"Thank you, Ken. It works very well."

You're welcome.

"Would you help me identify the problem in my script."

Happy to.

"I moved the print after unless block but it still does not work."

Unfortunately, that doesn't help me to help you. What exactly did you move? Where precisely did you move it to? What does "it still does not work" mean?

You need to provide code along with expected results, actual results, and any error or warnings messages. This is all described in more detail in the "How do I post a question effectively?" guidelines.

Here's what choroba was referring to:

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

    for (@fasta) {
        unless (/^>/) {
            s/^/ACGAGTGCGT/;
        }

        print;
    }
'
>dddd
ACGAGTGCGTabcdef
>eeee
ACGAGTGCGTbcdef
[download]

That may give you your answer. If not, post the requested information so that we can provide genuine help as opposed to guesswork.