When the SLO-scope feature is enabled, it assumes control of pins A and B and uses
them as analog inputs (or digital outputs controlled by the SLO-scope application).
Pins A and B temporarily lose their serial handshaking line associations while
the SLO-scope is active, but these associations are restored once the SLO-scope
is disabled. You can disable the SLO-scope via the SLO-scope application or by
unplugging the programmer and plugging it back in.
Pololu USB AVR Programmer User's Guide
© 2001–2010 Pololu Corporation
5. Communicating via the USB-to-TTL-Serial Adapter
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