This seems to be an answer from the SAM-BA boot loader that is not recognized by your PC. What make of a serial adapter on your PC do you use?
The 9 µs pulse is a single bit @ 110 kbit/s. Asynchronous serial communication is a start bit (low), 8 data bits, parity (optional) and at least one stop bit (high). Lets translate your sequence to data:
Quote:
70µs low, 18µs high, 70µs low, 18µs high, 8.5µs low, 18µs high, 25µs low, 9.5µs high, 18µs low.
This is 0_0000_0001_1 0_0000_0001_1 0_1100_0100_1. The first two are 0x80s, the third is a 0x23 ('#').
The answer from the device is 18µs low, 42µs high, 18µs low, which translates to 0_0111_1100_1 (slightly on the short side). The trouble is that the device isn't driven by a quartz. The boot loader tries to adjust the clock frequency to match the 110 kbit/s as closely as possible. The pattern reads 0x3e ('>') which is the supposed answer. The timing isn't correct and therefore the PC can't read it. Normally, the PC shall now repeat its request (0x80, 0x80, 0x23) and wait again for a new answer from the device at a slightly different rate.
All in all you can assume that your device is running the boot loader but the communication isn't working correctly.