Is it possible that the amplification failure products can be visualized in electrophoresis? Due to the failed amplification results it shows bands in my electrophoresis with bands that are quite clear. My amplification curve clearly shows amplification failure, but when I look back at it with electrophoresis there are some obvious bands, how is that possible?
I can think of several possibilities off the top of my head:
If the qPCR machine was not set up to detect the fluorescence that you were using (e.g. you are using SYBR, but picked something else), or if you forgot to add the SYBR/other to the PCR, or if the SYBR/other was degraded.
Depends what probe you are using. With qPCR the fluorescence is usually associated with the probe being displaced/cleaved by the amplification. If you are amplifying the wrong region of the template then your primers will not form an amplicon that interacts with the probe meaning no fluorescence.
I think this band is because of the primer bind with itself we call it dimer
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