Hi according to http://www.cse.unt.edu/~mikler/Courses/BioCom2011/slides/pdf/multiple_alignment.pdf.

Consider these 4 sequences s1 GATTCA s2 GTCTGA s3 GATATT s4 GTCAG

now there are 6 possible alignments possible. And the maximum alignment score happens to be between S2 and S4

So now we take S2 and S4 and do this

s2,4 GTCt/aGa/

after this step how do i find the optimal alignment score between s2,4 and s1 ?