I am using the code:
   ClientScript.RegisterStartupScript(typeof(Page), "message", message);
This code works fine in an ASP.NET page but does not in a UserControl. I need to use this functionality in UserControl.
You could try:
    string script = "<script language='JavaScript'>alert('hello');</script>";
    Page.RegisterStartupScript("myscript", script);
or
        ScriptManager.RegisterStartupScript(Page, Page.GetType(), "key", "<script>alert('Hello.')</script>", false);
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