Simple Tandem Repeats by TRF (TAGAAAAGAGTGAGCT)
 
Item: TAGAAAAGAGTGAGCT
Position: OU342673.1:14458349-14458415
Genomic Size: 67
View DNA for this feature (GCA_910589285.1/ilMytFerr1.1 Jul. 2021)

Length of repeat unit21
Mean number of copies of repeat3.2
Length of consensus sequence21
Percentage Match64
Percentage Indel26
Alignment Score = 2*match-7*mismatch-7*indel; minscore=5052
Percent of A's in repeat unit41
Percent of C's in repeat unit4
Percent of G's in repeat unit28
Percent of T's in repeat unit25
Entropy1.74
Sequence of repeat unit elementTAGAAAAGAGTGAGCTAGATT
View table schema

Go to Simple Repeats track controls


Description

This track displays simple tandem repeats (possibly imperfect repeats) on the 07 Jul 2021 Mythimna ferrago/GCA_910589285.1_ilMytFerr1.1/GCA_910589285.1 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 200,504 items in the track covering 25,994,303 bases, assembly size 861,042,006 bases, percent coverage % 3.02.

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This track was generated using a modification of a program developed by G. Miklem and L. Hillier (unpublished).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