51. The method of claim 49 , wherein the histogram for the known sequence is stored with the known sequence SSM Matrix, comprising the steps of: subtracting the histogram vector from one of the rows of the known sequence SSM Matrix without any of its entries becoming negative to unroll a first character of the known sequence; decrementing the histogram bin counter that corresponds to the first character; and repeating the steps of subtracting and decrementing for each subsequent element of the known sequence to be unrolled until the step of subtracting results in all rows of the known sequence SSM Matrix being equal to zero.
51. The method of claim 49 , wherein the histogram for the known sequence is stored with the known sequence SSM Matrix, comprising the steps of: subtracting the histogram vector from one of the rows of the known sequence SSM Matrix without any of its entries becoming negative to unroll a first character of the known sequence; decrementing the histogram bin counter that corresponds to the first character; and repeating the steps of subtracting and decrementing for each subsequent element of the known sequence to be unrolled until the step of subtracting results in all rows of the known sequence SSM Matrix being equal to zero. 52. The method of claim 51 , wherein at least one of the entries of the known sequence SSM Matrix is missing, further comprising the step of skipping the step of subtracting for that matrix element.