11) Select a position
The secondary structure that we have seen in previous steps should now be visible
We can use the mouse to drag and select a position on the loop we identified earlier
We are selecting a range on the secondary structure within which we wish to design a probe
A dialog box will appear telling us characteristics about the range we have chosen
If this is not an acceptable range, we can cancel by pressing "Cancel" and reselect a range
If the range is acceptable, then we can press "OK"
The secondary structure graphic will disappear to reveal our design grid with the appropriate range
NOTE: If your target is long, such as over 1500 nt or/and you have multiple targets, it is NOT necessary to simulate your target first. In the design algorithm, secondary structure of the target is already taken into consideration (see local target folding) when searching for optimal probes and primers. The example you see in this tutorial shows how you could select a target region first from a simulation, but it is not necessary, especially since you will be simulating your resulting probe/primer with your target after your design to assess for percent bound, effTm and other extensible sites.
