You haven't posted the relevant parts of the repeater markup so I can only guess it is like the below, and if so this should work, if not you'll need to update your question to include the markup as we can't give you a solution if we don't know your html structure.
<asp:Repeater ID="myRepeater" runat="server">
<HeaderTemplate>
<table id="myTable">
</HeaderTemplate>
<ItemTemplate>
<tr>
<td><asp:CheckBox ID="myCheckbox" CssClass="chk" runat="server" /></td>
</tr>
</ItemTemplate>
<FooterTemplate>
</table>
</FooterTemplate>
</asp:Repeater>
<button onclick="test();">test</button>
<script type="text/javascript">
function test() {
var selected = $("#myTable span.chk :checked");
alert(selected.length);
}
</script>