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Place the first 5 ingredients (including the adobo sauce with the chipotles) into a blender and puree until quite smooth. Pour into a small saucepan. At this point it will look like this:
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Add the water and on medium heat, bring the mixture to a boil. Immediately reduce the heat to medium low or low, enough to maintain a gentle simmer. Be careful because this mixture will splatter--you will want to stir it frequently, which will cut down on the splattering.
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Simmer for 30 minutes, stirring frequently.
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You are looking for it to thicken and darken a bit (but not as dark as the finished sauce), kind of like tomato paste.
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Remove from the heat and stir in the soy sauces. If you are using the dark soy sauce, which I definitely recommend for its depth of flavor, it will darken the sauce considerably. If needed, add a little water--you want a consistency like runny ketchup.
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Place in a sealed container and store in the fridge. Bayless says it will keep for a month or 2; I can confirm that the little I had left from July 23 was still fine this past weekend when I added it to the new batch I made.