Write a Perl program that prints the score of a sequence alignment given in
dna.txt (in FASTA format) but using match, mismatch, and gap open and extension 
scores provided in a file called matrix.txt. This file contains four rows and 
columns where the first row (and column) represents A, the second C, third G, 
and the fourth T.

For example if the file matrix.txt is

10   -1    2    1  -5  -.1 
-1    9    1    2  -5  -.1
2     1   11   -1  -5  -.1
1     2   -1   12  -5  -.1
-5   -5   -5   -5   0    0
-.1 -.1  -.1  -.1   0    0                              

then the score of aligning A with A is 10 (the number in the
the first row and first column) and C with A is -1 (the number in the 
second row and first column). The last two rows and columns represent
gap open and extension scores.

If dna.txt contains the alignment

>human
ACC--A
>mouse
ACGTAC

then its score according to matrix.txt is 10+9+1-5-.1-1=13.9. 

Your program should work for any set of numbers in matrix.txt and any pair of
aligned sequences in dna.txt.

Submit your solution as a file called <firstname>HW13.pl to Hareesh
hc44@njit.edu by Nov 13th and submit a hardcopy in class.