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Motivated by the Atiyah-Floer conjecture, we consider Santi-self-dual instantons on the product of the real line and a three-manifold with cylindrical end. We prove a Gromov-Uhlenbeck type compactness theorem, namely, any sequence of such instantons with uniform energy bound has a subsequence converging to a type of singular objects which may have both instanton and holomorphic curve components. This result is the first step towards constructing a natural bounding cochain proposed by Fukaya for the Atiyah-Floer conjecture.

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