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Why did my sequencing fail?

There can be lots of reasons for a sequencing failure: --- GC rich >60% can present problems --- Sequence repeats --- Secondary structure / hairpins --- long homopolymer runs, Poly-A / T. these polyA tails can cause polymerase slippage and poor readshere is a good article that covers some of these fundamentals: https: //www. ncbi. nlm. nih. gov/pmc/articles/PMC2291785/( J Biomol Tech. 2006 Jul; 17(3): 207-217. Jan Kieleczawa )and lastly, there could be a problem with the clone itself.