EDIT: question edited after I posted this answer, so it may not be relevant.

It's not clear from your question what part of the fasta file you are trying to count and what criteria specify a "unique read appearance".

If we assume that reads can appear more than once in the file myfile.fa and that the same read (sequence) will have the same ID - for example:

>id1
acgt...
>id1
acgt....
>id2
ggga...

then you can extract and count IDs like this:

grep -o -E "^>\w+" myfile.fa | tr -d ">" | uniq -c

  2 id1
  1 id2

Given your datasets--one query file and three seqnence files--the following produces your desired results:

use strict;
use warnings;
use File::Basename;
use Sort::Naturally;

local $/ = '>';
my ( %files, %query, %omit, @F );
$omit{$_}++ for ( $ARGV[0], basename $0);

while (<>) {
    chomp;
    $query{ $F[0] } = $F[1] if @F = split;
}

local $/ = "\n";
my @files = nsort @ARGV = grep !$omit{$_}, <*>;

while (<>) {
    next if /^>/;
    chomp;
    $files{$_}{$ARGV}++;
}

print join( "\t", 'tag', 'seq', @files ), "\n";

for my $key ( nsort keys %query ) {
    my @seqCount;
    push @seqCount, $files{ $query{$key} }->{$_} || 0 for @files;
    print join( "\t", $key, $query{$key}, @seqCount ), "\n";
}

Output on your datasets:

tag    seq    file1    file2    file3
tag1    TCGGA    1    0    1
tag2    TCTCA    2    2    0
tag3    TCTCGC    0    2    2

Place the script file in the same directory as all of your other files, and call it from the command line as follows:

perl script.pl queryFile

The script first processes the queryFile, creating a hash where the keys are the tags and the associated values are the sequences. Next, it reads all the file names in the directory, omitting (via grep) the query and script files. It builds a hash of hashes (HoH) to tally the sequences in the seq files. Finally, it prints the results.

Sort::Naturally is used to keep the alphanumeric tag and file names in proper order.

Hope this helps!

You tagged Perl. You can use a hash and for the key you can concatenate the FASTA id and sequence with a unique delimiter.

$key = join "~", $id,$seq;
$seqHash{$key}++;

....

foreach $key (sort keys %seqHash){
@temp = split /~/, $key;
print $temp[0]."\t".$seqHash{$key};
}