Simple Tandem Repeats by TRF (TGAGCTCATTGAGATC)
 
Item: TGAGCTCATTGAGATC
Position: PVJD01000001.1:550020-550058
Genomic Size: 39
View DNA for this feature (GCA_004026545.1/MorMeg_v1_BIUU Jan. 2019)

Length of repeat unit18
Mean number of copies of repeat2.1
Length of consensus sequence18
Percentage Match85
Percentage Indel4
Alignment Score = 2*match-7*mismatch-7*indel; minscore=5051
Percent of A's in repeat unit23
Percent of C's in repeat unit17
Percent of G's in repeat unit20
Percent of T's in repeat unit38
Entropy1.93
Sequence of repeat unit elementTGAGCTCATTGAGATCAT
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Description

This track displays simple tandem repeats (possibly imperfect repeats) on the 16 Jan 2019 Mormoops blainvillei/GCA_004026545.1_MorMeg_v1_BIUU/GCA_004026545.1 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 332,606 items in the track covering 14,842,025 bases, assembly size 2,111,750,309 bases, percent coverage % 0.70.

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This track was generated using a modification of a program developed by G. Miklem and L. Hillier (unpublished).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