G'day Nicpetbio23!,

Welcome to the Monastery.

As already pointed out, you'll need to be more specific to get the best answers; however, the following might get you started.

#!/usr/bin/env perl

use strict;
use warnings;

use Data::Dump;

my @src_strings = qw{A ABA ABBCCC AAABBCD BCDD CCD D};
my @re_strings = qw{A B C};
my %count;

for my $src (@src_strings) {
    for my $re (@re_strings) {
        $count{$src}{$re}++ while $src =~ /$re/g;
    }
}

dd \%count;
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Output:

{
  A => { A => 1 },
  AAABBCD => { A => 3, B => 2, C => 1 },
  ABA => { A => 2, B => 1 },
  ABBCCC => { A => 1, B => 2, C => 3 },
  BCDD => { B => 1, C => 1 },
  CCD => { C => 2 },
}
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Without seeing your data, that solution could be terribly slow, or may not work (in some way or another).

See also: perlintro (and the links it provides to more detailed information); and Data::Dump (the builtin Data::Dumper module provides equivalent functionality).