Simple Tandem Repeats by TRF (ATAGAACATAT)
 
Item: ATAGAACATAT
Position: NW_020653854.1:8772843-8772872
Genomic Size: 30
View DNA for this feature (GCF_003589595.1/ASM358959v1 Sep. 2018)

Length of repeat unit11
Mean number of copies of repeat2.7
Length of consensus sequence11
Percentage Match89
Percentage Indel0
Alignment Score = 2*match-7*mismatch-7*indel; minscore=5051
Percent of A's in repeat unit56
Percent of C's in repeat unit6
Percent of G's in repeat unit10
Percent of T's in repeat unit26
Entropy1.57
Sequence of repeat unit elementATAGAACATAT
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Description

This track displays simple tandem repeats (possibly imperfect repeats) on the 21 Sep 2018 Hyposmocoma kahamanoa/GCF_003589595.1_ASM358959v1/GCF_003589595.1 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 106,791 items in the track covering 6,266,395 bases, assembly size 731,440,758 bases, percent coverage % 0.86.

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This track was generated using a modification of a program developed by G. Miklem and L. Hillier (unpublished).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