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8.4.2.22. Max. # of G Bases in a Primer/Probe
OLIGO will eliminate all primers or probes that have more than this number of
guanosine residues if the “Restrict the Number of G Bases” sub-search is turned
on. This helps in finding primers or probes of a less secondary structure,
especially when multiplexing is considered down the road.
8.4.2.23. Frequency Table
In order to eliminate "Frequent Oligos", an oligonucleotide frequency table needs
to be specified. This table lists the frequencies of all oligonucleotide (6- or 7mers) combinations in various subsets of GenBank and is used by the
"Frequency Threshold" parameter. To choose a frequency table click on the
"Change" button and select a table from the "Frequencies" folder.
8.4.3. Search Parameters - Sequence Constraints
The Sequence Constraints search parameters window allows you to control
sequence contents of the actual primers and probes. You may type the actual 5’
or
Figure 8.4.3. The Search Parameters: Sequence Constraints and Scores windows.
3’-terminal sequence (ambiguous bases are possible), and OLIGO will select
primers only with those desired sequences. The check boxes in the Sequence
Constraints window indicate whether or not the particular constrain will be
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