After IP and reverse cross linking and DNA purification, I have done a standard semicuantitative PCR using control primers (GAPDH), which I expect bands around 166 bp.

In the results of my standard PCR, there's only the input with the product size. However, samples that were immunoprecipitated with the positive control, negative control, and for the interested target, appeared as many fragments up to 166 bp.

I haven't found an explanation for these results. Is it because the IP has failed? Or could it be the PCR conditions? It seems like dimer products.