Simple Tandem Repeats by TRF (TTCCGCCCCCACAAAG)
 
Item: TTCCGCCCCCACAAAG
Position: NW_022881603.1:17947948-17949323
Genomic Size: 1376
View DNA for this feature (GCF_003369915.1/D.miranda_PacBio2.1 Sep. 2019)

Length of repeat unit625
Mean number of copies of repeat2.2
Length of consensus sequence632
Percentage Match94
Percentage Indel2
Alignment Score = 2*match-7*mismatch-7*indel; minscore=502410
Percent of A's in repeat unit28
Percent of C's in repeat unit24
Percent of G's in repeat unit20
Percent of T's in repeat unit26
Entropy1.99
Sequence of repeat unit elementTTCCGCCCCCACAAAGGACGAAAATCTGTGGCATCCACAATATTAAAGATACGAGAAAACTAAAAACGCAGAATCATAGATAATGATCATATCTATCAGATTGCTGAATCTGGATCAGATCAGATCATTTTTATAGCCAAAAGGAACAAATCAATTTGCACTGGCTACGCAGCCCCGACGTCACGCTCAGACTGATTTTCTGTCTCTCTCGCACGCACTCTTTGTCGTGTCGTTTAATATAAGCGGCGTCTGCCGGACGAGAGCCATACTGACATAGTATCGGGTATAACCGTAGAGTTGCGGTGTCCGCAGCAACTCACAACGTTCCCCTCGTTATACCCGATACTCAAAATGAGTATTGGGGTATATTAGATTTGTGGTAAAAGTGGATGTGTGTAACGTCCAGAAGGAATCGTTTCCGACCCCATAAAGTATATATATTCTTGATCAGCATCAATAGCCGAGTCGATTGAGCCTCTGTCGTCGTCTGTCCGTCCGTCCGTCTGTCCGCTGTCCGCCCTATCAGCGCCTAGTGCTCAAAGACTATAAGAGCTAGAGCAACGATGTTTTGGATCCAGACTTCTGTGATATATCACTGCTACAAAAATATTTCAAAACTTCGCCCCGCCCAC
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This track was generated using a modification of a program developed by G. Miklem and L. Hillier (unpublished).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