Simple Tandem Repeats by TRF (AAAATTTCGCCACACC)
 
Item: AAAATTTCGCCACACC
Position: NW_022881603.1:17933960-17939956
Genomic Size: 5997
View DNA for this feature (GCF_003369915.1/D.miranda_PacBio2.1 Sep. 2019)

Length of repeat unit1914
Mean number of copies of repeat3.1
Length of consensus sequence1916
Percentage Match97
Percentage Indel0
Alignment Score = 2*match-7*mismatch-7*indel; minscore=5011362
Percent of A's in repeat unit31
Percent of C's in repeat unit23
Percent of G's in repeat unit17
Percent of T's in repeat unit26
Entropy1.97
Sequence of repeat unit elementAAAATTTCGCCACACCCCCTTCCGCCCCCGCAAAGGACGAAAATCTGGGGATATTCAAAAATCTCAGAGACTATTAAGGCTAGAGTAACCAAATTTGGTATCCGCACTCCTGTTAGATCTTACTATAAAACGTGTATCTAAAAGTTTCGCCCCACCCCTTTCCGCCCACACAAAGGACGAAAATCTGTTGCATCCACAATATTGCACATTCGAGAAAACTAAAAACGCAGAATCATTGATAATGACCATATCTATCAGATTGCTGAATCTGGATCAGATCAGATCATCCACAATTTTGAAGATACGAGAAAACCAAAAACGCAGAATCGTAGGGAATGACCATATCTTTTAGACTGCAGAATTTGAATTGGATCGTATTATTATTATAGCCAGCATCAAGAAAACAATTTAATTTTTTCTCGCCCTGTCTCTCTCTAACACACACGTAGCATAGCCGGCTTTGCTTAGAGTAAAACATTAGCGCCTAGATCTCAGAGACTATAAAAGCTAGAGCAACCAAATTTGGTATCCACACTCCTAATATATCGGACCGAGACGAGTTTGTTTCAAAATTTCGCCACACCCCCTTCCGCCCCCGCAAAGGATGAAAATCTGGGGATATTCACAAATCTCAGAGACTATTAGGGCTAGAGTAACCAAATTTGGTATCCGCACTCCTGTTTGATCTCACTATAAAACGTATATCTCGAAATTTCGTCCCACCCCTTTCCGCCCCACAAAGGACGAAAATCTATTGCCTCCACAATATTGAAGATACGAGAAAACAAAAAACGCAGAATCATAGATAATGATCATATCTATCAGATTGCTGAATCTGGATCAGATCAGATCATTTTTATAGCGAAAAGGAACAAATCAATTTGCACTGGCTACGCAGCCCCCGACGTCACGCTCAGACTGATTTTCTGTTTCTCTCGCACGCACTCTTTGTCGTGTCGTTTAATATTAGCGGCGTCTGCCGGAGGAGAGCCATACTGACATAGTATCGGGTATAACCGTAGAGTTGCGGTGTCCGCAGCAACTCACAACGTTCCCCCTCGTTATACCCGATACTCAAAATGAGTATTGGGGTATATTAGATTTGTGGTAAAAGTGGATGTGTGTAACGTCCAGAAGGAATCGTTTCCGACCCCATAAAGTATATATATTCTTGATCAGCATCAATAACCGAGTCGATTGAGCCATGTGTGTCTGTCCGTCTGTCCGTCCGTCCGTCTGTCCGTCTGTCCGTCCCTATTAGCGCCTAGTGCTCAAAGACTATAAGAGCTAGAGCAACGATGTTTTGGATCCAGACTTCTGTGATATGTCACTGCCACAAAAATATTTTAAAACTTCGCCCCGCCCACTTCCGCCCCCACAAAGGACGAAAATCTGGGGATATTCACAAATCTCAGAGACTATTAAGGCTAGAGTAACCAAATTTGGTATCCGCACTCCTGTTAGATCTTACTATAAAACGTGTATCTAAAAGTTTTGCCCCACCCCTTTCCGCCCACACAAAGGACGAAAATCTGTTGCATCCACAATATTGCACATTCGAGAAAACTAAAAACGCAGAATCATAGATAATGACCATATCTATCAGATTGCTGAATCTGGATCAGATCAGATCATCCACAATTTTAAAGATATGAGAAAACCAAAAACGTAGAATTGTAGAGAATGACCATATCTTTAAGACTGCGGAATCTGAATTGGATCGTATTATTATTATAGCCAGCATCAAGAAAACAATTTCATTTTTTCTCGCCCTGTCTCTCTCTAACACACACGTAGCATAGCCGGCTTTGCTTAGAGTAAAATATTAGCGCCTAGATCTCAGAGACTATAAAAGCTAGAGCAACCAAATTTGGTATCCACACTCCAAATATATCGGACCGAGACGAGTTTGTTTC
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Description

This track displays simple tandem repeats (possibly imperfect repeats) on the 23 Sep 2019 Drosophila miranda/GCF_003369915.1_D.miranda_PacBio2.1/GCF_003369915.1 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 157,163 items in the track covering 18,977,924 bases, assembly size 287,096,000 bases, percent coverage % 6.61.

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