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Why does a flush beat a straight in holdem?

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Because flushes are rarer than straights:

Seven Cards
Hand............Combinations
Royal Flush.........4,324
Straight Flush......37,260
4 of a Kind.........224,848
Full House........3,473,184
Flush.............4,047,644
Straight..........6,180,020
3 of a Kind.......6,461,620
Two Pair..........31,433,400
One Pair..........58,627,800
High Card.........23,294,460