I misunderstood the question. Yes, as long each molecule's outer sequences are still the two distinct P5 and P7 adapters, not identical, the innermost sequence can match. (The innermost dozen bases match on the original Solexa adapters too, not just Nextera, because that's the complementary portion of the Y-linker.)
But because of the Tm issue, it'll need to be a longer primer than that. On the other hand, because the inner sequences of the Illumina adapters match, it might still be the same primer for both ends.
Don't try this unless you really know what you're doing.
But because of the Tm issue, it'll need to be a longer primer than that. On the other hand, because the inner sequences of the Illumina adapters match, it might still be the same primer for both ends.
Don't try this unless you really know what you're doing.
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