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#!/usr/bin/perl -w
                                                                      
+          
...
        push( @sequence_1_arr, $protein_matrix[$row+1][0] );
        $dowhat = "diagonal";
}

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#TFD (Temporary for debug)>>
...
        $dowhat = "diagonal";
}
print "TFD> All 3 cell values defined, but NOT equal\n";