Eukaryote genomics is not a area of expertise for me so apologies if I miss some subtlety with the exons/introns here, but if the tasks is as simple as it appears you should just be able to do something like this:

from collections import Counter
from Bio.Seq import Seq

Array1 = [Seq("ATTCATTCGG"), Seq("GGCTAGATTG"), Seq("CATGTAATGC")]

for i in zip(*Array1):
    print(Counter(i))

Result:

Counter({'A': 1, 'G': 1, 'C': 1})
Counter({'T': 1, 'G': 1, 'A': 1})
Counter({'T': 2, 'C': 1})
Counter({'C': 1, 'T': 1, 'G': 1})
Counter({'A': 2, 'T': 1})
Counter({'T': 1, 'G': 1, 'A': 1})
Counter({'A': 2, 'T': 1})
Counter({'T': 2, 'C': 1})
Counter({'G': 2, 'T': 1})
Counter({'G': 2, 'C': 1})

This is just the printed representation, if you want to use the dicts produced by counter, you can simply assign them to a list or something.