In addition to the earlier comments, I'd suggest changing (as an example)

  $count_G = ( $seq =~ tr/G//);
  $ratio_G = ($count_G/$len);
# print "\n$ratio_G\n";
[download]

to

  $ratio_G = Calculate( 'G' );
[download]

Writing the sub Calculate is left as an exercise to the reader. The advantages are you

• get rid of all of the temporary $count_* variables
• remove duplicated code
• make future changes (e.g. you want percentage rather than ratio) more centralized
• make the intentions of your code much clearer

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