#!/usr/bin/env perl 
use strict;
use warnings;

my $text;
{
    local $/ = undef;
    $text = <DATA>;
}
$text =~ s/\n(?!>)/\t/g;
print "$text\n";

__DATA__
>1
AGTCGTAGCAT
>2
TGAGCTACG
>3
GGCATAGN
>4
CGCACNCAGCTACACC
>5
NGATAGCTACA