Simple Tandem Repeats by TRF (TGGGGCCACAATGGGG)
 
Item: TGGGGCCACAATGGGG
Position: AFTI02000070.1:766489-767573
Genomic Size: 1085
View DNA for this feature (GCA_000297895.2/ASM29789v2 Aug. 2019)

Length of repeat unit166
Mean number of copies of repeat6.5
Length of consensus sequence165
Percentage Match85
Percentage Indel4
Alignment Score = 2*match-7*mismatch-7*indel; minscore=501364
Percent of A's in repeat unit33
Percent of C's in repeat unit15
Percent of G's in repeat unit24
Percent of T's in repeat unit26
Entropy1.95
Sequence of repeat unit elementTGGGGCCACAATGGGGGTCGAAGTTTAACATAGGAATATATACAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCTGGGGGTAGGG

Item: TGGGGCCACAATGGGG
Position: AFTI02000070.1:766489-767573
Genomic Size: 1085
View DNA for this feature (GCA_000297895.2/ASM29789v2 Aug. 2019)

Length of repeat unit334
Mean number of copies of repeat3.3
Length of consensus sequence329
Percentage Match84
Percentage Indel5
Alignment Score = 2*match-7*mismatch-7*indel; minscore=501389
Percent of A's in repeat unit33
Percent of C's in repeat unit15
Percent of G's in repeat unit24
Percent of T's in repeat unit26
Entropy1.95
Sequence of repeat unit elementTGGGGCCACAATGGGGGATCGAAGTTTAACATAGGAATATATACAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCTGGGGGTAGGATGGGGCCACAATGGGGGTCGAAGTTTAACATAGGAATATAAAAAGTAATTCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCGGAAAGCTGGAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAATTTGTGAAAATCATGACCCCCGAGGGTAGGG
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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