primer design example - why is scoring matrix changed?

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Ekaterina Avershina
Ekaterina Avershina 2016-11-13
I need to design long primers of around 50 bp; and i follow the 'Exploring primer design' example (https://se.mathworks.com/help/bioinfo/examples/exploring-primer-design.html). When checking for cross-hybridization, the scoring matrix is changed from NUC44 to scr_mat = [-1,-1,-1,1;-1,-1,1,-1;-1,1,-1,-1;1,-1,-1,-1;]. I have 3 questions: (1) why? what do these numbers mean? (2) are these numbers specific for 18-30 bp, or are they valid for longer oligos? and (3) In this example, 'good' pair is the one with scr <=3, why? what does it mean? Is that 3 or less than 3 nucleotides hybridizing?

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