Local alignment

For this exercise, we will assign a match score of $1,$ a mismatch score of $-1,$ and a gap penalty of $-2.$

Let's work with the following sequences:

TTAAG

and

A AGC

$($Q$1)$ Substitution matrix

$\backslash$table$[[,$A$,$C$,$G$,$T$],[$A$,,,,],[$C$,,,,],[$G$,,,,],[$T$,,,,]]$

$($Q$2)$ Scoring matrix

$\backslash$table$[[,,$A$,$A$,$G$,$C$],[,,,,,],[$T$,,,,,],[$T$,,,,,],[$A$,,,,,],[$A$,,,,,],[$G$,,,,,]]$

$($Q$3)$ Alignment