SequenceJuxtaposer is a sequence visualization tool for the exploration and comparison of biomolecular sequences. We use an information visualization technique called “accordion drawing” that guarantees three key properties: context, visibility, and frame rate. We provide context through the navigation metaphor of a rubber sheet that can be smoothly stretched to show more details in the areas of focus, while the surrounding regions of context are correspondingly shrunk. Landmarks, such as motifs or differences between aligned base pairs, are guaranteed to be visible even if located in the shrunken areas of context. Our graphics infrastructure for progressive rendering provides immediate responsiveness to user interaction by guaranteeing that we redraw the scene at a target frame rate. SequenceJuxtaposer supports interaction at 20 frames per second when browsing collections of several hundred sequences that comprise over 1.7 million total base pairs.