Simple Tandem Repeats by TRF (TACATAGCATTCC)
 
Item: TACATAGCATTCC
Position: CM036558.1:56098118-56098147
Genomic Size: 30
View DNA for this feature (GCA_020745775.1/plumbeous ibis)

Length of repeat unit13
Mean number of copies of repeat2.3
Length of consensus sequence13
Percentage Match94
Percentage Indel0
Alignment Score = 2*match-7*mismatch-7*indel; minscore=5051
Percent of A's in repeat unit30
Percent of C's in repeat unit30
Percent of G's in repeat unit10
Percent of T's in repeat unit30
Entropy1.90
Sequence of repeat unit elementTACATAGCATTCC
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Description

This track displays simple tandem repeats (possibly imperfect repeats) on the 05 Nov 2021 Theristicus caerulescens/GCA_020745775.1_bTheCae1.pri.cur/GCA_020745775.1 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 188,606 items in the track covering 12,202,135 bases, assembly size 1,203,372,763 bases, percent coverage % 1.01.

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This track was generated using a modification of a program developed by G. Miklem and L. Hillier (unpublished).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