Simple Tandem Repeats by TRF (ATAATAATAATCACAA)
 
Item: ATAATAATAATCACAA
Position: NC_048272.1:14126654-14126731
Genomic Size: 78
View DNA for this feature (GCF_009762535.1/fNotCel1.pri Dec. 2019)

Length of repeat unit21
Mean number of copies of repeat3.6
Length of consensus sequence21
Percentage Match78
Percentage Indel10
Alignment Score = 2*match-7*mismatch-7*indel; minscore=5084
Percent of A's in repeat unit53
Percent of C's in repeat unit8
Percent of G's in repeat unit5
Percent of T's in repeat unit32
Entropy1.54
Sequence of repeat unit elementATAATAATAATCACAATTATA
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Description

This track displays simple tandem repeats (possibly imperfect repeats) on the 18 Dec 2019 Notolabrus celidotus/GCF_009762535.1_fNotCel1.pri/GCF_009762535.1 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 393,328 items in the track covering 46,882,675 bases, assembly size 846,744,125 bases, percent coverage % 5.54.

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This track was generated using a modification of a program developed by G. Miklem and L. Hillier (unpublished).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