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By 4:00 AM, he had a set of four primers. They were clean. No hairpins. Optimal GC content. He ran them through a secondary validation script he found on a bioinformatics forum. They were perfect. Please note that while these alternatives are available,
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Elias stared at the monitor, his eyes burning. He was trying to design primers for a notoriously difficult region of the Arabidopsis genome. The sequence was riddled with hairpins and repetitive motifs that turned standard calculations into a nightmare of false positives.