Find new candidate SSR markers/primer pairs in zebrafish Zv9 chromosome DNA sequence

 


Zebrafish Assembly Zv9
(updated 8/12/12)

Zebrafish Zv9 Chromosome

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Enter chromosome intervals (3,000,000 nt or less) based on nucleotide positions in the Zv9 zebrafish genome assembly.

To get results, interval size should be less than or equal to 3 Mb.

Enter full nucleotide numbers (i.e. 61000000, not 61Mb).

This form searches for all di- tri- and tetra-nucleotide repeat sequences in zebrafish Zv9 sequence, masks the sequence around the repeats for larger repetitive sequences, and then designs unique sequence primer pairs to amplify the simple sequence repeats. These are potentially polymorphic simple sequence repeats (SSRs) that can be used in genetic mapping/positional cloning projects.

Depending on amount of sequence to be processed, searches take between 1 and 3 minutes to complete. Input won't accept blank spaces.

Credits:This site uses software including repeatmasker, primer3 (Whitehead Institute), and components of the Emboss programs. Thanks to Gary Williams for fine tuning the eprimer3 program that makes primer selection possible.

Citing this site:"Candidate SSR marker primer pairs for this work were generated using the Zebrafish Genome SSR search website, Massachusetts General Hospital, Charlestown MA 02129; World Wide Web URL: http://danio.mgh.harvard.edu/chrMarkers/zfssr.html" (methods section).

Site created and maintained by Iain Drummond, Nephrology Division, Massachusetts General Hospital

Last updated 8/12/12