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dark urine and black spec

I have an orange, brown, reddish color settling in the toilet pretty much every time I pee lately and after having sharp left sided pains last night in my kidney area I noticed I had a black speck that was probably 1cm x 1cm so definitely noticeable.  Is this a stone?  I had a CT scan done about 1 month ago that came back normal.  I have also peed in a cup 3 times now and despite my pee looking dark in the cup everything comes back normal and they say I need to drink more water.  I drink a ton and regardless my pee still has this sediment?  It is a new thing for me within the last 6-8 months.  Has anybody come up with a diagnosis on this one yet?  Also, I'm not sure if this makes a difference, but the black flake isn't that hard...it pretty much crumbles apart when I rub it in between two fingers and separates into even smaller specs that are about the size of a grain of really fine sand.  Love to get some feedback on this since the doctors haven't been able to come up with anything...

Thanks! Danielle
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