function print_n(n)
 {
    text = ""
    for(j=0;j<n;j++) text=text"N"
    return text
 }

BEGIN {n=0}
$0 ~ "^>" {
    if(n<=i) {
        header = header" "substr($0,2)"";
        if(n > 0) seq=seq""print_n(1000)
        n++;
    }
    else {
        print ">"header"\n"seq;
        n=1;
        header=substr($0,2);
        seq=""
    }

    next;
}
{seq=seq$0}