Really you should switch to use strict and use warnings
Here is your code rewritten in 'pure perl', with this notes:
- my @xx= $str =~ /(xxx)/g # return array with matches
- scalar @xx # how many items are in @xx
- you should add use strict your self to the script
- it is not needed to go to #arr in the loop
- I really doesn't understand what you want to say in the last paragraph, so my code is only a guess
See perlretut for more info in first note

#! /usr/bin/perl

$str1='It is a guide to action which ensures that the military always 
+obey the commands of the party.'; chomp($str1);

$str2='It is a guide to action that ensures that the military will for
+ever heed Party commands is a guide.'; chomp($str2);



@arr1=split(/\s+/, $str1);

$n=0;

%result=();
%output=();
for($i=0; $i<$#arr1-1;$i++) {
      $t1="$arr1[$i] $arr1[$i+1] $arr1[$i+2]";
        if(@matchs=$str2=~/($t1)/g) {
                $result{@matchs}=$t1;
        print $i+1,"\t\t",scalar @matchs,"\t\t\t$t1\n";
                $n++;
              }
    if(@matchs=$str1=~/($t1)/g) {
        $output{@matchs}=$t1;
        print $i+1,"\t\t",scalar @matchs,"\t\t\t$t1\n";
    }
}
print "\n\nTotal Matches : $n\n";

if ((sort keys %output)[0] > (sort keys %result)[0])
{
    print "result has the minor value\n";
}
elsif ((sort keys %output)[0]  < (sort keys %result)[0])
{
    print "output has the minor value\n";
}
else 
{
    print "Both has the same minor value\n";
}
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PD to perlmonks admins: I really hate to have add <br> in every line :( when I'm commenting or posting

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