#!/usr/bin/perl

use warnings;

print ("Please input the first DNA-sequence: ");
chomp($dna1 = <STDIN>);

print ("Please input the second DNA-sequence: ");
chomp($dna2 = <STDIN>);

$dna1len = length($dna1);
$dna2len = length($dna2);
$itr = 0;
$num = 1;
if ($dna1len < $dna2len){
    for ($itr=0; $itr != $dna2len; $itr++){
    $sub1 = substr $dna1, $itr, $num;
    $sub2 = substr $dna2, $itr, $num;
    push(@dna1, $sub1);
    push(@dna2, $sub2);

}
}
elsif ($dna1len > $dna2len){
    for ($itr=0; $itr != $dna1len; $itr++){
    $sub1 = substr $dna1, $itr, $num;
    $sub2 = substr $dna2, $itr, $num;
    push(@dna1, $sub1);
    push(@dna2, $sub2);

    }
}
else {
    for ($itr=0; $itr != $dna1len; $itr++){
    $sub1 = substr $dna1, $itr, $num;
    $sub2 = substr $dna2, $itr, $num;
    push(@dna1, $sub1);
    push(@dna2, $sub2);

}
}
print ("DNA1 has $dna1len nucleotides, DNA2 has $dna2len nucleotides.\n");
print ("@dna1 and @dna2\n");
$itr1 = 0;

if ($dna2len < $dna1len){
    $lim = $dna2len;
    }
    else {
        $lim = $dna1len;
        }

while ($itr1 != $lim){
   for ($dna1[$itr1] eq $dna2[$itr1]){
    push(@dnaarray, $dna1[$itr1]);
    $itr1++
    }
}

#for ($itr1=0; $dna1[$itr1] eq $dna2[$itr1]; $itr1++){
#    push(@dnaarray, $dna1[$itr1]);
#    }
print ("lol $itr1 @dnaarray\n");