When filling the axes of the alignment matrix, start in the upper left corner and set it to 0. Next, assign a score for each letter in the row or column. Note that there is a penalty for gaps, and ...
One point is added if two letters match, and one point is subtracted if they do not. Using a value from either the upper (green) or left (dark blue) square, the final score is -2; however, using the ...
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