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[[830 - MaqIndex::CompareToIndex()]]
 
[[830 - MaqIndex::CompareToIndex()]]
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[[830 - BestAlignment::MaqAlignment()]]
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[[830 - BestAlignment::EvaluateAlignment() (main loop)]]
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[[830 - BestAlignment::EvaluateAlignment() (detailed comparison)]]
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[[830 - BestAlignment::isNewPosition()]]
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[[830 - BestAlignment::IterateCache()]]
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[[830 - BestAlignment::ClearPositions()]]

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