Mismatch level - This invokes a dialog box that allows the user
to specify the maximum number of base mismatches that will be allowed
between oligonucleotide and sequence record, during the analysis.
Default is for all oligonucleotides to tolerate up to 7 mismatches.
Length of minimum match at 3' end - The 3' end of primers are
most sensitive to base mismatches, such that a base mismatch at the 3'
end is more likely to result in a failure to anneal, than an equivalent
mismatch at the 5' end. OligoCheck allows the user to
specify
the minimum number of bases at the 3' end of the primer that must match
without mismatches. Note that although OligoCheck requires
that both forward and reverse primers are entered in their sense
form (i.e., correspond to the sense strand
of the target DNA molecule) within the main
window,
it is the 3' end of the reverse primer in its antisense form
that
the program considers here (since it is the antisense form that will be
used during PCR amplification).
Analyse one oligonucleotide only - This menu item enables /
disables the reverse primer text box on the main
window. Select this option when only one oligonucleotide
(e.g., a probe) is being considered.
Use 3' position information - This menu item enables / disables
the 3' position boxes on the main window