Simple Tandem Repeats by TRF (AAATTAAATACAAGCC)
 
Item: AAATTAAATACAAGCC
Position: NC_039364.1:90136059-90136146
Genomic Size: 88
View DNA for this feature (GCF_003573695.1/ASM357369v1 Sep. 2018)

Length of repeat unit21
Mean number of copies of repeat4.2
Length of consensus sequence21
Percentage Match76
Percentage Indel16
Alignment Score = 2*match-7*mismatch-7*indel; minscore=5076
Percent of A's in repeat unit57
Percent of C's in repeat unit22
Percent of G's in repeat unit4
Percent of T's in repeat unit14
Entropy1.55
Sequence of repeat unit elementAAATTAAATACAAGCCCACAA
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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This track was generated using a modification of a program developed by G. Miklem and L. Hillier (unpublished).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