Figure 3

Score differences between PRIME _piecewise and PRIME _affine on homologous region set. The horizontal axis denotes reference alignment ID, and the vertical axis, the difference in sum-of-pairs or column scores on respective alignments of the homologous region set using PRIME _piecewise and PRIME _affine . A positive difference score of an alignment is an indication that PRIME _piecewise shows better performance than PRIME _affine for the alignment, and vice versa.