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

Output linewrap width (0=no wrap)

Output UPPERCASE/lowercase

Invert SSR case(EX: ataaaTGTGTGTGcgatg)

Description processing

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

Ignore initial pair count

Number of intial base pairs in each sequence to ignore.

Ignore trailing pair count

Number of trailing base pairs in each sequence to ignore.

Aggressive join

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

2 (dinucleotide)

3 (trinucleotide)

4 (tetranucleotide)

5 (pentanucleotide)

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		Rpt₁	NRR₁		Rpt₂	NRR₂		Rpt₃	NRR₃
2 (dinucleotide)
3 (trinucleotide)
4 (tetranucleotide)
5 (pentanucleotide)
6
7
8
9
10