They "suspected" the balls may have been deflated, but then again it was pouring rain, and you know, science kicks in. Pressure+Water makes the ball heavy and deflated anyways. I know this because I'm a college football player who has rains games constantly. Plus, 45-7. The balls wouldn't have made a damn difference, as each team uses their own balls, as is the NFL rule.
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If you actually play football you know a deflated ball is easier to throw and catch. Patriots most likely were using a deflated ball and the colts were not. Adding the weight of the rain doesn't make the balls the same.
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I actually do, and I play constantly in rain and snow. Yes, it's easier, but do you have any idea how hard it would be to accomplish that?