Scenario $3$: $($A total of $2$ distinct indels are made, i$.$e$.,$ one where all Cs are deleted, and the second where TCCT is inserted.$)$

All Cs are deleted

TCCT is inserted

Suppose a version of NW that aligns Strings $1$ and $2$ above by making the least number of insertions$/$deletions$,$ i$.$e$.,$ implements Scenario $3$ above, is desired. Further suppose we have a DNA nucleotide scoring matrix where a $...$

Match between nucleotides $=+3$

Mismatch between nucleotides $=-3$

and the score to be placed in each cell in the final score matrix is determined as follows $...$

$S_{i,j}=$max$\{\begin{array}{cc}{S}_{i-1,j-1}+s(x_i,& y_j)\\ S_{i-1,j}+g\\ S_{i,j-1}+g\end{array}$

where $g$ in the above equation is one of the following $...$

$g=$ a constant gap penalty such as $-3.$

$g=-I-(n-1)E$ where $I=$ penalty of inserting a new gap $($i$.$e$.,$ no pre$-$existing gap exists next to it$)$ and $E$ is the penalty of inserting an additional gap, and $n$ is the number of gaps connected to and directly preceding the current location, and $-I=-1$ and $E=1.$

$g=-I-(n-1)E$ where $I=$ penalty of inserting a new gap $($i$.$e$.,$ no pre$-$existing gap exists next to it$)$ and $E$ is the penalty of inserting an additional gap, and $n$ is the number of gaps connected to and directly preceding the current location, and $-I=-2$ and $E=1.$

$g=-I-(n-1)E$ where $I=-1$ if previous nucleotide on reference string is $A,$ and $-I=-2$ if previous nucleotide on reference string is not $A,$ and $E=1,$ and $n$ is the number of gaps connected to and directly preceding the current location.

$g=-I-ln(n-1)E$ where $ln$ is the natural logarithm, $I=-1,E=1,$ and $n$ is the number of gaps connected to and directly preceding the current location.

None of the above equations for $g$ will accomplish the desired alignment.

Which above number represents a gap penalty equation, if any, that will accomplish the desired alignment? ANS: