3. Analyze - Duplex Formation
The "Duplex Formation" windows display potential duplexes in the forward (Upper Primer) and reverse (Lower Primer) primer. Potential dimers between the selected Upper and Lower Primer is displayed on a separate window.
DG and hairpin loop Tm values are calculated and displayed in association with each duplex (dimer or hairpin). If the Tm is not displayed for a given hairpin, then it is not likely that it can form (Tm>0).
The information shown in the Upper Primer Duplexes window
includes:
• The most stable 3' terminal dimer alignment of the primer
• The most stable primer dimer alignment overall
• The most stable hairpin structure in the primer, if any
• The stability values of the most stable uninterrupted duplex
(shown in bold) in each alignment, and of the hairpin structure is
expressed in kcal/mol and in Tm of the
hairpin.
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