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Do you have any information on ASCII termination characters in the integration mode?
If the user wants to exit the integration mode entirely, they may send the PhytoFlash an ASCII ESC character.

There is a nice tool available that may help answer any questions related to ASCII string characters:
http://www.serial-port-monitor.com/

This tool is a serial port monitor.  It allows the user to see data in the packets that are transmitted on a serial port.  In this case, the user could set up the PhytoFlash for integrated monitoring and see the actual raw data packets that are transmitted to Hyperterminal (or equivalent).  Seeing the raw data would answer any questions concerning formatting.  For instance, it will show that the numeric data is separated by tabs, not spaces.  It will also, of course, show the termination characters for each line.