thank u code but it retrieve "nothing to print" multiple times
I also tried again by using split().but it also print same as ur code
newly written code

#!/usr/bin/perl
use strict;
use warnings;

open(FH, "outputps_scan_chr1_.out") or die "Can't Open File1\n";
my @array1=<FH>;
close(FH);
open(BH, "chr1_1.txt") or die "Can't Open File2\n";
my @array2=<BH>;
close(BH);
my $pat='qr/^LOC_Os0.../';

foreach my $line1(@array1)
{ 
        my @array3= split(/ /, $line1);
    foreach my $line2(@array2)
    {
        my @array4= split(/ /, $line2);        
        foreach my $line3(@array3)
            {     
        foreach my $line4(@array4)
            {    
                $line3=~ $pat;
                $line4=~ $pat;
                if ($line3 eq $line4)
                    { 
                        print $line3;    
                    }
                else 
                    {
                    print "nothing to right\n";
                    }
            }
            }
    }
}
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