The ECU and tranny error codes are displayed the same way. If there were any ECU error codes, then the check-engine lamp would be flashing it's own codes while the S lamp flashes it's codes.

So you have to tell us which lamp was flashing... I guess it was the "S" lamp?

Also the pause between bunches of flashes is important. For example...
1 long followed immediately by 3 short = code 13
1 long followed by a pause, then 3 short = code 10 and code 3