while (<>) {
    chomp;
    my $offset = 0;
    my $limit = length();
    while (( my $found = index( $_, $graph, $offset )) >= 0 ) {
        my $bgn = ( $found - $num > 0 ) ? $found - $num : 0;
        my $end = ( $found + $num +1 < $limit ) ? $found + $num +1 : $limit;
        push @{$graph_contexts{substr( $_, $bgn, $end - $bgn )}}, $_;
        $offset = $found + 1;
    }
}

##</code><code>##

$sublen = $num * 2 + 1;

while (<INPUT>) {
    chomp;
    for my $ofs ( 0 .. length()-$sublen )
    {
        my $ngram = substr( $_, $ofs, $sublen );
        next unless $ngram =~ /^.{$num}$graph/;

         # store this ngram to your hash
    }
}