Hello, We are unable to duplicate. For the test, the example on the PCR page was used. http://genome.ucsc.edu/cgi-bin/hgPcr
If you would like to send a example pair that produces this behavior (or maybe two pairs, if you have them), we can test here and see what is going on. It is possible that the entire sequence did not align - 22 bases is nearing the lower-end threshold for minimum sequence length. You can check this yourself by examining the BLAT alignment produced by the PCR tool or send the data (you can send to me directly, not to the entire list, with the sequence just pasted into the email). Be sure to let me know the genome/assembly the primers are for and any setting that you changed from the default on the PCR tool page. Hopefully we will be able to work it out, Jennifer ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Tim Reddy" <[email protected]> wrote: > From: "Tim Reddy" <[email protected]> > To: "genome" <[email protected]> > Sent: Saturday, November 28, 2009 10:13:33 AM GMT -08:00 US/Canada Pacific > Subject: [Genome] PCR feature on genome browser > > Hello, > > A comment about how the PCR tracks are displayed that perhaps could > use a slight improvement: > > I was using the UCSC genome browser to design some experiments today, > and noticed something about the PCR feature that I thought was off. > Using the PCR tool, I like that you get thick bars indicating where > the primers anneal, and a thin region showing additional amplified > region. What was not clear to me until now, howe3ver, is that the > thick bars are not actually the primers: they seem fixed at 20bp. So, > for example, if you use a 22bp primer, the primers' 3'-most 2bp are > not displayed as thick. Usually a trivial point, but when carefully > designing experiments where the 3' end of the primer must be very > precise, it would be nice to have the full primer sequence in a thick > dark band. > > Many thanks! > Tim > > -- > Timothy E. Reddy, Ph.D. > Postdoctoral Fellow > Myers Lab > HudsonAlpha Institute for Biotechnology > > 256-684-0874 (cell) > [email protected] > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
