Simple Tandem Repeats by TRF (GAATAAGAGCAATTGT)
 
Item: GAATAAGAGCAATTGT
Position: NC_039364.1:90140051-90140177
Genomic Size: 127
View DNA for this feature (GCF_003573695.1/ASM357369v1 Sep. 2018)

Length of repeat unit55
Mean number of copies of repeat2.3
Length of consensus sequence55
Percentage Match86
Percentage Indel1
Alignment Score = 2*match-7*mismatch-7*indel; minscore=50173
Percent of A's in repeat unit29
Percent of C's in repeat unit20
Percent of G's in repeat unit24
Percent of T's in repeat unit25
Entropy1.99
Sequence of repeat unit elementGAATAAGAGCAATTGTTATCGCCATTCCATGGGACCAGTCGCAGATTCAACCATG
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Description

This track displays simple tandem repeats (possibly imperfect repeats) on the 18 Sep 2018 Papaver somniferum/GCF_003573695.1_ASM357369v1/GCF_003573695.1 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 1,050,181 items in the track covering 184,603,198 bases, assembly size 2,715,530,335 bases, percent coverage % 6.80.

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This track was generated using a modification of a program developed by G. Miklem and L. Hillier (unpublished).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