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I'm having a bit of trouble with this section of a biology paper:

"LSU was amplified in these species using F63.2 and Mollusc28R2, which amplified all but ~400 bases at the 3' end of the gene."

Does it mean it amplified almost all 400 bases, or every base except for those 400.

Thank you in advance. I don't study Biology though, I'm just translating this article for a friend.

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    The latter is correct. – Ricky Sep 27 '18 at 21:41
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"But" here is a preposition (not a conjunction) with the definition:

Except; apart from; other than.
‘supply currently exceeds demand in all but the most rural areas’
Oxford Dictionaries

Because it means exactly what it says, it's not an idiom either. Nor is it ambiguous.

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For clarity on the expression itself:

From Grammarist:

The adverbial phrase all but (no need to hyphenate it) means almost, nearly, or on the verge of. It signals that the following word is almost but not quite the case. For example, if I say, I all but ran to the door, it means I walked very fast to the door but did not run. Or if I say I’m all but finished making dinner, it means I’m putting the finishing touches on the meal.

In this case, you could rephrase it (at least in your mind) to read:

"which amplified nearly ~400 bases at the 3' end of the gene."

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