In-System Programming uses the target Atmel AVR®’s internal Serial Peripheral Interface (SPI) to download code into the flash and EEPROM memories. It is not a debugging interface. When designing an application PCB which includes an AVR with the SPI, the pinout on the image below should be used.
SPI Header Pinout
The SPI is effectively disabled when the debugWIRE enable fuse (DWEN) is programmed, even if Serial Peripheral Interface enable (SPIEN) is also programmed. To re-enable the SPI, the 'disable debugWIRE' command must be issued while in a debugWIRE debugging session. Disabling debugWIRE in this manner requires that the SPIEN fuse is already programmed. If Atmel Studio fails to disable debugWIRE, it is probable that the SPIEN fuse is NOT programmed. If this is the case, it is necessary to use a high-voltage programming interface to program the SPIEN fuse.
Connection to a 6-pin 100-mil SPI header
Use the 6-pin 100-mil tap on the flat cable (included in some kits) to connect to a standard 100-mil SPI header.
Connection to a 6-pin 50-mil SPI header
Use the adapter board (included in some kits) to connect to a standard 50-mil SPI header.
Connection to a custom 100-mil header
The 10-pin mini-squid cable should be used to connect between the Atmel-ICE AVR connector port and the target board. Six connections are required, as described in the table below.