"It is odd that a building of this extraordinarily large size would be located on their territorial frontier and that it would not be fortified," Muscutt said.
"It does not appear to be a military installation. And you would think that on the frontier they would be more interested in defensibility." So, Muscutt added, Chachapoya extended farther east than experts have suspected.
"What it is showing is that we don't really know what their territory was," he told the Reuters news service.
Muscutt said another oddity is that the structure doesn't seem to be the "nucleus of a larger site."
"You basically find a big building sitting there with nothing else in the immediate vicinity," he said. "Ordinarily when you find a significant monument it's usually central to a residential or administration complex. The fact it sits on its own is baffling."
Muscutt said the penitentiary resembles only one other Chachapoya building, a structure known as Pirca Pirca.
But he added that one feature has never before been seen in a Chachapoya find: an elevated masonry plaza about the size of a football field that projects horizontally from the main building.
Muscutt added that almost no other Chachapoya structure is as large as La Penitenciaría.
Adriana von Hagen is co-director of Peru's Leymebamba Museum in the city of Chachapoyas. She said, "It's an amazing find that is hard to relate to anything we've known about the Chachapoya."
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