You are including the first line when you are counting your characters so you are counting the two A's in

gb|AE008689|:2073051-2073458, Atu4895
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so your counts are off by 2. If you strip off the first line you will get the right answer. You also don't need the strip off the newlines since tr[ACGT][ACGT] will only count the "ACGT" characters.