Works with huge 1.fa file.

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


while (my $line =<DATA>)
{
   $line =~ s/^\s*|\s*$//g;
   
   if ($line =~ /^\d/)
   {
      print "$line\t";
   }
   else
   {   
      print "$line\n";
   }
}

=Prints
1       AGTCGTAGCAT
2       TGAGCTACG
3       GGCATAGN
4       CGCACNCAGCTACACC
5       NGATAGCTACA
=cut


__DATA__
1
AGTCGTAGCAT
2
TGAGCTACG
3
GGCATAGN
4
CGCACNCAGCTACACC
5
NGATAGCTACA
[download]

To prevent blank lines in output caused by blank lines in 1.fa, add next unless $line =~ /\S/; or similar after removing leading and trailing spaces.

Update: looking back this, if the ">" actually appears in the 1.fa file, then just delete it if seen while processing the line and use the above logic.