How to go through CheckBox in WebForms automatically generated with JQuery

How to go through several CheckBox in the Click event of a button with C # and these CheckBoxes were automatically generated with JQuery? Home The HTML of the automatically generated CheckBox is this:

<div class="col-md-12">
    <div id="MainContent_pnlCheckbox">
        <div id="MainContent_divCheckboxes">
            <div>
                <a>
                    <input type="checkbox" name="chkCI" id="2" runat="server" checked="checked" value="2">
                        <span>CI 2</span>
                </a>
            </div>
            <div>
                <a>
                    <input type="checkbox" name="chkCI" id="4" runat="server" checked="checked" value="4">
                        <span>CI 4</span>
                </a>
            </div>
        </div>
    </div>
</div>

The code to go through the CheckBox is ess:

foreach(Control item in divCheckboxes.Controls)
{
    if(item is CheckBox)
    {
        CheckBox c = item as CheckBox;
        if (c != null && c.Checked)
        {
            CIModel ci = new CIModel();
            ci.idci = int.Parse(c.ClientID);
            lCI.Add(ci);
        }
    }
}

But the above code does not find the CheckBox object:

Note: I am using a MasterPage.