use warnings;
use strict;

my $prevline;
while ( my $curline = <DATA> ) {
	next unless defined $prevline;
	if ( $prevline=~/^>/ && $curline=~/^[ATCGN]/ ) {
		$prevline =~ s/\n\z/\t/;
	}
	print $prevline;
} continue { $prevline = $curline }
print $prevline if defined $prevline;

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

##</code><code>##

>1	AGTCGTAGCAT
foo
bar
>2	TGAGCTACG
>3	GGCATAGN
quz
>4	CGCACNCAGCTACACC
>5	NGATAGCTACA