According to your experience, is it possible to sequence weak PCR products like the ones shown in lanes A and B? In this case I can not get better amplicons.
Hot spot PCR possible Lane A and B product may be good amplification
Is the PCR product long enough to allow nested PCR (re-amplify purified PCR product with internal primers specific to your fragment) before purification and sequencing? In that case you can try that out. Ensure clean environment to eliminate the risk of contamination since it will be many PCR cycles in total. For example, 1st PCR 30 cycles, 2nd PCR 35 cycles.
Hello, you can also try to clone your PCR product in a topoTA plasmid and than perform the sequencing of this region thanks the universal primers delivered with this kit.
All the best
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