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The pain in the knees suggest that you could be developing an early age arthritis. In the arthritis there occurs an inflammation of knee joint and it may occur due to the continuous work with bending down on the knees. An x-ray of the knee can confirm the same. In case if found to have the arthritis, then you will have to consider changing your job profile. Meanwhile you should avoid squatting and temporary pain relief can be obtained by using knee caps and painkillers like ibuprofen or tylenol.
Do meet your doctor and get an x-ray done and consider the options mentioned above.
Hope I am able to answer your concerns.
Wish you good health!
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