You should start your Perl program with these two pragmas:

use warnings;
use strict;
[download]

They will help you find mistakes in your code, like why $ofound is not visible at the end of the subroutine.

     12     my $seq =();
[download]

It looks like you are attempting to assign a list to a scalar variable, but that is impossible as there is no such thing as a list in scalar context.

     23       $o{$header} = "$seq";

     27     print "$line";
     28     $header = "$line";

     33     $seq .= "$line";
[download]

What's wrong with always quoting "$vars"?

     35 #Q: How many times is the $search found inside all the hash va
+lues??

     37     while (my ($key,$value) = each(%o)) {
     38       $hits++ while $value =~ /$search/gi;
     39     }
     40   
     41 #Q: How many hash values contain at least one <93>$search<94> 
+inside of them?
     42     ####################
     43     #FOREACH LOOP START#
     44     ####################
     45     foreach my $key (keys %o) {
     46       $searchline = $o{$key};
     47       if ($searchline =~ /$search/gi) {
     48         $contains ++;
     49       }
     50     }
     51     ###################
     52     # FOREACH LOOP END#
     53     ###################
[download]

These two loops do the same thing.    So that code could be simplified to:

my $hits;
$hits += () = /$search/gi for values %o;
my $contains = $hits;
[download]

     68     if ($count) {
     69       my $ofound = ($hits)/($count);
     70     } elsif ($count ==0) {
     71     }
[download]

my creates a variable that is lexically scoped inside the current block or file so $ofound can only be seen on line 69 of your program.    You need to declare it outside of that block:

     my $ofound;
     if ($count) {
       $ofound = ($hits)/($count);
     } elsif ($count ==0) {
     }
[download]

Or just return that value:

     if ($count) {
       return $hits / $count;
     } elsif ($count ==0) {
     }
[download]