Write a Perl subroutine called alignmentscore that computes
the score of a sequence alignment. The parameters to the subroutine
are

1. aligned sequence 1
2. aligned sequence 2
3. match score
4. mismatch score
5. gap score

Use the following code to test your subroutine:

open(DNA, "dna.txt"); @file=<DNA>; 
$seq1 = $file[1]; $seq2 = $file[3];
$match=2; $mismatch=-1; $gap=-2;
$score = &alignmentscore($seq1, $seq2, $match, $mismatch, $gap);

The input is in FASTA format in a file called "dna.txt".

For example if the file contains 

>human
ATTCTA
>mouse
ATACTT

then the subroutine should return the score 6. 

Your subroutine should work for **any** pair of aligned sequences and
not just the one provided in the example. 

If the input file dna.txt contains

>human
ATTCTA
>mouse
-ATCT-

then your subroutine should return 1.

Submit a hardcopy in class on Oct 6th.