Simple Tandem Repeats by TRF (CTCGATCCATCGAGAA)
 
Item: CTCGATCCATCGAGAA
Position: NW_019826381.1:767977-768091
Genomic Size: 115
View DNA for this feature (GCF_002906115.1/CorkOak1.0 Jan. 2018)

Length of repeat unit49
Mean number of copies of repeat2.3
Length of consensus sequence51
Percentage Match80
Percentage Indel15
Alignment Score = 2*match-7*mismatch-7*indel; minscore=50116
Percent of A's in repeat unit19
Percent of C's in repeat unit28
Percent of G's in repeat unit15
Percent of T's in repeat unit36
Entropy1.92
Sequence of repeat unit elementCTCGATCCATCGAGAATTTTTCCTATGCTCTCGATACTTCTCAACAATTTC
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Description

This track displays simple tandem repeats (possibly imperfect repeats) on the 29 Jan 2018 Quercus suber/GCF_002906115.1_CorkOak1.0/GCF_002906115.1 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 491,126 items in the track covering 56,718,649 bases, assembly size 953,298,670 bases, percent coverage % 5.95.

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This track was generated using a modification of a program developed by G. Miklem and L. Hillier (unpublished).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