Simple Tandem Repeats by TRF (CATGCGCAGTGCCGGC)
 
Item: CATGCGCAGTGCCGGC
Position: NC_047505.1:17818303-17818414
Genomic Size: 112
View DNA for this feature (GCF_902827115.1/fPseGeo1.1 Apr. 2020)

Length of repeat unit45
Mean number of copies of repeat2.5
Length of consensus sequence45
Percentage Match85
Percentage Indel5
Alignment Score = 2*match-7*mismatch-7*indel; minscore=50138
Percent of A's in repeat unit16
Percent of C's in repeat unit33
Percent of G's in repeat unit35
Percent of T's in repeat unit13
Entropy1.88
Sequence of repeat unit elementCATGCGCAGTGCCGGCTGGAGCTGAAAGGGCACCACCGTCACACG
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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This track was generated using a modification of a program developed by G. Miklem and L. Hillier (unpublished).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