#! perl -slw
use strict;
use Data::Dump qw[ pp ];

my %seqs;
{
    local $/ = ">";
    my @seqs = <DATA>;
    chomp @seqs;
    s[\n][\t] for @seqs;
    tr[\n][]d for @seqs;
    shift @seqs;
    %seqs = map split( "\t" ), @seqs;
}

pp \%seqs;

__DATA__
>sequence header 1.
AAATATTATATATATTGCG
ATTATTATATGCGCGGCGC
>sequence header 2
AATTGGGCTCGCTGCTTTT
AGGAGGAGGAGCCCTCTCC
>sequence header 3
AATTGGCTGCTCGCTGCTC
AATGTGTCGGCGCGCGTGC

##</code><code>##

[ 4:34:55.96] c:\test>junk40
{
  "sequence header 1." => "AAATATTATATATATTGCGATTATTATATGCGCGGCGC",
  "sequence header 2"  => "AATTGGGCTCGCTGCTTTTAGGAGGAGGAGCCCTCTCC",
  "sequence header 3"  => "AATTGGCTGCTCGCTGCTCAATGTGTCGGCGCGCGTGC",
}