This may sound a bit strange as you're not typing it into your calculator, but the difference is parentheses. When you multiply two negative numbers like -3x-3 you should get a positive result without parentheses. When you put in -3^2, the calcluator squares 3 first and then makes the result negative, because of the order of operations. If you put in (-3)^2, the calculator will square -3. Depending on how parentheses are used it can effect whether the result is positive or negative. For more information check out Purple Math's Exponents and Negative numbers.
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