Simple Tandem Repeats by TRF (CTCGAGTTTCGGGTCA)
 
Item: CTCGAGTTTCGGGTCA
Position: HG995366.1:13540524-13540742
Genomic Size: 219
View DNA for this feature (GCA_905333075.2/moth A.centrago)

Length of repeat unit121
Mean number of copies of repeat1.8
Length of consensus sequence121
Percentage Match81
Percentage Indel5
Alignment Score = 2*match-7*mismatch-7*indel; minscore=50273
Percent of A's in repeat unit23
Percent of C's in repeat unit13
Percent of G's in repeat unit31
Percent of T's in repeat unit31
Entropy1.93
Sequence of repeat unit elementCTCGAGTTTCGGGTCATATGATTCGGTTTGACGAGTCCAATAGACTAGGCTTGGTAACGACGGTCTGATGATAGAGCCAGCAGGTGGATAGTGGAACTTTTGAGTGGCTACTAATAAAACG
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Description

This track displays simple tandem repeats (possibly imperfect repeats) on the 26 Mar 2021 Atethmia centrago/GCA_905333075.2_ilAteCent1.2/GCA_905333075.2 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 171,734 items in the track covering 23,349,498 bases, assembly size 926,655,310 bases, percent coverage % 2.52.

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This track was generated using a modification of a program developed by G. Miklem and L. Hillier (unpublished).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