I cannot understand this sentence:

if (($head =~ /$_/) .. ($_ =~ /\/\//))
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What are you doing here?

In fact, the most sensible way to do your job is to load the FASTA sequence file into a hash:

my %fasta_source;

my $tmp_title;
open INSEQ,"<$file_fasta";
while (<INSEQ>) {
    chomp;
    if ($_=~/^>/) {
        $tmp_title=$_;
    }
    else {
        $fasta_source{$tmp_title}.=$_;
    }
}
close INSEQ;
[download]

This should put the FASTA file into the hash "fasta_source", and you would easy to do what you want.