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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 reads
here 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.