Simple Tandem Repeats by TRF (GTCTGTCC)
 
Item: GTCTGTCC
Position: NW_022881603.1:17941553-17941595
Genomic Size: 43
View DNA for this feature (GCF_003369915.1/D.miranda_PacBio2.1 Sep. 2019)

Length of repeat unit8
Mean number of copies of repeat5.4
Length of consensus sequence8
Percentage Match94
Percentage Indel0
Alignment Score = 2*match-7*mismatch-7*indel; minscore=5077
Percent of A's in repeat unit0
Percent of C's in repeat unit39
Percent of G's in repeat unit25
Percent of T's in repeat unit34
Entropy1.56
Sequence of repeat unit elementGTCTGTCC
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Description

This track displays simple tandem repeats (possibly imperfect repeats) on the 23 Sep 2019 Drosophila miranda/GCF_003369915.1_D.miranda_PacBio2.1/GCF_003369915.1 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 157,163 items in the track covering 18,977,924 bases, assembly size 287,096,000 bases, percent coverage % 6.61.

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This track was generated using a modification of a program developed by G. Miklem and L. Hillier (unpublished).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