Putative Simple Sequence Repeats (SSRs) in the Rice Genome Pseudomolecules

The Rice Genome Annotation Project pseudomolecules (Release 7) were scanned with the Simple Sequence Repeat Identification Tool* to identify putative perfect mono-, di-, tri-, tetra-, penta-, and hexanucleotide simple sequence repeats. The minimum sizes for the putative SSRs are: 20 repeats for mononucleotides, 9 repeats for dinucleotides, 6 repeats for trinucleotides, 5 repeats for tetranucleotides, 4 repeats for pentanucleotides, and 3 repeats for hexanucleotides.

This page allows the display of the putative SSRs filtered by type and/or chromosome. If you are interested in finding the locations where a repeated motif is found, the bottom form can be used to conduct a search by motif.

*Temnykh S, DeClerck G, Lukashova A, Lipovich L, Cartinhour S, McCouch S. (2001) Computational and experimental analysis of microsatellites in rice (Oryza sativa L. ): frequency, length variation, transposon associations, and genetic marker potential. Genome Research, 2001, 11, pp.1441-1452

  
Please choose a chromosome, SSR type, and output type:
Chromosome:

SSR type:
Mononucleotide: 
Dinucleotide: 
Trinucleotide: 
Tetranucleotide: 
Pentanucleotide: 
Hexanucleotide: 
All Types: 

Output type:
HTML
(500 rows/page): 
Tab-delimited Text: 

OR

  
Enter a SSR motif to search for (i.e., at, ctg, tagt):
Motif: 
Chromosome:


NSF Logo This work is supported by grants (DBI-0321538/DBI-0834043) from the National Science Foundation.