#!/usr/bin/env perl

use 5.014;
use strict;
use warnings;

{
    local $/ = "\n>";

    while (<DATA>) {
        chomp;
        substr $_, 0, 1, '' if $. == 1;
        my ($head, $seq) = split /\n/, $_, 2;
        printf "%-15s %s\n", $head, $seq =~ y/\n//dr;
    }
}

__DATA__
>SEQ1
AAA
>SEQ2
AAA
CCC

>SEQ3

AAA
CCC
GGG

>SEQ4 plus ...
AAA
CCC
GGG
TTT

##</code><code>##

SEQ1            AAA
SEQ2            AAACCC
SEQ3            AAACCCGGG
SEQ4 plus ...   AAACCCGGGTTT