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Occasionally, you can't use just a /g to get all the changes to occur.
+ Here are two common cases:

...

    # expand tabs to 8-column spacing
    1 while s/\t+/' ' x (length($&)*8 - length($`)%8)/e;

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# patterns to search with are stored in @pattern Array
# patterns are strings of uc DNA (i.e. TTTAGT, etc)
...
   }

$text_seqs[$i] =~ s{$rxHaystack[$j]}{<span class=$class[$a]>$1</span>}
+gemx;