1     M         1.681   1.701   1.747   1.903   1.939   2.010   1.850   1.877   1.948
2     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
3     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
4     W         0.335   0.316   0.367   0.412   0.362   0.441   0.023  -0.016   0.056
5     K        -0.983  -1.028  -0.993  -1.033  -1.133  -1.051  -0.890  -0.930  -0.873
6     A        -0.428  -0.370  -0.390  -0.516  -0.442  -0.455  -0.585  -0.512  -0.518
7     V        -0.219  -0.237  -0.309  -0.114  -0.151  -0.266  -0.281  -0.309  -0.399
8     M        -1.537  -1.515  -1.466  -1.223  -1.184  -1.110  -1.194  -1.164  -1.090
9     N        -1.537  -1.515  -1.466  -1.546  -1.533  -1.433  -1.194  -1.164  -1.090
10    A         0.335   0.316   0.367   0.062   0.021   0.095   0.023  -0.016   0.056
11    W        -0.219  -0.313  -0.342  -0.008  -0.179  -0.257  -0.281  -0.408  -0.444
12    N        -0.428  -0.398  -0.401  -0.452  -0.399  -0.402  -0.585  -0.538  -0.528
13    G        -0.219  -0.313  -0.342  -0.178  -0.308  -0.359  -0.281  -0.408  -0.444
14    -        -0.516  -0.504  -0.446  -0.734  -0.711  -0.622  -0.687  -0.666  -0.584
15    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
16    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
17    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
18    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
19    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
20    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
21    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
22    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
23    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
24    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
25    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
26    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
27    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
28    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
29    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
30    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
31    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
32    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
33    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
34    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
35    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
36    -         0.408   0.398   0.417   0.349   0.325   0.348   0.159   0.137   0.150
37    -        -0.516  -0.504  -0.446  -0.769  -0.756  -0.657  -0.687  -0.666  -0.584
38    -        -0.516  -0.504  -0.446  -0.699  -0.681  -0.588  -0.687  -0.666  -0.584
39    -        -0.516  -0.504  -0.446  -0.713  -0.698  -0.601  -0.687  -0.666  -0.584
40    -        -0.516  -0.504  -0.446  -0.693  -0.679  -0.581  -0.687  -0.666  -0.584
41    -        -0.516  -0.504  -0.446  -0.547  -0.517  -0.435  -0.687  -0.666  -0.584
42    -        -0.516  -0.504  -0.446  -0.748  -0.729  -0.636  -0.687  -0.666  -0.584
43    -         0.408   0.398   0.417   0.255   0.233   0.262   0.159   0.137   0.150
44    -        -0.516  -0.504  -0.446  -0.483  -0.472  -0.372  -0.687  -0.666  -0.584
45    -         0.408   0.398   0.417   0.179   0.152   0.187   0.159   0.137   0.150
46    -        -0.516  -0.504  -0.446  -0.659  -0.640  -0.547  -0.687  -0.666  -0.584
47    -        -0.516  -0.504  -0.446  -0.748  -0.731  -0.636  -0.687  -0.666  -0.584
48    -         0.408   0.398   0.417   0.408   0.403   0.392   0.159   0.137   0.150
49    -        -0.516  -0.504  -0.446  -0.713  -0.694  -0.601  -0.687  -0.666  -0.584
50    -         1.681   1.701   1.747   1.739   1.769   1.847   1.850   1.877   1.948
51    T        -0.398  -0.430  -0.401  -0.399  -0.450  -0.415  -0.528  -0.568  -0.524
52    E        -0.983  -1.006  -0.980  -0.870  -0.882  -0.853  -0.890  -0.908  -0.859
53    S        -0.983  -0.886  -0.959  -0.933  -0.753  -0.909  -0.890  -0.772  -0.837
54    Q        -1.537  -1.515  -1.466  -1.371  -1.354  -1.258  -1.194  -1.164  -1.090
55    S        -0.983  -1.028  -0.993  -1.085  -1.149  -1.082  -0.890  -0.930  -0.873
56    K        -1.537  -1.515  -1.466  -1.371  -1.315  -1.258  -1.194  -1.164  -1.090
57    N        -0.983  -0.886  -0.959  -0.940  -0.773  -0.896  -0.890  -0.772  -0.837
58    V        -0.983  -1.006  -0.980  -0.970  -1.006  -0.951  -0.890  -0.908  -0.859
59    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
60    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
61    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
62    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
63    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
64    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
65    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
66    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
67    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
68    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
69    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
70    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
71    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
72    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
73    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
74    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
75    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
76    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
77    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
78    S        -0.219  -0.146  -0.286  -0.312  -0.209  -0.404  -0.281  -0.176  -0.367
79    N        -0.983  -0.957  -0.973  -0.937  -0.905  -0.918  -0.890  -0.856  -0.852
80    I        -1.537  -1.515  -1.466  -1.330  -1.270  -1.217  -1.194  -1.164  -1.090
81    Q        -0.983  -0.944  -0.954  -0.756  -0.678  -0.718  -0.890  -0.838  -0.832
82    S        -1.537  -1.515  -1.466  -1.538  -1.523  -1.425  -1.194  -1.164  -1.090
83    Y         0.680   0.678   0.562   0.853   0.860   0.673   0.632   0.627   0.415
84    S        -0.983  -0.996  -0.976  -0.961  -0.977  -0.956  -0.890  -0.898  -0.855
85    F        -0.219  -0.313  -0.342  -0.035  -0.178  -0.226  -0.281  -0.408  -0.444
86    E        -0.983  -1.028  -0.993  -1.018  -1.111  -1.045  -0.890  -0.930  -0.873
87    D         0.557   0.608   0.487   0.515   0.602   0.386   0.423   0.509   0.280
88    M         0.295   0.316   0.366   0.268   0.295   0.378  -0.053  -0.017   0.054
89    K         0.557   0.562   0.481   0.485   0.498   0.344   0.423   0.430   0.268
90    R        -1.091  -1.074  -1.020  -1.206  -1.195  -1.093  -1.004  -0.976  -0.901
91    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
92    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
93    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
94    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
95    I        -0.983  -0.992  -0.968  -0.946  -0.963  -0.935  -0.890  -0.893  -0.847
96    V        -1.537  -1.515  -1.466  -1.416  -1.343  -1.303  -1.194  -1.164  -1.090
97    G        -0.983  -0.957  -0.973  -0.912  -0.877  -0.882  -0.890  -0.856  -0.852
98    K        -0.983  -0.904  -0.951  -0.855  -0.738  -0.806  -0.890  -0.793  -0.829
99    H        -0.983  -1.028  -0.993  -0.805  -0.892  -0.858  -0.890  -0.930  -0.873
100   D        -0.219  -0.211  -0.308  -0.141  -0.119  -0.278  -0.281  -0.265  -0.397
101   P        -0.428  -0.469  -0.409  -0.529  -0.584  -0.497  -0.585  -0.622  -0.539
102   N         0.335   0.330   0.372   0.090   0.060   0.122   0.023   0.009   0.065
103   V         0.335   0.330   0.372   0.112   0.088   0.173   0.023   0.009   0.065
104   V         0.335   0.348   0.383   0.112   0.125   0.189   0.023   0.042   0.086
105   L         1.681   1.701   1.747   1.694   1.754   1.801   1.850   1.877   1.948
106   V        -0.219  -0.290  -0.324  -0.233  -0.334  -0.385  -0.281  -0.378  -0.419
107   D         1.681   1.701   1.747   1.686   1.722   1.794   1.850   1.877   1.948
108   V         1.681   1.701   1.747   1.582   1.607   1.690   1.850   1.877   1.948
109   R         1.681   1.701   1.747   1.781   1.806   1.889   1.850   1.877   1.948
110   E         1.681   1.701   1.747   1.657   1.680   1.765   1.850   1.877   1.948
111   P         1.681   1.701   1.747   1.701   1.740   1.809   1.850   1.877   1.948
112   S        -0.428  -0.398  -0.401  -0.653  -0.585  -0.586  -0.585  -0.538  -0.528
113   E         1.681   1.701   1.747   1.657   1.680   1.765   1.850   1.877   1.948
114   Y         0.680   0.780   0.576   0.851   0.981   0.707   0.632   0.791   0.439
115   S        -0.428  -0.398  -0.401  -0.717  -0.658  -0.654  -0.585  -0.538  -0.528
116   I        -0.983  -1.006  -0.980  -0.864  -0.874  -0.864  -0.890  -0.908  -0.859
117   V         0.335   0.316   0.367   0.043   0.001   0.085   0.023  -0.016   0.056
118   H        -0.219  -0.290  -0.324   0.080  -0.028  -0.091  -0.281  -0.378  -0.419
119   I         1.681   1.701   1.747   1.745   1.772   1.853   1.850   1.877   1.948
120   P         0.680   0.574   0.542   0.744   0.590   0.529   0.632   0.451   0.379
121   A        -0.219  -0.237  -0.309  -0.209  -0.236  -0.348  -0.281  -0.309  -0.399
122   S         0.680   0.678   0.562   0.545   0.539   0.367   0.632   0.627   0.415
123   I        -0.219  -0.290  -0.324  -0.095  -0.205  -0.266  -0.281  -0.378  -0.419
124   N         1.681   1.701   1.747   1.716   1.744   1.823   1.850   1.877   1.948
125   V        -0.983  -1.028  -0.993  -0.891  -0.938  -0.874  -0.890  -0.930  -0.873
126   P         1.681   1.701   1.747   1.701   1.740   1.809   1.850   1.877   1.948
127   Y         0.335   0.316   0.367   0.209   0.148   0.227   0.023  -0.016   0.056
128   R        -0.428  -0.469  -0.409  -0.519  -0.593  -0.491  -0.585  -0.622  -0.539
129   S         0.680   0.574   0.542   0.539   0.368   0.325   0.632   0.451   0.379
130   H        -0.983  -1.028  -0.993  -0.728  -0.804  -0.765  -0.890  -0.930  -0.873
131   P         0.680   0.574   0.542   0.744   0.590   0.529   0.632   0.451   0.379
132   D        -0.428  -0.423  -0.398  -0.556  -0.544  -0.503  -0.585  -0.569  -0.525
133   A         0.680   0.759   0.574   0.671   0.798   0.508   0.632   0.757   0.436
134   F        -0.428  -0.469  -0.409  -0.371  -0.392  -0.316  -0.585  -0.622  -0.539
135   A        -0.428  -0.472  -0.401  -0.708  -0.772  -0.661  -0.585  -0.627  -0.530
136   L         0.680   0.710   0.565   0.773   0.846   0.614   0.632   0.678   0.419
137   D        -0.428  -0.398  -0.401  -0.664  -0.629  -0.621  -0.585  -0.538  -0.528
138   P        -0.428  -0.416  -0.396  -0.522  -0.483  -0.464  -0.585  -0.559  -0.522
139   L        -0.219  -0.088  -0.284  -0.214  -0.010  -0.323  -0.281  -0.095  -0.365
140   E         0.680   0.759   0.574   0.722   0.823   0.572   0.632   0.757   0.436
141   F         1.681   1.701   1.747   1.774   1.796   1.882   1.850   1.877   1.948
142   E        -0.428  -0.472  -0.402  -0.653  -0.741  -0.613  -0.585  -0.627  -0.531
143   K        -0.428  -0.385  -0.394  -0.543  -0.487  -0.468  -0.585  -0.530  -0.522
144   Q        -0.219  -0.129  -0.289  -0.066   0.054  -0.171  -0.281  -0.152  -0.371
145   I        -0.219  -0.237  -0.309  -0.019  -0.056  -0.152  -0.281  -0.309  -0.399
146   G         1.681   1.701   1.747   1.627   1.660   1.735   1.850   1.877   1.948
147   I        -0.219  -0.088  -0.284  -0.019   0.166  -0.113  -0.281  -0.095  -0.365
148   P        -0.219  -0.254  -0.316  -0.207  -0.277  -0.386  -0.281  -0.330  -0.409
149   K         1.681   1.701   1.747   1.612   1.636   1.720   1.850   1.877   1.948
150   P         1.681   1.701   1.747   1.701   1.740   1.809   1.850   1.877   1.948
151   D        -0.983  -0.992  -0.968  -1.037  -1.063  -1.027  -0.890  -0.893  -0.847
152   S        -1.537  -1.515  -1.466  -1.530  -1.475  -1.417  -1.194  -1.164  -1.090
153   A        -1.537  -1.515  -1.466  -1.542  -1.493  -1.429  -1.194  -1.164  -1.090
154   K        -0.983  -0.886  -0.959  -0.867  -0.703  -0.824  -0.890  -0.772  -0.837
155   E        -0.219  -0.254  -0.316  -0.107  -0.172  -0.236  -0.281  -0.330  -0.409
156   L         0.680   0.574   0.542   0.718   0.580   0.493   0.632   0.451   0.379
157   I         0.335   0.400   0.412   0.112   0.211   0.237   0.023   0.139   0.141
158   F         0.680   0.574   0.542   0.798   0.621   0.569   0.632   0.451   0.379
159   Y         0.680   0.710   0.565   0.872   0.915   0.706   0.632   0.678   0.419
160   C         1.681   1.701   1.747   1.952   1.984   2.059   1.850   1.877   1.948
161   A        -0.219  -0.313  -0.342  -0.116  -0.234  -0.275  -0.281  -0.408  -0.444
162   S         0.335   0.348   0.383  -0.019   0.000   0.056   0.023   0.042   0.086
163   G         1.681   1.701   1.747   1.627   1.660   1.735   1.850   1.877   1.948
164   K        -0.219  -0.155  -0.287  -0.070   0.026  -0.184  -0.281  -0.189  -0.368
165   R         1.681   1.701   1.747   1.781   1.806   1.889   1.850   1.877   1.948
166   G        -0.428  -0.398  -0.401  -0.705  -0.663  -0.657  -0.585  -0.538  -0.528
167   G        -1.537  -1.515  -1.466  -1.538  -1.468  -1.425  -1.194  -1.164  -1.090
168   E        -1.537  -1.515  -1.466  -1.359  -1.337  -1.246  -1.194  -1.164  -1.090
169   A         1.681   1.701   1.747   1.635   1.677   1.742   1.850   1.877   1.948
170   Q        -0.983  -1.006  -0.980  -0.820  -0.887  -0.839  -0.890  -0.908  -0.859
171   K        -0.983  -0.957  -0.973  -1.121  -1.085  -1.098  -0.890  -0.856  -0.852
172   V        -0.983  -1.028  -0.993  -1.014  -1.065  -1.020  -0.890  -0.930  -0.873
173   A         0.680   0.574   0.542   0.687   0.552   0.480   0.632   0.451   0.379
174   S        -1.537  -1.515  -1.466  -1.583  -1.533  -1.470  -1.194  -1.164  -1.090
175   S        -0.983  -0.932  -0.957  -1.049  -0.973  -1.010  -0.890  -0.825  -0.835
176   H        -1.537  -1.515  -1.466  -1.178  -1.136  -1.066  -1.194  -1.164  -1.090
177   G         1.681   1.701   1.747   1.627   1.660   1.735   1.850   1.877   1.948
178   Y         1.681   1.701   1.747   1.803   1.833   1.910   1.850   1.877   1.948
179   S        -0.983  -0.996  -0.976  -0.903  -0.935  -0.901  -0.890  -0.898  -0.855
180   N         0.680   0.678   0.562   0.767   0.773   0.590   0.632   0.627   0.415
181   T        -1.537  -1.515  -1.466  -1.334  -1.285  -1.221  -1.194  -1.164  -1.090
182   S        -0.219  -0.313  -0.342  -0.364  -0.515  -0.562  -0.281  -0.408  -0.444
183   L        -0.983  -0.886  -0.959  -0.885  -0.721  -0.847  -0.890  -0.772  -0.837
184   Y         1.681   1.701   1.747   1.803   1.833   1.910   1.850   1.877   1.948
185   P        -0.219  -0.290  -0.324  -0.178  -0.289  -0.361  -0.281  -0.378  -0.419
186   G         1.681   1.701   1.747   1.627   1.660   1.735   1.850   1.877   1.948
187   S         1.681   1.701   1.747   1.506   1.528   1.614   1.850   1.877   1.948
188   M        -0.983  -1.028  -0.993  -0.593  -0.651  -0.607  -0.890  -0.930  -0.873
189   N         0.680   0.574   0.542   0.767   0.617   0.557   0.632   0.451   0.379
190   D         0.680   0.574   0.542   0.729   0.572   0.515   0.632   0.451   0.379
191   W         1.681   1.701   1.747   1.917   1.951   2.024   1.850   1.877   1.948
192   V        -0.219  -0.313  -0.342  -0.310  -0.471  -0.522  -0.281  -0.408  -0.444
193   S        -0.219  -0.237  -0.309  -0.261  -0.277  -0.420  -0.281  -0.309  -0.399
194   H         0.335   0.369   0.387   0.226   0.274   0.315   0.023   0.082   0.094
195   G         0.557   0.450   0.464   0.507   0.345   0.364   0.423   0.231   0.238
196   G         0.557   0.450   0.464   0.446   0.256   0.275   0.423   0.231   0.238
197   D         0.557   0.450   0.464   0.477   0.280   0.286   0.423   0.231   0.238
198   K         0.557   0.652   0.511   0.495   0.614   0.434   0.423   0.582   0.323
199   L         1.681   1.701   1.747   1.740   1.770   1.848   1.850   1.877   1.948
200   D        -0.398  -0.318  -0.393  -0.344  -0.200  -0.361  -0.528  -0.412  -0.514
201   L         0.557   0.490   0.464   0.566   0.450   0.399   0.423   0.303   0.238
* gap fraction no less than  0.50; conservation set to M-S
  M: mean;  S: standard deviation

al2co - The parameters are:

Input alignment file - ../mafft-mac/clustal/Q12305
Output conservation file - output/Q12305
All 9 methods are used - true 
   1. unweighted entropy measure; 2. Henikoff entropy measure;
   3. independent count entropy measure;
   4. unweighted variance measure; 5. Henikoff variance measure;
   6. independent count variance measure;
   7. unweighted matrix-based sum-of-pairs measure;
   8. Henikoff matrix-based sum-of-pairs measure;
   9. independent count matrix-based sum-of-pairs measure;
Window size - 1
Conservation normalized to zero mean and unity variance
Gap fraction to suppress calculation -  0.50
