The following tools are located in the upper right of the Primer Design view:
| Selection Mode
||To enable selection of a region of sequence using the mouse. After selecting this tool, click on a translated amino acid to select its codon. Click and hold on a restriction enzyme to show the cut sites, represented by thin blue lines. Click and hold on a restriction enzyme while holding down the Alt (Win) or Option (Mac) key to show the cut represented by bold black arrows, as well as the recognition sequence.|
| Introduce Restriction Site
||To introduce a restriction site into the sequence. After selecting this tool, click between the residues where the restriction site should be added, and choose an enzyme from the list provided. The restriction enzymes identified to cleave the sequence at your specified location will be organized into 3 groups: Silent substitutions, Non-silent substitutions, and Introduce a stop.|
| Introduce Codon Change/Mutation
||To introduce a mutation into your sequence. After selecting this tool, the cursor will highlight each codon as you hover over the sequence. Click the codon of interest to display a list of alternate codons available for a silent mutation, as well as a list of alternate amino acids available for non-silent mutations. Selecting an alternate amino acid will replace the sequence via the least disruptive alternate codon.|
| Show Top Primer Strand
||To change the focus of the Residue Pane to the top primer. The Mispriming Pane is updated automatically to reflect the associated primer.|
| Show Bottom Primer Strand
||To change the focus of the Residue Pane to the bottom primer. The Mispriming Pane is updated automatically to reflect the associated primer.|
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