Simple Tandem Repeats by TRF (GAGCTAGATTTAGAAT)
 
Item: GAGCTAGATTTAGAAT
Position: OU342673.1:14458237-14458458
Genomic Size: 222
View DNA for this feature (GCA_910589285.1/ilMytFerr1.1 Jul. 2021)

Length of repeat unit41
Mean number of copies of repeat5.4
Length of consensus sequence41
Percentage Match86
Percentage Indel8
Alignment Score = 2*match-7*mismatch-7*indel; minscore=50267
Percent of A's in repeat unit41
Percent of C's in repeat unit6
Percent of G's in repeat unit23
Percent of T's in repeat unit28
Entropy1.78
Sequence of repeat unit elementGAGCTAGATTTAGAATTAAGATTTGAGAGCTAGAAAAGAGA
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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This track was generated using a modification of a program developed by G. Miklem and L. Hillier (unpublished).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