The growth of the Reconfigurable Computing (RC) systems community exposes diverse requirements with regard to functionality of Electronic Design Automation (EDA) tools. Low-level design tools are increasingly required for RC bitstream debugging and IP core design assurance, particularly in multiparty Partially Reconfigurable (PR) designs. While tools for low-level analysis of design netlists do exist, there is increasing demand for automated and customisable bitstream analysis tools.This article discusses the need for low-level IP core verification within PR-enabled FPGA systems and reports FDAT (FPGA Design Analysis Tool), a versatile, modular and open tools framework for low-level analysis and verification of FPGA designs. FDAT provides a set of high-level Application Programming Interfaces (APIs) abstracting the Xilinx FPGA fabric, the implemented design (e.g., placed and routed netlist) and the related bitstream. A lightweight graphic front-end allows custom visualisation of the design within the FPGA fabric. The operation of FDAT is governed by "recipe" scripts which support rapid prototyping of the abstract algorithms for system-level design verification. FDAT recipes, being Python scripts, can be ported to embedded FPGA systems, for example, the previously reported Secure Reconfiguration Controller (SeReCon) which enforces an IP core spatial isolation policy in order to provide run-time protection to the PR system.The paper illustrates the application of FDAT for bit-pattern analysis of Virtex-II Pro and Virtex-5 inter-tile routing and verification of the spatial isolation between designs.