$ perl -Mstrict -Mwarnings -e '
    my @fasta = (">dddd\n", "abcdef\n", ">eeee\n", "bcdef\n");

    for (@fasta) {
        print "aaaa" unless /^>/;
        print;
    }
'
>dddd
aaaaabcdef
>eeee
aaaabcdef