thank you.Yes, by conserved I mean columns where there is more than one letter. Could you please explain the following lines more verbosely. Also, I need the position, so I guess in your case instead of printing I could feed it into and array or hash and then print out the positions with an X 

 $template |= $first ^ $_;

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 print ord == 0 ? '.' : 'X';

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In reply to Re^2: manipulating alignment data by AWallBuilder
in thread manipulating alignment data by AWallBuilder

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