I think you need adapter cables. J11 (10 pin) connector is 0.05" pitch in pcb and Intel/Altera uses 0.1" pitch connector.
Also signal placement didn't seems to match. Not sure did they do that you can just cut cable and solder it to pcb.
J7 (6 pin) is for SAMD21 debug connector. Haven't checked if that pinout is OK.
I currently use USB BLaster emulator for SAMD21 and I tested it with signaltap with continuous capture.