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Event sequence data analysis is common in many domains, including web and software development, transportation, and medical care. Few have investigated visualization techniques for comparative analysis of multiple event sequence datasets. Grounded in the real-world characteristics of web clickstream data, we explore visualization techniques for comparison of two clickstream datasets collected on different days or from users with different demographics. Through iterative design with web analysts, we designed MatrixWave, a matrix-based representation that allows analysts to get an overview of differences in traffic patterns and interactively explore paths through the website. We use color to encode differences and size to offer context over traffic volume. User feedback on MatrixWave is positive. Our study participants made fewer errors with MatrixWave and preferred it over the more familiar Sankey diagram.