Try cutting your file down (half the size each time would be normal) until you get the bit that causes the problem. Then print out the problem bit in delimiters like angle brackets. You might also print out the length of that string. This may help you see what characters are really there, not just what characters you can see.
OMG, dear OP, don't do that! Use Perl instead, really. 
$ echo -n $'atcg\r\nhello\r\n' > ATCG_FILE # this is our test file

$ perl -mcharnames -e 'my $s = join "", <>; printf "%s: %d\n",  charna
+mes::viacode(ord $1), pos($s) while $s =~ m/([^atcg])/ig' ATCG_FILE

CARRIAGE RETURN: 5
LINE FEED: 6
LATIN SMALL LETTER H: 7
LATIN SMALL LETTER E: 8
LATIN SMALL LETTER L: 9
LATIN SMALL LETTER L: 10
LATIN SMALL LETTER O: 11
CARRIAGE RETURN: 12
LINE FEED: 13

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In reply to Re^2: =~ matches non-existent symbols by Anonymous Monk
in thread =~ matches non-existent symbols by Anonymous Monk

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