Is it will affect the final result?
Yes, You can.
But the AFLP signals will be unstable among different samples owing to the unestimated amount DNA affects the efficiency of AFLP amplification.
Nur,
Pure DNA is one of critical conditions for reproducible AFLP. It is better to use commercial kits with magnetic beads or resin.
I think for AFLP you need very clean and purified DNA.IT IS REALLY CRITICAL
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