Simple Tandem Repeats by TRF (CATGCTGATAAAATGA)
 
Item: CATGCTGATAAAATGA
Position: HG995286.1:10134152-10134273
Genomic Size: 122
View DNA for this feature (GCA_905332915.1/ilHecDyso1.1 Mar. 2021)

Length of repeat unit61
Mean number of copies of repeat2.0
Length of consensus sequence61
Percentage Match95
Percentage Indel3
Alignment Score = 2*match-7*mismatch-7*indel; minscore=50219
Percent of A's in repeat unit43
Percent of C's in repeat unit10
Percent of G's in repeat unit22
Percent of T's in repeat unit23
Entropy1.84
Sequence of repeat unit elementCATGCTGATAAAATGAAAAAGCAGTTTCCAGGAAATGGAAAATAAGGCGTATTAATTGAAG
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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This track was generated using a modification of a program developed by G. Miklem and L. Hillier (unpublished).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