Simple Tandem Repeats by TRF (CTAAAGCTGTGTTGCC)

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Simple Tandem Repeats by TRF (CTAAAGCTGTGTTGCC)

Item: CTAAAGCTGTGTTGCC
Position: NC_045956.1:64396052-64396130
Genomic Size: 79
View DNA for this feature (GCF_010909765.2/sAmbRad1.1.pri Feb. 2020)

Length of repeat unit	31
Mean number of copies of repeat	2.5
Length of consensus sequence	31
Percentage Match	100
Percentage Indel	0
Alignment Score = 2match-7mismatch-7*indel; minscore=50	158
Percent of A's in repeat unit	18
Percent of C's in repeat unit	15
Percent of G's in repeat unit	27
Percent of T's in repeat unit	37
Entropy	1.91
Sequence of repeat unit element	CTAAAGCTGTGTTGCCTTTGGTTTGGAAATG

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Description

This track displays simple tandem repeats (possibly imperfect repeats) on the 21 Feb 2020 Amblyraja radiata/GCF_010909765.2_sAmbRad1.1.pri/GCF_010909765.2 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 1,176,348 items in the track covering 97,024,358 bases, assembly size 2,558,784,953 bases, percent coverage % 3.79.

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This track was generated using a modification of a program developed by G. Miklem and L. Hillier (unpublished).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