[DIYbio] PCR trouble

I'm trying to amplify the LuxC-LuxG (or LuxC-LuxE) section of pVIB (pJE202).

This is the forward primer
CATATG ATGAATAAATGTATTCCAATGA I added the Ndel sequence to the 5' end

This is the reverse primer
CTCGAG TTATACGTATGCAAAAGCATCGG I added the Xhol sequence to the 5' end

I also tried a different primer made to bind LuxE but I don't have its sequence with me I can get it when I get home.

I'm consistently getting some small product when I run it on a gel with both primer combinations. On the gel it's smaller than 1kb and very bright. I've done a lot of variations with time, temp concentration, template purity etc. I've made fresh working stock (though my original dilution make still be contaminated if that's the issue) I plan to run a PCR of each primer alone and in combination with no template and see if I still get that same product.

Since I don't have a sequence for the plasmid I'm using I'm using the V. Fischeri genomic sequence from gene bank for the Lux gene sequence. The one submitted by Thomas Knight.

Does anyone see any mistakes in my primer design or elsewhere?

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