Simple Tandem Repeats by TRF (AAAAAGACAGCAAA)
 
Item: AAAAAGACAGCAAA
Position: CM022047.1:6587079-6587118
Genomic Size: 40
View DNA for this feature (GCA_011316535.1/beet armyworm)

Length of repeat unit15
Mean number of copies of repeat2.7
Length of consensus sequence14
Percentage Match84
Percentage Indel7
Alignment Score = 2*match-7*mismatch-7*indel; minscore=5053
Percent of A's in repeat unit67
Percent of C's in repeat unit12
Percent of G's in repeat unit17
Percent of T's in repeat unit2
Entropy1.33
Sequence of repeat unit elementAAAAAGACAGCAAA
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Description

This track displays simple tandem repeats (possibly imperfect repeats) on the 17 Mar 2020 Spodoptera exigua/GCA_011316535.1_NJAU_Sexi_v1/GCA_011316535.1 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 56,338 items in the track covering 4,976,213 bases, assembly size 446,801,326 bases, percent coverage % 1.11.

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This track was generated using a modification of a program developed by G. Miklem and L. Hillier (unpublished).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