Simple Tandem Repeats by TRF (A)
 
Item: A
Position: CM023913.1:51496715-51496756
Genomic Size: 42
View DNA for this feature (GCA_013407035.1/jackdaw)

Length of repeat unit1
Mean number of copies of repeat42.0
Length of consensus sequence1
Percentage Match85
Percentage Indel0
Alignment Score = 2*match-7*mismatch-7*indel; minscore=5057
Percent of A's in repeat unit92
Percent of C's in repeat unit0
Percent of G's in repeat unit7
Percent of T's in repeat unit0
Entropy0.37
Sequence of repeat unit elementA
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Description

This track displays simple tandem repeats (possibly imperfect repeats) on the 13 Jul 2020 Coloeus monedula/GCA_013407035.1_ASM1340703v1/GCA_013407035.1 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 173,436 items in the track covering 10,600,873 bases, assembly size 1,035,863,955 bases, percent coverage % 1.02.

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This track was generated using a modification of a program developed by G. Miklem and L. Hillier (unpublished).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