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As most runners know, but we sometimes forget, the quads and hamstrings are opposing muscle groups. When you tighten your quads, you relax your hamstrings, and vice versa.
As I have learned from yoga classes, it's you can often get a better stretch in a muscle that is slightly warmed up. Before you stretch your hamstrings, stand up straight, then bend your knees slightly, as if you were going to sit in a chair. Your quads should be active, which means that your hamstrings are relaxing. Hold this position for 30 seconds, then try doing your regular hamstring stretches.