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End free-space alignment

In this variant, any indel operations at the end or the beginning of the alignment contribute a weight of zero, no matter what weight other spaces contribute.

Example 2.16   Consider the alignment
S = - - c a c - d b d v l
T = l t c a b d d b - - -

the two leading spaces at the left end of the alignment are free, as well as the three trailing spaces at the right end.



 

Itshack Pe`er
1999-01-03