use strict;
use warnings;

my $str1 = "LTIEAVPSNAAEGKEVLLLVHNLPQDPRGYNWYKGETVDANRRIIGYVISNQQITPGPAYSNRETIYPNASLLMRNVTRNDTGSYTLQVIKLNLMSEEVTGQ-FSVHPETPKPSISSNNSNPVEDKDAVAFTCEPETQNTTYLWWVNGQSLPVSP";
my $str2 = "PTISPSYTYYRPGVNLSLSCHAASNPPAQYSWLIDGNIQQHTQE---------------------------LFISNITEKNSGLYTCQANNSASGHSRTTVKTITVSAELPKPSISSNNSKPVEDKDAVAFTCEPEAQNTTYLWWVNGQSLPVSP";
my %hash;
my @a = split('',$str1);
my @b = split('',$str2);

my $a_index = 36; #Start counting at residue number
my $b_index = 206;
for my $i (0 .. $#b) { #Loop through arrays
	
	if ($b[$i] eq "-") { #Check for a gap in str2, if so increment a_index and go to the next residue
		$a_index++;
		next;
	}
	if ($a[$i] eq "-") { #Check for a gap in str1, if so store the gap in the hash without a residue #, increment b_index, and go to the next residue
		$hash{$b[$i].$b_index}=$a[$i];
		$b_index++;
		next;
	}
	$hash{$b[$i].$b_index}=$a[$i].$a_index; #Else store residue pair in hash
	$b_index++;
	$a_index++;
}

print "value of N254 is $hash{'N254'}\n";
print "value of I255 is $hash{'I255'}\n";
print "value of K280 is $hash{'K280'}\n";
print "value of T281 is $hash{'T281'}\n";
print "value of I282 is $hash{'I282'}\n";