Simple Tandem Repeats by TRF (GTCC)
 
Item: GTCC
Position: AFTI02000070.1:765028-765081
Genomic Size: 54
View DNA for this feature (GCA_000297895.2/ASM29789v2 Aug. 2019)

Length of repeat unit4
Mean number of copies of repeat13.8
Length of consensus sequence4
Percentage Match84
Percentage Indel3
Alignment Score = 2*match-7*mismatch-7*indel; minscore=5074
Percent of A's in repeat unit0
Percent of C's in repeat unit42
Percent of G's in repeat unit25
Percent of T's in repeat unit31
Entropy1.55
Sequence of repeat unit elementGTCC
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Description

This track displays simple tandem repeats (possibly imperfect repeats) on the 08 Aug 2019 Crassostrea gigas/GCA_000297895.2_ASM29789v2/GCA_000297895.2 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 210,258 items in the track covering 33,870,954 bases, assembly size 564,789,775 bases, percent coverage % 6.00.

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This track was generated using a modification of a program developed by G. Miklem and L. Hillier (unpublished).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