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We have developed a simple elegant system based on an array of thin-film magnetic bars for creating a two-dimensional array of paramagnetic polymer beads that can be functionalized to bind fluorescently labeled DNA fragments. The resulting array can be scanned using conventional optical fluorescence instruments, to quantify the relative abundance of specific DNA sequence fragments in a biological sample. Parallel analysis for a large number of target DNA fragments is possible with such a system. The magnetic array generation system is inexpensive to fabricate, easy to use, and reusable. It has applications in DNA variation detection, pathogen detection, and DNA fingerprinting.