Table 1.

Notations

Symbol	Description
q, t	Strings: $q=q_0{q}_1\dots q_{n-1},\hspace{0.17em}t=t_0{t}_1\dots t_{m-1}$
$p=\{a,x,o,e\}$	Gap-affine penalty scores
M, I, D	SWG alignment matrices
${\mathcal{F}}_{s,k}$	Furthest-reaching (f.r.) point on diagonal k with score s
${\tilde{M}}_{s,k}$	Offset in the diagonal to the corresponding f.r. point ${\mathcal{F}}_{s,k}$
$\widetilde{I_s},\hspace{0.17em}\widetilde{D_s},\hspace{0.17em}\widetilde{M_s}$	Components of the wavefront WFs
WFs	Wavefront of score s
${\tilde{M}}^{hi}$	Index of the rightmost diagonal in the component
${\tilde{M}}^{lo}$	Index of the lowest diagonal in the component
WFmin	Minimum wavefront length
WFdiff	Maximum difference distance