<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; ">Hi Melissa,<DIV><BR class="khtml-block-placeholder"></DIV><DIV>The positions of the SSRs in Gramene are based on the current rice pseudomolecules, as assemblies from TIGR. We re-run the pipeline that positions these SSRs on the rice genome (based on e-PCR with the primer pairs) with every build of Gramene. Thus, as the assemblies of the rice pseudomolecules are updated in Gramene, the bp positions of the SSRs change, reflecting their current positions on the latest assembly of the pseudomolecules. Thus, with each build of Gramene, the positions of the SSRs may change slightly.</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>In addition, you will find that the positions of the SSRs published in 2005 (and downloaded as a supplemental file that I shared with you at that time) were based on the 2005 assembly of the rice pseudomolecule by the IRGSP. That assembly differs from the TIGR pseudomolecules, even though the underlying sequence information is the same. </DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>I hope this answers your questions. I would suggest that you use the most recent positions of the SSRs as published in Gramene, but please cite the version of the pseudomolecules (i.e., TIGR v. 5) so that as they continue to change, it is clear where you referenced your positions.</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Best regards,</DIV><DIV>Susan</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><BR><DIV><DIV>On Sep 19, 2007, at 11:52 AM, Melissa Jia wrote:</DIV><BR class="Apple-interchange-newline"><BLOCKQUOTE type="cite"><FONT size="2">About two years ago, Dr. McCouch provided me with an excel file listing the 18,000 Class I SSR's. The location and sequence listed in gramene are different from this one. I assume gramene lists correct one. Is this so? For reference I've attached the original table Dr. McCouch gave me.</FONT><SPAN><DIV><18000_Class1_SSrs.xls></DIV></SPAN><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">_______________________________________________</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Gramene mailing list</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><A href="mailto:Gramene@brie4.cshl.edu">Gramene@brie4.cshl.edu</A></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><A href="http://mail.gramene.org/mailman/listinfo/gramene">http://mail.gramene.org/mailman/listinfo/gramene</A></DIV> </BLOCKQUOTE></DIV><BR></DIV></BODY></HTML>