Which prefix means 'against, contrary'?

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The prefix that means "against" or "opposite" is contra-. It comes from Latin and shows up in words like contradict, which means to speak against a statement; contrary, meaning opposite in nature or direction; and contraindicate, meaning to indicate something is not advisable or against a recommended course. The other prefixes point to different ideas—inter- means between or among, se- means apart or away, and circum- means around—so contra- is the one that best conveys the sense of opposition.