Long MIS and short BO

If I am long on a scrip (e.g.) Nifty futures in an MIS order, and another intraday strategy requires me to go short on the same scrip, can I go short with say e.g. BO? Would these positions cancel each other out?

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You can do it. Both the Positions will show you separately.

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MIS and BO are intraday products and these two are totally different , so you can place these orders and system interprets these orders separately.