8. Analyze - Oligonucleotide Frequency
This window shows the relative frequency of nucleic acid subsequences (6- or 7-mers) throughout the entire loaded sequence. Oligonucleotides having 3'-ends which are common in a specific database (subset of GenBank) have a greater likelihood of false priming. The tables of frequencies (located in the Frequencies folder) are user-selected and contain normalized frequencies of GenBank sub-sequences (6- or 7-mer). By choosing oligos with infrequent 3'-ends, in a given database, you are decreasing the likelihood of selecting a primer that primes on many sites in a complex substrate, such as genomic DNA. In other words using oligos with low frequency numbers decreases a chance of unspecific PCR.
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