Fig. 10

Realignment algorithm dependencies and penalties for computing cell i, j in the five matrices \(D\blacksquare , I\blacklozenge , M\bigstar , S\bullet , L\blacktriangle\), which represent the states Deleting, Inserting, Matching, Shortening, and Lengthening, respectively. Computation for cell i, j occurs in that order, and large symbols (e.g. \(\blacksquare\)) denote where the result is stored. Superscript symbols (e.g. \(^\blacksquare\)) represent cell dependencies, and a penalty score accompanies it. Each result is the minimum value of all dependency cells plus their accompanying penalty scores. n-polymer shortening and lengthening is only allowed if certain conditions are met (\(c_1, c_2, c_3\)), described in the text