Optimal Mismatch example

First attempt
G C A T C G C A G A G A G T A T A C A G T A C G
  1           2  
G C A G A G A G  

Shift by: 3 (adaptedGs[1])

Second attempt
G C A T C G C A G A G A G T A T A C A G T A C G
  1   4   3   2  
  G C A G A G A G  

Shift by: 2 (qsBc[A]=adaptedGs[3])

Third attempt
G C A T C G C A G A G A G T A T A C A G T A C G
  5 1 8 4 7 3 6 2  
  G C A G A G A G  

Shift by: 9 (qsBc[T])

Fourth attempt
G C A T C G C A G A G A G T A T A C A G T A C G
  1  
  G C A G A G A G  

Shift by: 7 (qsBc[C])

The Optimal Mismatch algorithm performs 15 character comparisons on the example.

Optimal Mismatch algorithm