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Why did 5' sequencing work and 3' sequencing fail with my cDNA clone?

This could be the result of a long polyA tail. Sequencing through the polyA tail can be difficult due to thermodynamic slippage of the polymerase during extension. The reference below has good suggestions. Reference: http://nar.oxfordjournals.org/cgi/pdf_extract/19/7/1715

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