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The dark rectangle is one of the skylights for the Capitol Visitor Center, which is located underneath the plaza you see in this panorama. The time for this picture is about 7 in the morning on a Saturday and the only people around are the guards and joggers.
For the pano enthusiasts out there: I shot this using a Nodal Ninja and a tripod. Be aware that tripods and monopods are not *at all* popular with the Capitol Police and you will need to get a permit to use your tripod on the Capitol grounds.