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Dan Stieneke with Imad Eujayl
United States Department of Agriculture
Agricultural Research Service
Northwest Irrigation and Soils Research Lab
3793 N 3600 E
Kimberly, ID 83341

Web interface: v1.10
SSR finder: v1.00

Instructions

Modify options on this page as necessary, then press the "Go to Step 2" button. At Step 2, you will be prompted to upload a FASTA-formatted sequence file. You can also bookmark the "Step 2" page with your most-frequently-used parameters. More detailed instructions.

Abbreviations

SSR
Simple Sequence Repeat - a repeating pattern of nucleotides, also known as a microsatellite or Short Tandem Repeat (STR)
NRR
Non-Repeating Region - seemingly random nucleotides

General Options




Leave the description-line alone, or change it as described in the dropdown box.

Number of intial base pairs in each sequence to ignore.

Number of trailing base pairs in each sequence to ignore.

Yes: Join NRR-separated SSRs if only one "wants" to join.
No: Join NRR-separated SSRs only if both "want" to join.

(EX: With (ag)12-(NRR)6-(tca)2, (ag)12 would likely "want" to join, but (tca)2 would likely "not want" to join.

Perfect SSR Minimums

The minimum number of times a microsatellite must repeat before being reported. A blank means that type of microsatellite will not be reported.

Microsatellite
type Repeat









Imperfect SSR Minimums

The minimum number of times a microsatellite must repeat before being reported, taking into acount an adjacent microsatellite separated by a NRR.

For example, the default value for trinucleotides (4,6 ; 3,2 ; blank,blank) means that at least 4 repeats are required when adjacent to an NRR of up to 6 nucleotides long, but only 3 repeats are needed when adjacent to an NRR of 2 or fewer nucleotides. Blanks are ignored.

Microsatellite type   Rpt1NRR1  Rpt2NRR2  Rpt3NRR3
2 (dinucleotide)      
3 (trinucleotide)      
4 (tetranucleotide)      
5 (pentanucleotide)      
6      
7      
8      
9      
10