Simple Tandem Repeats by TRF (TA)
 
Item: TA
Position: OU015585.1:7944817-7944906
Genomic Size: 90
View DNA for this feature (GCA_907165245.1/ilHabPyri1.1 May 2021)

Length of repeat unit2
Mean number of copies of repeat43.5
Length of consensus sequence2
Percentage Match86
Percentage Indel6
Alignment Score = 2*match-7*mismatch-7*indel; minscore=50126
Percent of A's in repeat unit46
Percent of C's in repeat unit1
Percent of G's in repeat unit5
Percent of T's in repeat unit46
Entropy1.33
Sequence of repeat unit elementTA
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Description

This track displays simple tandem repeats (possibly imperfect repeats) on the 17 May 2021 Habrosyne pyritoides/GCA_907165245.1_ilHabPyri1.1/GCA_907165245.1 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 50,304 items in the track covering 5,277,194 bases, assembly size 400,568,986 bases, percent coverage % 1.32.

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This track was generated using a modification of a program developed by G. Miklem and L. Hillier (unpublished).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