use warnings;
use strict;

use Data::Dumper;
use List::Util qw(first);

my %hits;
my $index;

open my $fh, '<', 'file.txt' or die $!;

while (<$fh>){
    chomp;
    my @F = split ' ';

    if (/Strand/){
        $index = first { $F[$_] eq 'Strand' } 0..$#F;
        next;
    }

    if (! exists $hits{$F[$index+1]}{$F[$index+2]}) {
        $hits{$F[$index+1]}{$F[$index+2]}{'w'} = 0;
        $hits{$F[$index+1]}{$F[$index+2]}{'c'} = 0;
    }
    $hits{$F[$index+1]}{$F[$index+2]}{$F[$index]}++;
}

print Dumper \%hits;

##</code><code>##

Strand
1   4   1   0
1   5   1   0
1   31  1   0
1   74  1   0