That does not complile (missing $ sigil).

did you mean the second line to read 

++$counts{uc($_)} for $a =~ /[TCAG]{3}/sg;

[download]
With that, I get the counts the OP expects.

             All great truths begin as blasphemies.
                   ― George Bernard Shaw, writer, Nobel laureate (1856-1950)

In reply to Re^2: How can I get correct result in counting 3-letter words? by NetWallah
in thread How can I get correct result in counting 3-letter words? by supriyoch_2008

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