I had always heard she was held in the Bell Tower, but I decided to check my copy of Anna Keay's "The Elizabethan Tower of London" which has a gazetteer section with some good, well-sourced info on the buildings in the Tower complex that existed in the 1597 survey. And sure enough, she says (as does Starkey in "Elizabeth: Struggle for the Throne") that she was NOT in the Bell Tower, but in the royal apartments, next to the Lanthorn Tower. She says that four chambers were allocated to Elizabeth and had permission to walk in the Great Chamber, which were next to her chambers.
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