Check your file with 
perl -mcharnames -e '<> =~ m/([^atcg])/i; print charnames::viacode(ord
+ $1), "\n"' ATCG_FILE

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I created one file in Vim, typed 'atcgATCG' there, saved it, run the one-liner and got: 
LINE FEED

[download]
Many editors add newline to the end of a file when they save it.

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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