Getting the frequency of letters in each position
That's a crazy amount of code for such a simple task.  There's no need to generate any intermediate files.  There's no need to create nine separate variables for the nine columns.

To process an input file (whether from sys.stdin or as a named argument on the command line), use fileinput.  That way, you don't have to hard-code 'infile.txt'.  Then, simply ignore the lines that start with &gt; and strip off the newlines.

To work on columns rather than rows, use zip().

Suggested solution

These seven lines could replace your entire code.

import fileinput
from collections import Counter

def nucleotide_lines(f):
    for line in f:
        if not line.startswith('&gt;'):
            yield line.rstrip()

print([Counter(col) for col in zip(*nucleotide_lines(fileinput.input()))])