PCR and Gel conundrum

[antonyviridae]

Why is it that when I run the exact same PCR reaction (with the same sample) on two different PCR platforms, that when I run it on a gel or on Qiaxcel I see that the bands are running at different sizes? The difference isn't significant but enough to be noticable.

[merv]

I dont know.
Agarose gels are different technology to the patented system to which you refer, so I would ask the Qiagen reps to pay you a visit and explain it. or email them. or call.
it may be related to the pH of the gel and buffer, gel concentration, etc.

[JackBean]

I understood the question that there is difference between two PCRs; not between home-made gel and Qiaxcel.

[tranglee]

you could check your technique, maybe have some mistakes during your working