Simple Tandem Repeats by TRF (CTTCCTTCTTTCCTTC)
 
Item: CTTCCTTCTTTCCTTC
Position: NW_024407213.1:81768509-81768561
Genomic Size: 53
View DNA for this feature (GCF_016881025.1/HiC_Itri_2 Feb. 2021)

Length of repeat unit20
Mean number of copies of repeat2.6
Length of consensus sequence20
Percentage Match87
Percentage Indel3
Alignment Score = 2*match-7*mismatch-7*indel; minscore=5079
Percent of A's in repeat unit0
Percent of C's in repeat unit47
Percent of G's in repeat unit1
Percent of T's in repeat unit50
Entropy1.12
Sequence of repeat unit elementCTTCCTTCTTTCCTTCCTCC
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Description

This track displays simple tandem repeats (possibly imperfect repeats) on the 17 Feb 2021 Ictidomys tridecemlineatus/GCF_016881025.1_HiC_Itri_2/GCF_016881025.1 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 640,624 items in the track covering 40,556,393 bases, assembly size 2,478,965,571 bases, percent coverage % 1.64.

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This track was generated using a modification of a program developed by G. Miklem and L. Hillier (unpublished).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