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The Saturday fixture was a play-off match for ninth to 12th positions in the tournament where the Indian colts are taking part as part of an exposure tour to Russia, AIFF said in a release here on Sunday, January 15.
India led 1-0 at the interval after a 37th-minute goal but lost the advantage thereafter.
Estonia equalised in the 70th minute and sealed the match in the 87th.
India will now contest for positions between 13th to 16th after the loss.