1×SCM I/O instruction and arrangement. A. Bit partition of custom instruction for the 1×SCM. The input_A and input_B are two 32-bit data containing the scores and flags from the three neighbouring cells (north, northwest and west). The output is one 32-bit data containing the final scores and the direction of alignment gap. The grey areas indicate the unused data bits. B. Schematic design of the inputs and outputs from one 1×SCM.