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Blood in urine could be due to surgery or due to exercise too. The most common cause of blood in urine is UTI (ruled out in your case). The next possible diagnosis is stone. The stone can be anywhere in the urinary system from kidney to urethra. Cancers of urinary system or some drugs too cause blood in urine. Bladder infections and cysts too can cause similar symptoms.
The granulosa cell ovarian tumor has potential to turn cancerous and cause bladder metastasis. Also this can cause endometriosis of bladder. All of these can cause blood in urine.
Since a confirmed diagnosis cannot be given on net please discuss these possibilities with your doctor once. A comprehensive investigation is required keeping all the points in mind. Hope this helps. Please let me know if there is any thing else and do keep me posted. Take care!