Simple Tandem Repeats by TRF (AAAATCTAAATAAAAA)
 
Item: AAAATCTAAATAAAAA
Position: LR990987.1:11823680-11823722
Genomic Size: 43
View DNA for this feature (GCA_905163435.1/ilMamBras1.1 Jan. 2021)

Length of repeat unit19
Mean number of copies of repeat2.3
Length of consensus sequence19
Percentage Match84
Percentage Indel8
Alignment Score = 2*match-7*mismatch-7*indel; minscore=5052
Percent of A's in repeat unit76
Percent of C's in repeat unit4
Percent of G's in repeat unit0
Percent of T's in repeat unit18
Entropy0.95
Sequence of repeat unit elementAAAATCTAAATAAAAAAAA
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Description

This track displays simple tandem repeats (possibly imperfect repeats) on the 28 Jan 2021 Mamestra brassicae/GCA_905163435.1_ilMamBras1.1/GCA_905163435.1 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 86,624 items in the track covering 13,640,306 bases, assembly size 576,184,143 bases, percent coverage % 2.37.

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This track was generated using a modification of a program developed by G. Miklem and L. Hillier (unpublished).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