DNA for this feature (GCF_902827115.1/fPseGeo1.1 Apr. 2020)

Length of repeat unit18
Mean number of copies of repeat2.6
Length of consensus sequence18
Percentage Match100
Percentage Indel0
Alignment Score = 2*match-7*mismatch-7*indel; minscore=5092
Percent of A's in repeat unit10
Percent of C's in repeat unit52
Percent of G's in repeat unit26
Percent of T's in repeat unit10
Entropy1.69
Sequence of repeat unit elementCACGGCTCCCGCGAGTCC
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Description

This track displays simple tandem repeats (possibly imperfect repeats) on the 15 Apr 2020 Pseudochaenichthys georgianus/GCF_902827115.1_fPseGeo1.1/GCF_902827115.1 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 474,032 items in the track covering 73,834,875 bases, assembly size 1,026,101,545 bases, percent coverage % 7.20.

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This track was generated using a modification of a program developed by G. Miklem and L. Hillier (unpublished).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