Internal Stability Windows
The Analyze Internal Stability command plots the free energy of pentamers (internal stability) of the active sequence, Current Oligo, and Upper and Lower Primers. The "Internal Stability" (Current Oligo) window is displayed along with the "Melting Temperature" window on the main screen immediately after an active sequence is opened. There are two display styles available for this window: "bar" and "dot" that may be switched using the Options-Style.
Each base of the Current Oligo pentamer is represented by an open red circle or a deep-green bar, while the rest of the sequence pentamers are represented by solid black circles or light green bars. Each pentamer is marked at the 5'-end of the positive strand.
The "Internal Stability" window can be used to check that an oligo is specific and will prime efficiently on its intended target. An oligo with a relatively unstable 3'-end, but with higher stability along the remainder of its length, should possess both these characteristics, assuming that other design characteristics are optimized.
The primer stability window provides stability information about a selected primer. An ideal primer in a complex PCR has a stable 5' end ("GC Clamp") and a relatively unstable 3' end to minimize false priming. Two types of display are available.
