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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