Simple Tandem Repeats by TRF (TCTGCGCCATTTTCAT)
 
Item: TCTGCGCCATTTTCAT
Position: NC_044916.1:12696665-12696757
Genomic Size: 93
View DNA for this feature (GCF_003576645.1/ASM357664v1 Sep. 2018)

Length of repeat unit50
Mean number of copies of repeat1.9
Length of consensus sequence50
Percentage Match86
Percentage Indel6
Alignment Score = 2*match-7*mismatch-7*indel; minscore=50138
Percent of A's in repeat unit19
Percent of C's in repeat unit38
Percent of G's in repeat unit8
Percent of T's in repeat unit33
Entropy1.82
Sequence of repeat unit elementTCTGCGCCATTTTCATTCACCACATCCCTCTCCCAAATCTCCATATATTG
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Description

This track displays simple tandem repeats (possibly imperfect repeats) on the 19 Sep 2018 Ipomoea triloba/GCF_003576645.1_ASM357664v1/GCF_003576645.1 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 335,317 items in the track covering 49,226,649 bases, assembly size 461,989,178 bases, percent coverage % 10.66.

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This track was generated using a modification of a program developed by G. Miklem and L. Hillier (unpublished).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