Mouse genome build m36
(updated 7/11/07)

Enter chromosome intervals (3,000,000 nt or less) based on nucleotide positions in the m36 mouse genome assembly (NCBI build 36).

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

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

search Mouse genome build 37

This form searches for all di- tri- and tetra-nucleotide repeat sequences in mouse genome build 36 sequence, masks the sequence around the repeats for larger mouse 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.

The ends of NCBI mouse chromosomes may contain many "N"'s, so low range nt. numbers (1-1000000) sometimes do not yield results.

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 Mouse Genome SSR search website, Massachusetts General Hospital, Charlestown MA 02129; World Wide Web URL: http://danio.mgh.harvard.edu/mouseMarkers/musssr.html" (methods section).

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

Last updated 7/11/07