To show another way to calculate the matches. 
#!/usr/bin/perl
use strict;
use warnings;

my $fasta1 = 'GGGTATTCCTTCTCCACCTTGCAGCTAACATCAGTGTTTCGTCTACTCAAGCACGC
+CAAC';
my $fasta2 = 'ACGCCCTAGAGCGCCCTGTCCAGGGGATGGCAACCAACTCTGACCCTGCAAGTGCA
+GCAG';

my $matched = ($fasta1 ^ $fasta2) =~ tr/\0//;
my $non_match = length($fasta1) - $matched;

print "matched: $matched\n";
print "non_matched: $non_match\n";

[download]
This prints: 
matched: 15
non_matched: 45

[download]

In reply to Re: nested foreach loop, match DNA sequences and calculate score by Cristoforo
in thread nested foreach loop, match DNA sequences and calculate score by NadjaPadjala

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