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PAM1 := MutationMatrix:
lnPAM1 := ln(MutationMatrix):
...

PrintMatrix(transpose(transpose(PAM1[1..10])[1..10]),'% .5f ');

the mutation matrix i used was:

...
    }
    print "\n";
}

 0.99002  0.00040  0.00048  0.00048  0.00193  0.00090  0.00115  0.0011
+2  0.00031  0.00018 
 0.00024  0.99072  0.00052  0.00013  0.00035  0.00140  0.00045  0.0001
+9  0.00075  0.00011 
...
 0.00104  0.00030  0.00117  0.00050  0.00027  0.00026  0.00034  0.9958
+9  0.00024  0.00002 
 0.00008  0.00031  0.00065  0.00026  0.00008  0.00057  0.00017  0.0000
+6  0.99023  0.00001 
 0.00015  0.00014  0.00019  0.00003  0.00032  0.00008  0.00004  0.0000
+2  0.00005  0.98765

0.9876  0.9712  0.9670  0.9662  0.9586  0.9726  0.9654  0.9654  0.9677
+  0.9605  0.9644  0.9670  0.9694  0.9646  0.9607  0.9717  0.9710  0.9
+700  0.9714  0.9615  
0.9607  0.9891  0.9504  0.9522  0.9552  0.9458  0.9567  0.9588  0.9543
+  0.9515  0.9513  0.9513  0.9462  0.9505  0.9555  0.9614  0.9589  0.9
+572  0.9592  0.9606  
...
0.9726  0.9704  0.9550  0.9598  0.9633  0.9608  0.9630  0.9813  0.9656
+  0.9720  0.9766  0.9600  0.9625  0.9643  0.9632  0.9657  0.9715  0.9
+900  0.9592  0.9661  
0.9561  0.9545  0.9424  0.9348  0.9514  0.9338  0.9337  0.9446  0.9185
+  0.9355  0.9327  0.9279  0.9513  0.9491  0.9311  0.9445  0.9514  0.9
+416  0.9950  0.9621  
0.9567  0.9664  0.9512  0.9545  0.9774  0.9464  0.9758  0.9546  0.9584
+  0.9603  0.9593  0.9582  0.9539  0.9563  0.9588  0.9592  0.9559  0.9
+587  0.9726  0.9888