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1. Wash the clams well under cold running water in colander. Place clams in a large pot, and add enough water to cover clams by 2 inches. Cover the pan and place over high heat.
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2. When the water comes to a boil, give the pan a good shake. Turn the heat to low, and cook clams another 30 seconds or so. Remove from the heat, and take out all the clams that have opened, using a slotted spoon. If any clams remain closed, put back on the heat, with the lid on the pan, and cook another 1-2 minutes. Remove remaining clams, reserve, discard any clams that have not opened.
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3. Pour the clam juice through a fine strainer and set aside. You will need 6 cups of broth. If you have more than enough clam broth, reduce it to 6 cups. If you have too little clam brother, add some bottled clam juice or water to make 6 cups total.
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4. Put the bacon into a large, heavy saucepan and cook over moderate heat, stirring, until the bacon begins to brown. Pour off excess fat, leaving behind the bacon and about 3 tablespoons of fat in the pan.
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5. Add the onion, celery, and carrot to the pan and cook until soft, about 10 minutes. Add potatoes, and cook mixture for 10 minutes more. Add tomatoes and reserved clam juice to the pan. Bring chowder to a boil over high heat.
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6. While chowder is coming to a boil, remove clams from their shells and chop coarsely. Add to chowder and reduce heat to low. Add thyme leaves. Cook over low heat for another 5 minutes; check to make sure potatoes are soft and chowder is well seasoned. Remove and allow to sit for 5 minutes. Serve in warm bowls.
