Consider the following alignment:

TCGAC$-$ATT

CC$--$GAA$-$T

What is the score of this alignment if the match score is $1,$ the mismatch penalty is $1,$ and the indel penalty is affine

with a gap opening penalty of $4$ and a gap extension penalty of $1?$

True or False: Using a Manhattan with long indel edges is quicker than using a three$-$level Manhattan to solve the

Alignment with Affine Gap Penalties Problem.

True

False

True or False: Different longest paths in an alignment graph may have different middle nodes.

True

False

There is a unique multiple longest common subsequence of CGGAACTGGT, TGAGACGGTA, and TGCGACGGCT. What

is it$?$

True or False: Optimal pairwise alignments of three strings always can be assembled into an optimal $3-$way

alignment.

True

False

Compute the number of steps required by GreedySorting to sort the following permutation

into the identity parmutation$)$

$(+2+6-8-17+7-14+18+3-5-16-11-19-4+10+13-20-1+9-12+15)$

Compute the number of breakpoints in the following permutation

$(-16-20*11+12-14-13-15-6-4-19-18-17-10+4-5-2*7-1*1-9)$

What is the maximum number of breakpoints that a single revertal can eliminate?