use strict;
use warnings;

my @data = grep { !/^(>|\s)/ } <DATA>;
chomp @data;
print join "nnnnncattccattcattaattaattaatgaatgaatgnnnnn", @data;

__DATA__
>contig number 11

tttgctcggaggggatc
>contig number 23

gaaaacacttccttattatacaggtaaaccgtatttggat
>contig number 3

aaagctcggaggggatcccct


##</code><code>##

perl -e "undef $/; print  join 'nnnnncattccattcattaattaattaatgaatgaatgnnnnn', <> =~ /^([tcag]+)$/gm;"  input_file.txt >output_file.txt