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The April soybean contract closed 1.4 percent higher at 2,940 Indian rupees ($45.61) per 100 kg on the National Commodity & Derivatives Exchange Ltd (NCDEX).
The April soyoil futures were down 0.4 percent at 634 rupees per 10 kg as of 1313 GMT, tracking weakness in palm oil on the Bursa Malaysia Derivatives Exchange.
The April rapeseed contract was largely flat at 3,840 rupees per 100 kg.
Indian commodities market will be shut on Friday on account of Ambedkar Jayanti, a day commemorating the birth anniversary of the country's social reformer B.R Ambedkar.