Simple Tandem Repeats by TRF (AT)
 
Item: AT
Position: NC_051386.1:21960963-21961135
Genomic Size: 173
View DNA for this feature (GCF_015228065.1/NSTDA_Pmon_1 Nov. 2020)

Length of repeat unit2
Mean number of copies of repeat91.5
Length of consensus sequence2
Percentage Match83
Percentage Indel15
Alignment Score = 2*match-7*mismatch-7*indel; minscore=50190
Percent of A's in repeat unit50
Percent of C's in repeat unit4
Percent of G's in repeat unit0
Percent of T's in repeat unit44
Entropy1.25
Sequence of repeat unit elementAT
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Description

This track displays simple tandem repeats (possibly imperfect repeats) on the 05 Nov 2020 Penaeus monodon/GCF_015228065.1_NSTDA_Pmon_1/GCF_015228065.1 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 7,028,944 items in the track covering 524,601,632 bases, assembly size 2,394,347,767 bases, percent coverage % 21.91.

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This track was generated using a modification of a program developed by G. Miklem and L. Hillier (unpublished).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