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I would have just gone ahead and raised the flop in case anyone wanted to get cute behind me or had a strong draw thast they would call two bets with.

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Given the size of the pot I think raising the flop would make it correct to call for anyone chasing the flush draw on both the turn and the river. Its even worse if they 2 players behind Hero decide to CC the 2 bets and come along for the ride. I think calling and raising the turn is the better line to take. The two players behind hero might also decide to come along for one bet and fold to the turn raise, whereas had they paid 2SB, they may call the turn because of the larger pot and the fact it would only be 1BB to them see as it is likely MP1 would just c/c the turn.

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Also MP1 might not bet again on the turn.

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True MP1 might not bet again on the turn, but in micro limits the average player usually tend to lead again on the turn until their opponents show some strength.