Find new candidate SSR markers/primer pairs in the Sanger Center Zv9 assembly of the zebrafish genome, or in BAC sequence.

Sequence name format: Use bac names (i.e. zK146H10) for searches instead of accession numbers. BAC accession numbers (i.e. BX465862.7) are not accepted as input.

Enter the name of a Zv9 scaffold, or BAC name. Sanger BAC name formats:

Library name Prefix
CHORI-211 zC
DanioKey zK
DanioKey pilot zKp
RPCI-71 bZ

Name translation:

DKEY-146N1 = zK146N1

Example accepted formats:

zC237K17, etc.


Searches take between 1 and 3 minutes to complete. Input is case sensitive and won't accept blank spaces.

This form will not search for Zv3, Zv4, Zv5, Zv6 Zv7 or Zv8 contigs.

This form searches for a Zv9 scaffold, finished or unfinished BAC clone by name, derives all di-, tri-, and tetra- nucleotide repeats in the sequence, masks the sequence around the repeats for larger zebrafish repetitive sequences, and then designs unique 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.

Note: Due to the possibility of mis-assembly in zebrafish genome assemblies, marker linkage should be independently confirmed.

Credits:This site uses the Sanger Center zebrafish Zv9 assembly, and bac sequence, and software including repeatmasker, primer3 (Whitehead Institute), and components of the Emboss programs. Zebrafish repeat libraries compiled by Rick Waterman and Zhirong Bao. 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 SSR search website, Massachusetts General Hospital, Charlestown MA 02129; World Wide Web URL:" (methods section).

Created and maintained by Iain Drummond,
Renal Unit, Massachusetts General Hospital

Last updated 8/12/2012