Simple Tandem Repeats by TRF (TATTATGCACATGCAA)
 
Item: TATTATGCACATGCAA
Position: HG995286.1:10131818-10131870
Genomic Size: 53
View DNA for this feature (GCA_905332915.1/ilHecDyso1.1 Mar. 2021)

Length of repeat unit19
Mean number of copies of repeat2.8
Length of consensus sequence19
Percentage Match71
Percentage Indel5
Alignment Score = 2*match-7*mismatch-7*indel; minscore=5054
Percent of A's in repeat unit37
Percent of C's in repeat unit16
Percent of G's in repeat unit18
Percent of T's in repeat unit26
Entropy1.93
Sequence of repeat unit elementTATTATGCACATGCAAGAT
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Description

This track displays simple tandem repeats (possibly imperfect repeats) on the 19 Mar 2021 Hecatera dysodea/GCA_905332915.1_ilHecDyso1.1/GCA_905332915.1 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 133,312 items in the track covering 17,687,792 bases, assembly size 640,911,641 bases, percent coverage % 2.76.

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This track was generated using a modification of a program developed by G. Miklem and L. Hillier (unpublished).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