Simple Tandem Repeats by TRF (TTCACT)
 
Item: TTCACT
Position: CM001582.2:91806014-91806044
Genomic Size: 31
View DNA for this feature (GCA_000298735.2/Oar_v4.0 Nov. 2015)

Length of repeat unit6
Mean number of copies of repeat5.0
Length of consensus sequence6
Percentage Match92
Percentage Indel7
Alignment Score = 2*match-7*mismatch-7*indel; minscore=5053
Percent of A's in repeat unit16
Percent of C's in repeat unit32
Percent of G's in repeat unit0
Percent of T's in repeat unit51
Entropy1.44
Sequence of repeat unit elementTTCACT
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Description

This track displays simple tandem repeats (possibly imperfect repeats) on the 20 Nov 2015 Ovis aries/GCA_000298735.2_Oar_v4.0/GCA_000298735.2 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 540,267 items in the track covering 42,833,190 bases, assembly size 2,615,499,683 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This track was generated using a modification of a program developed by G. Miklem and L. Hillier (unpublished).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