use strict; use warnings; my @data = grep { !/^(>|\s)/ } ; chomp @data; print join "nnnnncattccattcattaattaattaatgaatgaatgnnnnn", @data; __DATA__ >contig number 11 tttgctcggaggggatc >contig number 23 gaaaacacttccttattatacaggtaaaccgtatttggat >contig number 3 aaagctcggaggggatcccct