The ispVM software only provides a way to control the length of the low pulse of the clock. You can change the duration of the low pulse using the ispVM Project->Project Settings dialog and clicking on the Advanced button. Using the TCK Low Pulse Width Delay control you can stretch the TCK low pulse width. Setting TCK Low Pulse Width Delay to 2 will stretch the Low state 2x. Setting it to 3 will stretch the Low state 3x. The high pulse width is not changed.
The exact frequency and duty cycle will vary from system to system. This feature can be used to debug programming issues due to noise. It does not provide exact frequency or duty cycle control.