[Genome] isPcr doesn't find an amplicon?

[Amir Karger]

Hi.

I put the following primer pair into isPcr (command line and web
version), and got no results. I've confirmed that I can get results with
other primers, so I know I'm using it correctly.

ENSG00000000457_E13A_P14        TTCCACCTCCGCGTGC        AGCTTTAGGACCCTC

isPcr should be finding chr20:59,627,734-59,627,760 on the + strand.

I've confirmed with the Genome Browser that the forward primer and the
complement of the reverse primer do appear at those positions on chr20.

Could you tell me why isPcr isn't finding it? I thought maybe one of the
primers was a repeat, but at least my command-line version isn't doing
any masking: I just did isPcr chr20.fa primers.tab primers.fasta.

Thanks,
- Amir Karger
Research Computing
Life Sciences Division
Harvard University
617-496-0626