It is often convenient to start a puzzle by filling in every base pair in target mode. This starting sequence can then be modified as needed. When creating a starting sequence, your goal is not to solve the puzzle. Instead, try to quickly create a sequence that is close to the solution.
- Before starting, enable the options "view free energy" and "view base pair numbering" in the settings menu.
- Fill in all long stacks with AU pairs.
- Fill in all short stacks and closing base pairs to with GC pairs.
The line between a "short" and a "long" stack is a fuzzy one that may depend on how many GC pairs are allowed in your solution.