Simple Tandem Repeats by TRF (CA)
 
Item: CA
Position: NC_047153.1:10899492-10899526
Genomic Size: 35
View DNA for this feature (GCF_009819705.1/fHipHip1.pri Dec. 2019)

Length of repeat unit2
Mean number of copies of repeat17.5
Length of consensus sequence2
Percentage Match93
Percentage Indel0
Alignment Score = 2*match-7*mismatch-7*indel; minscore=5061
Percent of A's in repeat unit51
Percent of C's in repeat unit48
Percent of G's in repeat unit0
Percent of T's in repeat unit0
Entropy1.00
Sequence of repeat unit elementCA
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Description

This track displays simple tandem repeats (possibly imperfect repeats) on the 31 Dec 2019 Hippoglossus hippoglossus/GCF_009819705.1_fHipHip1.pri/GCF_009819705.1 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 256,153 items in the track covering 22,271,519 bases, assembly size 596,792,615 bases, percent coverage % 3.73.

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This track was generated using a modification of a program developed by G. Miklem and L. Hillier (unpublished).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