into sequence x. This column of cells were filled by integers

g to how many gaps were inserted. For instance, the cell (1, 0)

d by a one and the cell (2, 0) was filled by a two.

ext stage was to consider how to fill a value for the cell (1, 1) via

g three incremental alignments. The move was either a diagonal

a horizontal move or a vertical move. The horizontal move for

was the move from the left cell, i.e., the cell (1, 0). The cell (1, 0)

ignment between the first residue (T) of sequence x and a gap. It

dy a unit penalty due to the gap inserted into sequence y. The

t of this horizontal move is shown below, where a bar was used

te between aligned residues and the current alignment and the #

followed by all remaining residues of two sequences which were

sed in the current alignment.

൜^ݔ:

T | െ

#GGCT

ݕ:

െ | T

#GCT ^{ൠ⟹cost ൌ1 ൅1 ൌ2}

s horizontal move, the first residue (T) of sequence y was picked

no residue was picked up from sequence x meaning a gap was

nto sequence x. In the above equation, the first one stands for the

when align the residue T of sequence x with a gap and the second

ds for the penalty when align the residue T of sequence y with a

refore this horizontal move had a cost two. After this alignment,

ning residues of two sequences were GGCT and GCT.

tical move was to move from the cell above of the current cell,

ing from the cell (0, 1) to the cell (1, 1). The cell (0, 1) was an

t between a gap, which was inserted into sequence x and the first

T) of sequence y. This alignment is shown below, where the first

T) of sequence x was picked up for the alignment but a gap was

nto sequence y. Remaining residues of two sequences were the

above.

൜^ݔ:

െ | T

#GGCT

ݕ:

T | െ

#GCT ^{ൠ⟹cost ൌ1 ൅1 ൌ2}

gonal move was from the upper-left cell, i.e., moving from the