Simple Tandem Repeats by TRF (GTGACTGGGAG)
 
Item: GTGACTGGGAG
Position: NW_024356505.1:13256366-13256416
Genomic Size: 51
View DNA for this feature (GCF_014805655.1/ASM1480565v1 Sep. 2020)

Length of repeat unit11
Mean number of copies of repeat4.6
Length of consensus sequence11
Percentage Match100
Percentage Indel0
Alignment Score = 2*match-7*mismatch-7*indel; minscore=50102
Percent of A's in repeat unit17
Percent of C's in repeat unit9
Percent of G's in repeat unit52
Percent of T's in repeat unit19
Entropy1.72
Sequence of repeat unit elementGTGACTGGGAG
View table schema

Go to Simple Repeats track controls


Description

This track displays simple tandem repeats (possibly imperfect repeats) on the 30 Sep 2020 Passer montanus/GCF_014805655.1_ASM1480565v1/GCF_014805655.1 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 492,684 items in the track covering 41,418,192 bases, assembly size 1,039,966,254 bases, percent coverage % 3.98.

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This track was generated using a modification of a program developed by G. Miklem and L. Hillier (unpublished).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