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When you choose to generate a puzzle with a custom alignment, a dialog box will appear giving you simple instructions on how to procede.
Simply highlight the cells you want the givens to be in, and when you're finished press any key. The generator will then calculate a puzzle that fits your chosen skill level for the cells you've chosen. Since there is the possibility you may choose an alignment that can not contain a unique solution puzzle, the generator will quit after about ten seconds.
Note that due to the difficulty of finding an adequate puzzle using limitted cells, there is a high chance that this method will not yield a puzzle. You may have to try this command several times before you get a result.
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