Shouldn't stackmm value for TA_AA be 4700 instead of inf?

primer3-org / primer3

Primer3 is a command line tool to select primers for polymerase chain reaction (PCR).

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Shouldn't stackmm value for TA_AA be 4700 instead of inf? #35

Open Curley-Joe opened 4 years ago

Curley-Joe commented 4 years ago

The ds value for stackmm AA_AT is 4700, which seems correct, but the dh value for TA_AA is "inf" due to commit 8c2aa6960c1befe4cdba0870078814844e548a15. I think the value for TA_AA should have been left at 4700.

untergasser commented 2 years ago

Hi, we try to trace back what lead to this changes. Can you provide more information why this change was incorrect? Best, Andreas

Curley-Joe commented 2 years ago

It was a long time ago that I reported this, so my memory is faint, but I think I was looking at the SantaLucia papers and they have 4.7 for AA_AT dh. See "Nearest-Neighbor Thermodynamics and NMR of DNA Sequences with Internal A-A, C-C, G-G, and T-T Mismatches".