Simple Tandem Repeats by TRF (GACTCGGAGGCTC)
 
Item: GACTCGGAGGCTC
Position: NC_047505.1:17816718-17816742
Genomic Size: 25
View DNA for this feature (GCF_902827115.1/fPseGeo1.1 Apr. 2020)

Length of repeat unit13
Mean number of copies of repeat1.9
Length of consensus sequence13
Percentage Match100
Percentage Indel0
Alignment Score = 2*match-7*mismatch-7*indel; minscore=5050
Percent of A's in repeat unit16
Percent of C's in repeat unit28
Percent of G's in repeat unit40
Percent of T's in repeat unit16
Entropy1.89
Sequence of repeat unit elementGACTCGGAGGCTC
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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This track was generated using a modification of a program developed by G. Miklem and L. Hillier (unpublished).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