I am guessing a lot of variables here for your setup. But, a few probable reasons:
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If you are using secondary index queries. You are required to upgrade to 3.5.15 or higher. Current release is 3.6.0. Release notes for 3.5.9 has a disclaimer: “NOTICE [AER-4062] - Secondary index query has noticeable performance degredation. Fix released in 3.5.15”
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Enable micro-benchmarks and use asloglatency tool to analyse the exact bottleneck. A few useful links here:
-samir