1     M         2.262   2.263   2.334   2.511   2.511   2.628   2.544   2.543   2.659
2     V        -0.867  -0.862  -0.820  -0.922  -0.914  -0.848  -0.805  -0.798  -0.739
3     S        -0.084  -0.073  -0.070  -0.201  -0.182  -0.186  -0.246  -0.231  -0.228
4     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
5     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
6     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
7     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
8     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
9     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
10    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
11    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
12    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
13    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
14    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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    F        -0.867  -0.862  -0.820  -0.642  -0.634  -0.564  -0.805  -0.798  -0.739
35    I         0.993   0.991   0.933   1.037   1.033   0.921   0.870   0.865   0.735
36    T        -1.370  -1.362  -1.328  -1.328  -1.312  -1.259  -1.028  -1.018  -0.965
37    S        -0.744  -0.732  -0.743  -0.691  -0.675  -0.673  -0.671  -0.656  -0.655
38    R        -1.370  -1.362  -1.328  -1.195  -1.179  -1.125  -1.028  -1.018  -0.965
39    Q        -0.119  -0.095  -0.092  -0.226  -0.196  -0.179  -0.313  -0.286  -0.270
40    L        -0.119  -0.138  -0.114  -0.358  -0.383  -0.342  -0.313  -0.335  -0.296
41    K         0.117   0.131   0.023   0.032   0.056  -0.132   0.044   0.062  -0.094
42    G        -0.119  -0.093  -0.104  -0.311  -0.271  -0.289  -0.313  -0.283  -0.284
43    L        -0.744  -0.767  -0.738  -0.679  -0.710  -0.658  -0.671  -0.696  -0.650
44    I        -0.119  -0.138  -0.114  -0.198  -0.211  -0.166  -0.313  -0.335  -0.296
45    E        -0.744  -0.767  -0.738  -0.691  -0.724  -0.679  -0.671  -0.696  -0.650
46    N        -0.744  -0.699  -0.741  -0.651  -0.580  -0.644  -0.671  -0.617  -0.653
47    Q        -0.744  -0.767  -0.738  -0.704  -0.741  -0.699  -0.671  -0.696  -0.650
48    R        -1.370  -1.362  -1.328  -1.381  -1.375  -1.313  -1.028  -1.018  -0.965
49    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
50    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
51    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
52    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
53    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
54    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
55    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
56    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
57    K         0.117   0.119   0.056   0.166   0.170   0.063   0.044   0.045  -0.046
58    D        -0.119  -0.126  -0.097  -0.226  -0.235  -0.185  -0.313  -0.321  -0.276
59    F        -0.119  -0.101  -0.096  -0.286  -0.264  -0.252  -0.313  -0.291  -0.276
60    Q        -0.744  -0.744  -0.764  -0.675  -0.667  -0.713  -0.671  -0.669  -0.679
61    V         0.743   0.758   0.788   0.422   0.451   0.482   0.401   0.429   0.455
62    V         1.133   1.110   1.030   1.136   1.100   0.983   1.115   1.074   0.915
63    D         2.262   2.263   2.334   2.307   2.308   2.421   2.544   2.543   2.659
64    L         0.117   0.101   0.035   0.106   0.079  -0.018   0.044   0.019  -0.076
65    R         2.262   2.263   2.334   2.267   2.269   2.381   2.544   2.543   2.659
66    R         0.117   0.063   0.023   0.169   0.086   0.019   0.044  -0.035  -0.094
67    E        -0.119  -0.103  -0.101  -0.236  -0.215  -0.200  -0.313  -0.294  -0.280
68    D         2.262   2.263   2.334   2.307   2.308   2.421   2.544   2.543   2.659
69    F        -0.119  -0.138  -0.114  -0.029  -0.057  -0.005  -0.313  -0.335  -0.296
70    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
71    A        -0.744  -0.767  -0.738  -0.749  -0.786  -0.742  -0.671  -0.696  -0.650
72    R         0.117   0.131   0.023   0.052   0.074  -0.104   0.044   0.062  -0.094
73    D         1.133   1.174   1.051   1.091   1.151   0.970   1.115   1.183   0.953
74    H         0.743   0.758   0.788   0.766   0.797   0.828   0.401   0.429   0.455
75    I         1.133   1.158   1.045   1.217   1.256   1.078   1.115   1.157   0.942
76    T        -0.744  -0.721  -0.734  -0.778  -0.738  -0.766  -0.671  -0.643  -0.644
77    N         0.117   0.171   0.073   0.077   0.159   0.010   0.044   0.120  -0.021
78    A         0.743   0.758   0.788   0.442   0.470   0.500   0.401   0.429   0.455
79    W        -0.119  -0.138  -0.114  -0.069  -0.098  -0.064  -0.313  -0.335  -0.296
80    H         0.117   0.131   0.023   0.426   0.442   0.287   0.044   0.062  -0.094
81    V        -0.119  -0.138  -0.114  -0.343  -0.366  -0.325  -0.313  -0.335  -0.296
82    P         2.262   2.263   2.334   2.473   2.472   2.589   2.544   2.543   2.659
83    V        -0.119  -0.138  -0.114  -0.358  -0.394  -0.355  -0.313  -0.335  -0.296
84    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
85    A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
86    Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
87    I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
88    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
89    E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
90    K        -1.370  -1.362  -1.328  -1.146  -1.142  -1.075  -1.028  -1.018  -0.965
91    Q        -0.119  -0.138  -0.114  -0.243  -0.262  -0.217  -0.313  -0.335  -0.296
92    L        -0.119  -0.106  -0.105  -0.191  -0.172  -0.145  -0.313  -0.298  -0.285
93    N        -1.370  -1.362  -1.328  -1.127  -1.126  -1.056  -1.028  -1.018  -0.965
94    Q        -0.744  -0.764  -0.739  -0.651  -0.688  -0.644  -0.671  -0.692  -0.651
95    L        -0.119  -0.138  -0.114  -0.351  -0.380  -0.348  -0.313  -0.335  -0.296
96    I        -0.744  -0.732  -0.727  -0.766  -0.743  -0.735  -0.671  -0.657  -0.637
97    K        -0.744  -0.767  -0.738  -0.631  -0.671  -0.616  -0.671  -0.696  -0.650
98    G        -1.370  -1.362  -1.328  -1.392  -1.370  -1.324  -1.028  -1.018  -0.965
99    L         1.133   1.152   1.040   1.106   1.138   0.969   1.115   1.146   0.933
100   S        -0.744  -0.756  -0.762  -0.643  -0.668  -0.692  -0.671  -0.684  -0.676
101   D        -0.744  -0.764  -0.739  -0.643  -0.675  -0.632  -0.671  -0.692  -0.651
102   T        -0.744  -0.732  -0.743  -0.655  -0.639  -0.651  -0.671  -0.656  -0.655
103   F         0.993   0.973   0.944   1.139   1.113   1.066   0.870   0.832   0.755
104   S        -0.084  -0.055  -0.100  -0.134  -0.080  -0.172  -0.246  -0.205  -0.270
105   S        -0.744  -0.732  -0.743  -0.745  -0.725  -0.731  -0.671  -0.656  -0.655
106   S         0.117   0.131   0.023   0.100   0.119  -0.070   0.044   0.062  -0.094
107   Q        -0.744  -0.756  -0.762  -0.829  -0.850  -0.856  -0.671  -0.684  -0.676
108   F        -1.370  -1.362  -1.328  -1.185  -1.175  -1.115  -1.028  -1.018  -0.965
109   V        -0.744  -0.744  -0.764  -0.757  -0.760  -0.785  -0.671  -0.669  -0.679
110   K         0.117   0.063   0.023   0.178   0.092   0.022   0.044  -0.035  -0.094
111   V         1.133   1.152   1.040   1.121   1.145   0.978   1.115   1.146   0.933
112   I         0.743   0.763   0.790   0.503   0.537   0.570   0.401   0.438   0.458
113   F         2.262   2.263   2.334   2.346   2.346   2.461   2.544   2.543   2.659
114   H         0.743   0.758   0.788   0.846   0.873   0.913   0.401   0.429   0.455
115   C         2.262   2.263   2.334   2.454   2.452   2.569   2.544   2.543   2.659
116   T        -0.119  -0.138  -0.114  -0.289  -0.312  -0.273  -0.313  -0.335  -0.296
117   G        -1.370  -1.362  -1.328  -1.387  -1.368  -1.319  -1.028  -1.018  -0.965
118   S         2.262   2.263   2.334   2.146   2.148   2.258   2.544   2.543   2.659
119   K        -0.744  -0.744  -0.764  -0.704  -0.700  -0.738  -0.671  -0.669  -0.679
120   N        -0.119  -0.138  -0.114  -0.219  -0.247  -0.213  -0.313  -0.335  -0.296
121   R         2.262   2.263   2.334   2.267   2.269   2.381   2.544   2.543   2.659
122   G         2.262   2.263   2.334   2.177   2.181   2.289   2.544   2.543   2.659
123   P         1.133   1.152   1.040   1.344   1.371   1.189   1.115   1.146   0.933
124   K         0.117   0.113   0.046   0.169   0.163   0.057   0.044   0.035  -0.061
125   V        -0.744  -0.724  -0.742  -0.607  -0.576  -0.613  -0.671  -0.647  -0.654
126   A         1.133   1.110   1.030   1.178   1.141   1.021   1.115   1.074   0.915
127   A        -0.119  -0.126  -0.093  -0.254  -0.263  -0.209  -0.313  -0.320  -0.272
128   K        -0.744  -0.756  -0.762  -0.457  -0.477  -0.493  -0.671  -0.684  -0.676
129   F        -0.744  -0.744  -0.764  -0.548  -0.546  -0.570  -0.671  -0.669  -0.679
130   E         0.117   0.153   0.023   0.122   0.176  -0.040   0.044   0.094  -0.093
131   T        -0.744  -0.756  -0.762  -0.728  -0.754  -0.764  -0.671  -0.684  -0.676
132   Y         1.133   1.086   1.023   1.361   1.289   1.191   1.115   1.034   0.903
133   L        -0.119  -0.126  -0.097  -0.226  -0.226  -0.180  -0.313  -0.321  -0.276
134   Q        -1.370  -1.362  -1.328  -1.210  -1.203  -1.140  -1.028  -1.018  -0.965
135   E        -0.119  -0.104  -0.096  -0.268  -0.248  -0.228  -0.313  -0.294  -0.275
136   E        -0.744  -0.699  -0.741  -0.821  -0.745  -0.816  -0.671  -0.617  -0.653
137   D         0.743   0.742   0.785   0.457   0.457   0.515   0.401   0.397   0.448
138   I        -1.370  -1.362  -1.328  -1.425  -1.418  -1.357  -1.028  -1.018  -0.965
139   T        -0.744  -0.756  -0.762  -0.724  -0.748  -0.759  -0.671  -0.684  -0.676
140   S        -0.084  -0.082  -0.076  -0.303  -0.301  -0.294  -0.246  -0.244  -0.236
141   K         0.826   0.787   0.820   0.692   0.622   0.664   0.560   0.485   0.518
142   F        -0.744  -0.744  -0.764  -0.671  -0.667  -0.710  -0.671  -0.669  -0.679
143   E        -0.119  -0.127  -0.105  -0.229  -0.242  -0.206  -0.313  -0.322  -0.285
144   S         0.117   0.063   0.023   0.006  -0.083  -0.153   0.044  -0.035  -0.094
145   C        -0.119  -0.103  -0.092  -0.069  -0.049  -0.023  -0.313  -0.295  -0.270
146   I         0.117   0.165   0.066   0.109   0.179   0.028   0.044   0.112  -0.031
147   L         1.133   1.158   1.045   1.153   1.192   1.041   1.115   1.157   0.942
148   V        -0.744  -0.736  -0.724  -0.762  -0.756  -0.734  -0.671  -0.661  -0.634
149   G         1.133   1.152   1.040   1.081   1.110   0.939   1.115   1.146   0.933
150   G         2.262   2.263   2.334   2.177   2.181   2.289   2.544   2.543   2.659
151   F        -0.119  -0.127  -0.105  -0.116  -0.124  -0.079  -0.313  -0.322  -0.285
152   Y        -0.744  -0.744  -0.764  -0.514  -0.510  -0.550  -0.671  -0.669  -0.679
153   A        -0.119  -0.138  -0.114  -0.387  -0.418  -0.385  -0.313  -0.335  -0.296
154   W         2.262   2.263   2.334   2.530   2.531   2.647   2.544   2.543   2.659
155   E        -0.084  -0.103  -0.103  -0.246  -0.278  -0.287  -0.246  -0.273  -0.274
156   T        -0.867  -0.860  -0.820  -0.874  -0.860  -0.799  -0.805  -0.796  -0.739
157   H        -0.867  -0.860  -0.820  -0.596  -0.594  -0.518  -0.805  -0.796  -0.739
158   C        -0.084  -0.103  -0.103   0.048   0.012   0.003  -0.246  -0.273  -0.274
159   R        -0.867  -0.860  -0.820  -0.903  -0.896  -0.829  -0.805  -0.796  -0.739
160   E        -0.084  -0.097  -0.076  -0.265  -0.287  -0.261  -0.246  -0.264  -0.236
161   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
162   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
163   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
164   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
165   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
166   S         0.698   0.702   0.757   0.384   0.393   0.474   0.312   0.318   0.394
167   N        -0.084  -0.067  -0.063  -0.181  -0.160  -0.148  -0.246  -0.222  -0.217
168   -        -0.084  -0.094  -0.079   0.063   0.045   0.071  -0.246  -0.261  -0.240
169   -         0.993   0.978   0.933   1.008   0.985   0.908   0.870   0.840   0.735
170   -        -0.084  -0.094  -0.079  -0.177  -0.192  -0.170  -0.246  -0.261  -0.240
171   -        -0.867  -0.861  -0.820  -0.778  -0.770  -0.703  -0.805  -0.798  -0.739
172   -        -0.867  -0.861  -0.820  -1.028  -1.019  -0.956  -0.805  -0.798  -0.739
173   L        -0.744  -0.756  -0.762  -0.404  -0.417  -0.434  -0.671  -0.684  -0.676
174   K        -0.744  -0.767  -0.738  -0.631  -0.665  -0.616  -0.671  -0.696  -0.650
175   L        -1.370  -1.362  -1.328  -1.225  -1.203  -1.155  -1.028  -1.018  -0.965
176   I        -0.119  -0.138  -0.114  -0.226  -0.242  -0.200  -0.313  -0.335  -0.296
177   V        -1.370  -1.362  -1.328  -1.425  -1.405  -1.357  -1.028  -1.018  -0.965
178   S         0.117   0.063   0.023   0.035  -0.050  -0.115   0.044  -0.035  -0.094
179   G        -1.370  -1.362  -1.328  -1.414  -1.400  -1.346  -1.028  -1.018  -0.965
180   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
181   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
182   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
183   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
* 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/Q06597
Output conservation file - output/Q06597
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
