Simple Tandem Repeats by TRF (AAATATTAAAATTACA)
 
Item: AAATATTAAAATTACA
Position: HG992305.1:7016557-7016680
Genomic Size: 124
View DNA for this feature (GCA_905220615.1/moth T.trinotella)

Length of repeat unit28
Mean number of copies of repeat4.4
Length of consensus sequence28
Percentage Match79
Percentage Indel8
Alignment Score = 2*match-7*mismatch-7*indel; minscore=50128
Percent of A's in repeat unit60
Percent of C's in repeat unit3
Percent of G's in repeat unit1
Percent of T's in repeat unit34
Entropy1.22
Sequence of repeat unit elementAAATATTAAAATTACAATTAATAAATAA
View table schema

Go to Simple Repeats track controls


Description

This track displays simple tandem repeats (possibly imperfect repeats) on the 16 Feb 2021 Tinea trinotella/GCA_905220615.1_ilTinTrin1.1/GCA_905220615.1 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 72,850 items in the track covering 8,365,462 bases, assembly size 371,738,977 bases, percent coverage % 2.25.

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This track was generated using a modification of a program developed by G. Miklem and L. Hillier (unpublished).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