If you have amplification in a negative control then you have post pcr contamination which is a serious problem. First check its size....it may be primer dimer if less than 100 bp but if it is a clean band and sharply defined then you have a serious problem. You can redesign primers for a larger pcr product and then it will not matter as the contamination cannot amplify but you will have to clean up your pipettes and working area and change all of your reagents. In the first instance borrow pipettes and pcr machine and reagents from another researcher and using your primers and their pcr reagents and pipettes set up a pcr.If the no template control is clean then your primers are probably ok and just change all other reagents. A thorough clean up of your working area is still needed

If your negative control is your non-template control (meaning that you use water instead of the PCR product obtained in the first step), than this does indicate a contamination (and following Paul's suggestions will help you identify the source). Simply changing your molecular-grade water (used as your NTC) might be a first step. If you are not using water as your template for the negative controls, it depends on the respective template. If it is the pre-PCR DNA used as template, you may of course be amplifying both your target and the pseudogene (as your allele-specific primers may not be as specific as your target-specific primers).

Good luck with your experiments!

Sounds like typical contamination. As Paul said, throw away ALL of your reagents (water, buffer, enzyme, primers, etc.), clean your work area, and try agin. Also, do NOT use the same micropipettes for handling amplified PCR products that use use for setting up PCR.

Supposed to be so