where to store certifcates in windows for the software

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I am developing windows service as part of msi. when we select msi, it will install the service and creates certficates example bootstrap cert and client cert. These certifcates are used for rest api calls(as request body these certs are send). Can anyone help me as per security reasons where can I store client and ca certifcates in windows? Guide me whether it should be in some folders or certifcate store.

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