How A Weight Matrix Works Sequence matrix, s(b,l,j) for sequence j has 4 rows (base b: ACGT) and -3 to 6 columns (position l: CAGGTCTGCA). Each column has 3 zeros and a 1 corrsponding to that base. Individual information weight matrix, Riw(b,l) has the same form as the sequence matrix but has positive and negative numbers in it. Add the numbers that correspond to 1's in the first matrix to get the total. Sequence walker - a graphic 5' to 3' showing the sequence and then the same letters but with heights corresponding to the individual information weight matrix. The letters are rotated 90 degrees counterclockwise to represent the direction of the donor site shown.

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