A Search for Sequencing Primers
The "Selected Oligos" window lists all oligonucleotide selections from the most recent search. Check the "R1" button at the upper left corner of the window to display all positive strand oligonucleotide positions. Checking "R2" displays all negative strand positions.
The "Primer Pairs" window contains a table of primer pairs data from the most recent PCR primer search. To find the most optimal pair click on the "Sort %GC" button. In general, the lower the GC% of the template the easier to amplify the product. Similar results will provide sorting by Opt. Ta (choosing the highest Ta within the same percentage of GC ensures the most stable primers). By clicking on any of the listed primer pairs in the table, you select that pair as the Upper and Lower Primer. Clicking on a pair also calls up the PCR window that displays a graphic of the PCR product's location on the active sequence, along with other data for running PCR with the selected primer pair.