Simple Tandem Repeats by TRF (ATTGTCGTGTCGTTTA)
 
Item: ATTGTCGTGTCGTTTA
Position: NW_022881603.1:17939953-17943050
Genomic Size: 3098
View DNA for this feature (GCF_003369915.1/D.miranda_PacBio2.1 Sep. 2019)

Length of repeat unit1345
Mean number of copies of repeat2.3
Length of consensus sequence1346
Percentage Match97
Percentage Indel0
Alignment Score = 2*match-7*mismatch-7*indel; minscore=505876
Percent of A's in repeat unit30
Percent of C's in repeat unit24
Percent of G's in repeat unit18
Percent of T's in repeat unit27
Entropy1.98
Sequence of repeat unit elementATTGTCGTGTCGTTTAATATTAGCGGCGTCTGCCGGAGGAGAGCCATACTGACTTAGTATCGGGTATAACCGTAGAGTTGCGGTGTCCGCAGCAGCTCACAACGTTCCCCCTCGTTATACCCGATACTCAAAATGAGTATTGGGGTATATTAGATTTGTGGTAAAAGTGGATGTGTGTAACGTCCAGAAGGAATCGTTTCCGACCCCATAAAGTATATATATTCTTGATCAGCATCAATAACCGAGTCGATTGAGCCATGTGTGTCTGTCCGTCTGTCCGTCCGTCCGTCTGTCCGTCTGTCCGTCCCTATTAGCGCCTAGTGCTCAAAGACTATAAGAGCTAGAGCAACGATGTTTTGGATCCAGACTTCTGTGATATGTCACTGCCACAAAAATATTTTAAAACTTCGCCCCGCCCACTTCCGCCCCACAAAGGACGAAAATCTGGGGATATTCACAAATCTCAGAGACTATTAAGGCTAAAGTAACCAAATTTGGTATCCGCACTCCTGTTAGATCTTACTATAAAACGTGTATCTAAAAGTTTCGCCCCACCCCTTTCCGCCCACACAAAGGACGAAAATCTGTTGCATCCACAATATTGCACATTCGAGAAAACTAAAAACACAGAATCATAGATAATGACCATATCTATCAGATTGCTGAATCTGGATCAGATCAGATCATCCACAATTTTAAAGATACGAGAAAACCAAAAACGCAGAATTGTAGGAATGACCATATCTTTTAGACTGCAGAATTTGAATTGGATCGTATTATTATTATAGCCAGCATCAAGAAAACAATTTCATTTTTTCTCACCCTGTCTCTCTCTAACACACACGTAGCATAGCCGGCTTTGCTTAGAGTAAAACATTAGCGCCTAGATCTCAGAGACTATAAAAGCTAGAGCAACCAAATTTGGTATCCACACTCCTAATATATCGGACCGAGACGAGTTTGTTTCAAAATTTCGCCACACCCCCTTCCGCCCCCGCAAAGGACGAAAATCTGGGGATATTCAAAAATCTCAGAGACTATTAGGGCTAGAGTAACCAAATTTGGTATCCGCACTCCTGTTAGATCTCACTATAAAACGTATATCTCGAAATTTCACCCCACCCCTTTCCGCCCCACAAAGGACGAAAATCTATTACATCCACAATATTGAAGATACGAGAAAACTAAAAACGCAGAATCATAGATAATGATCATATCTATCAGATTGCTGAATCTGGATCAGATCAGATCATTTTTATAGCCAAAAGGAACAAATCAATTTGCACTGGCTACGCAGCCCCCGACGTCACGCTCAGACTGATTTTCTGTCTCTCTCGCAAGCACTC
View table schema

Go to Simple Repeats track controls


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