Pattern matching is a versatile task which has a variety of applications including genome sequencing as a major application. During the analysis, short read mapping technique is used where short DNA sequences are mapped relative to a known reference sequence. This paper discusses the use of reconfigurable hardware to accelerate the short read mapping problem. The proposed design is based on the FM-index algorithm. Although several pattern matching techniques are available, FM-index based pattern search is perfectly suitable for genome sequencing due to the fastest mapping from known indices. In order to make use of inherent parallelism, a multi-FPGA system called Flow-in-Cloud (FiC) is used. FiC consists of multiple boards, mounting middle scale Xilinx’s FPGAs and SDRAMs, which are tightly coupled with high speed serial links. By distributing the input data transfer with I/O ring network and broadcasting I-Table, C-Table and Suffix-Array with the board-to-board interconnection network, about 10 times performance improvement was achieved when compared to the software implementation. Since the proposed method is scalable to the number of boards, we can obtain the required performance by increasing the number of boards.