1     M         0.897   0.903   0.946   1.117   1.123   1.171   0.950   0.957   1.019
2     S        -1.094  -1.163  -1.161  -1.129  -1.259  -1.250  -1.139  -1.216  -1.166
3     E        -1.556  -1.537  -1.513  -1.489  -1.453  -1.411  -1.437  -1.424  -1.327
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     K        -0.763  -0.764  -0.719  -0.751  -0.727  -0.675  -0.995  -0.982  -0.912
9     A        -1.271  -1.235  -1.169  -1.365  -1.296  -1.224  -1.338  -1.292  -1.174
10    V        -0.880  -0.884  -0.747  -1.230  -1.239  -1.014  -1.139  -1.142  -0.949
11    R        -0.189  -0.191  -0.117  -0.367  -0.375  -0.269  -0.542  -0.549  -0.446
12    R         0.897   0.903   0.946   0.944   0.952   1.014   0.950   0.957   1.019
13    K         0.897   0.903   0.946   0.891   0.900   0.965   0.950   0.957   1.019
14    L         0.279   0.276  -0.009   0.207   0.205  -0.195   0.254   0.249  -0.244
15    V         0.897   0.903   0.946   0.772   0.777   0.856   0.950   0.957   1.019
16    I         0.279   0.219  -0.017   0.383   0.301  -0.108   0.254   0.161  -0.260
17    I        -0.241  -0.225  -0.124  -0.561  -0.547  -0.364  -0.641  -0.614  -0.459
18    G         0.897   0.903   0.946   0.888   0.894   0.962   0.950   0.957   1.019
19    D         0.897   0.903   0.946   0.897   0.906   0.970   0.950   0.957   1.019
20    G         0.897   0.903   0.946   0.888   0.894   0.962   0.950   0.957   1.019
21    A         0.897   0.903   0.946   0.830   0.834   0.909   0.950   0.957   1.019
22    C         0.897   0.903   0.946   1.041   1.047   1.101   0.950   0.957   1.019
23    G         0.897   0.903   0.946   0.888   0.894   0.962   0.950   0.957   1.019
24    K         0.897   0.903   0.946   0.891   0.900   0.965   0.950   0.957   1.019
25    T         0.897   0.903   0.946   0.929   0.937   0.999   0.950   0.957   1.019
26    S         0.897   0.903   0.946   0.922   0.927   0.993   0.950   0.957   1.019
27    L         0.897   0.903   0.946   0.752   0.759   0.838   0.950   0.957   1.019
28    L         0.897   0.903   0.946   0.752   0.759   0.838   0.950   0.957   1.019
29    Y        -1.094  -1.169  -1.161  -0.930  -1.044  -1.023  -1.139  -1.221  -1.166
30    V         0.897   0.903   0.946   0.772   0.777   0.856   0.950   0.957   1.019
31    F         0.897   0.903   0.946   1.022   1.031   1.085   0.950   0.957   1.019
32    T         0.897   0.903   0.946   0.929   0.937   0.999   0.950   0.957   1.019
33    L         0.279   0.201  -0.012   0.232   0.138  -0.134   0.254   0.133  -0.250
34    G         0.897   0.903   0.946   0.888   0.894   0.962   0.950   0.957   1.019
35    K        -1.948  -1.959  -1.816  -1.814  -1.824  -1.576  -1.636  -1.638  -1.443
36    F         0.897   0.903   0.946   1.022   1.031   1.085   0.950   0.957   1.019
37    P         0.897   0.903   0.946   1.016   1.022   1.079   0.950   0.957   1.019
38    E        -1.164  -1.193  -1.167  -1.271  -1.296  -1.251  -1.238  -1.257  -1.173
39    Q        -0.672  -0.692  -0.703  -0.736  -0.752  -0.778  -0.869  -0.878  -0.891
40    Y         0.897   0.903   0.946   1.015   1.025   1.078   0.950   0.957   1.019
41    H        -0.865  -0.976  -1.138  -0.506  -0.678  -1.019  -0.840  -0.974  -1.140
42    P         0.897   0.903   0.946   1.016   1.022   1.079   0.950   0.957   1.019
43    T         0.897   0.903   0.946   0.929   0.937   0.999   0.950   0.957   1.019
44    V         0.897   0.903   0.946   0.772   0.777   0.856   0.950   0.957   1.019
45    F         0.897   0.903   0.946   1.022   1.031   1.085   0.950   0.957   1.019
46    E         0.279   0.201  -0.012   0.306   0.210  -0.131   0.254   0.133  -0.250
47    N         0.897   0.903   0.946   1.050   1.057   1.110   0.950   0.957   1.019
48    Y         0.897   0.903   0.946   1.025   1.034   1.087   0.950   0.957   1.019
49    V         0.897   0.903   0.946   0.772   0.777   0.856   0.950   0.957   1.019
50    T        -0.311  -0.440  -0.657  -0.177  -0.361  -0.732  -0.343  -0.519  -0.826
51    D         0.897   0.903   0.946   0.897   0.906   0.970   0.950   0.957   1.019
52    C         0.897   0.903   0.946   1.041   1.047   1.101   0.950   0.957   1.019
53    R         0.897   0.903   0.946   0.944   0.952   1.014   0.950   0.957   1.019
54    V         0.279   0.297  -0.008   0.227   0.249  -0.177   0.254   0.281  -0.243
55    D         0.897   0.903   0.946   0.897   0.906   0.970   0.950   0.957   1.019
56    G         0.897   0.903   0.946   0.888   0.894   0.962   0.950   0.957   1.019
57    I        -0.189  -0.132  -0.102  -0.381  -0.276  -0.245  -0.542  -0.438  -0.418
58    K        -1.164  -1.142  -1.167  -1.229  -1.192  -1.198  -1.238  -1.208  -1.173
59    V         0.897   0.903   0.946   0.772   0.777   0.856   0.950   0.957   1.019
60    S        -0.581  -0.594  -0.684  -0.470  -0.479  -0.679  -0.741  -0.741  -0.865
61    L         0.897   0.903   0.946   0.752   0.759   0.838   0.950   0.957   1.019
62    T        -0.026   0.054  -0.062  -0.160  -0.036  -0.232  -0.244  -0.107  -0.341
63    L         0.897   0.903   0.946   0.752   0.759   0.838   0.950   0.957   1.019
64    W         0.897   0.903   0.946   1.144   1.151   1.196   0.950   0.957   1.019
65    D         0.897   0.903   0.946   0.897   0.906   0.970   0.950   0.957   1.019
66    T         0.897   0.903   0.946   0.929   0.937   0.999   0.950   0.957   1.019
67    A         0.897   0.903   0.946   0.830   0.834   0.909   0.950   0.957   1.019
68    G         0.897   0.903   0.946   0.888   0.894   0.962   0.950   0.957   1.019
69    Q         0.897   0.903   0.946   1.062   1.067   1.121   0.950   0.957   1.019
70    E         0.897   0.903   0.946   0.859   0.873   0.935   0.950   0.957   1.019
71    E         0.279   0.287  -0.010   0.306   0.324  -0.127   0.254   0.265  -0.246
72    Y         0.897   0.903   0.946   1.025   1.034   1.087   0.950   0.957   1.019
73    E         0.897   0.903   0.946   0.859   0.873   0.935   0.950   0.957   1.019
74    R         0.897   0.903   0.946   0.944   0.952   1.014   0.950   0.957   1.019
75    L         0.897   0.903   0.946   0.752   0.759   0.838   0.950   0.957   1.019
76    R         0.897   0.903   0.946   0.944   0.952   1.014   0.950   0.957   1.019
77    P         0.897   0.903   0.946   1.016   1.022   1.079   0.950   0.957   1.019
78    F        -0.703  -0.711  -0.715  -0.851  -0.849  -0.787  -0.940  -0.929  -0.909
79    S        -0.026  -0.065  -0.086  -0.102  -0.180  -0.252  -0.244  -0.316  -0.387
80    Y         0.897   0.903   0.946   1.025   1.034   1.087   0.950   0.957   1.019
81    S        -0.703  -0.700  -0.714  -0.846  -0.868  -0.815  -0.940  -0.944  -0.910
82    K        -1.094  -1.115  -1.149  -1.054  -1.083  -1.137  -1.139  -1.159  -1.154
83    A        -0.026  -0.017  -0.074  -0.162  -0.153  -0.256  -0.244  -0.230  -0.364
84    D        -0.703  -0.724  -0.712  -0.628  -0.618  -0.614  -0.940  -0.944  -0.904
85    I        -0.189  -0.168  -0.114  -0.486  -0.453  -0.353  -0.542  -0.505  -0.440
86    I         0.897   0.903   0.946   0.954   0.961   1.022   0.950   0.957   1.019
87    L         0.897   0.903   0.946   0.752   0.759   0.838   0.950   0.957   1.019
88    I         0.279   0.219  -0.017   0.383   0.301  -0.108   0.254   0.161  -0.260
89    G        -0.026   0.011  -0.086  -0.136  -0.076  -0.280  -0.244  -0.182  -0.387
90    F         0.897   0.903   0.946   1.022   1.031   1.085   0.950   0.957   1.019
91    A        -0.189  -0.167  -0.116  -0.451  -0.417  -0.332  -0.542  -0.503  -0.443
92    V        -0.703  -0.688  -0.708  -0.957  -0.938  -0.943  -0.940  -0.923  -0.903
93    D         0.279   0.201  -0.012   0.366   0.271  -0.039   0.254   0.133  -0.250
94    N        -1.663  -1.645  -1.527  -1.695  -1.690  -1.489  -1.537  -1.516  -1.338
95    F        -0.311  -0.210  -0.646  -0.083   0.046  -0.625  -0.343  -0.208  -0.811
96    E        -0.189  -0.132  -0.102  -0.426  -0.310  -0.292  -0.542  -0.438  -0.418
97    S         0.897   0.903   0.946   0.922   0.927   0.993   0.950   0.957   1.019
98    L         0.897   0.903   0.946   0.752   0.759   0.838   0.950   0.957   1.019
99    I        -1.379  -1.298  -1.497  -1.221  -1.110  -1.415  -1.238  -1.154  -1.312
100   N         0.897   0.903   0.946   1.050   1.057   1.110   0.950   0.957   1.019
101   A        -0.189  -0.215  -0.121  -0.533  -0.600  -0.436  -0.542  -0.594  -0.454
102   R        -0.865  -0.976  -1.138  -0.701  -0.871  -1.166  -0.840  -0.974  -1.140
103   T        -1.379  -1.374  -1.483  -1.153  -1.164  -1.312  -1.238  -1.234  -1.299
104   K         0.897   0.903   0.946   0.891   0.900   0.965   0.950   0.957   1.019
105   W         0.897   0.903   0.946   1.144   1.151   1.196   0.950   0.957   1.019
106   A        -1.271  -1.228  -1.177  -1.503  -1.441  -1.316  -1.338  -1.298  -1.183
107   D        -1.379  -1.375  -1.483  -1.318  -1.311  -1.517  -1.238  -1.235  -1.299
108   E         0.897   0.903   0.946   0.859   0.873   0.935   0.950   0.957   1.019
109   A        -0.703  -0.724  -0.711  -0.994  -1.011  -0.947  -0.940  -0.950  -0.905
110   L        -1.556  -1.487  -1.514  -1.474  -1.337  -1.413  -1.437  -1.361  -1.328
111   R        -1.271  -1.308  -1.186  -1.383  -1.439  -1.247  -1.338  -1.368  -1.192
112   Y        -0.581  -0.663  -0.708  -0.510  -0.648  -0.773  -0.741  -0.853  -0.898
113   C         0.897   0.903   0.946   1.041   1.047   1.101   0.950   0.957   1.019
114   P         0.897   0.903   0.946   1.016   1.022   1.079   0.950   0.957   1.019
115   D        -1.094  -1.061  -1.150  -0.988  -0.924  -1.116  -1.139  -1.093  -1.154
116   A        -0.880  -0.859  -0.743  -1.236  -1.208  -0.999  -1.139  -1.109  -0.944
117   P         0.897   0.903   0.946   1.016   1.022   1.079   0.950   0.957   1.019
118   I        -1.271  -1.274  -1.172  -1.326  -1.305  -1.154  -1.338  -1.329  -1.178
119   V        -0.880  -0.840  -0.739  -1.235  -1.169  -0.997  -1.139  -1.089  -0.938
120   L         0.897   0.903   0.946   0.752   0.759   0.838   0.950   0.957   1.019
121   V        -0.581  -0.605  -0.701  -0.692  -0.741  -0.827  -0.741  -0.786  -0.890
122   G         0.897   0.903   0.946   0.888   0.894   0.962   0.950   0.957   1.019
123   L         0.279   0.219  -0.017   0.232   0.160  -0.142   0.254   0.161  -0.260
124   K         0.897   0.903   0.946   0.891   0.900   0.965   0.950   0.957   1.019
125   K        -0.311  -0.328  -0.651  -0.226  -0.251  -0.778  -0.343  -0.369  -0.819
126   D         0.897   0.903   0.946   0.897   0.906   0.970   0.950   0.957   1.019
127   L         0.897   0.903   0.946   0.752   0.759   0.838   0.950   0.957   1.019
128   R         0.897   0.903   0.946   0.944   0.952   1.014   0.950   0.957   1.019
129   Q        -2.045  -2.028  -1.822  -2.026  -2.006  -1.699  -1.702  -1.684  -1.447
130   E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
131   A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
132   H        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
133   F        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
134   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
135   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
136   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
137   K        -1.647  -1.611  -1.529  -1.564  -1.491  -1.418  -1.518  -1.481  -1.340
138   E        -1.647  -1.598  -1.524  -1.669  -1.596  -1.469  -1.518  -1.472  -1.336
139   N        -1.972  -1.940  -1.818  -1.810  -1.783  -1.583  -1.648  -1.619  -1.444
140   A        -1.948  -1.920  -1.808  -1.780  -1.730  -1.595  -1.636  -1.611  -1.438
141   T        -1.948  -1.895  -1.812  -1.839  -1.759  -1.638  -1.636  -1.593  -1.441
142   D        -2.232  -2.184  -2.053  -1.957  -1.897  -1.737  -1.736  -1.697  -1.513
143   E        -2.232  -2.188  -2.048  -1.975  -1.900  -1.743  -1.736  -1.700  -1.511
144   M        -1.094  -1.104  -1.139  -0.848  -0.850  -0.903  -1.139  -1.134  -1.142
145   V         0.279   0.201  -0.012   0.227   0.125  -0.183   0.254   0.133  -0.250
146   P        -1.948  -1.920  -1.808  -1.650  -1.627  -1.447  -1.636  -1.611  -1.438
147   I        -1.948  -1.959  -1.814  -1.826  -1.852  -1.656  -1.636  -1.638  -1.442
148   E        -1.556  -1.625  -1.524  -1.500  -1.587  -1.396  -1.437  -1.492  -1.336
149   D        -1.271  -1.248  -1.170  -1.241  -1.208  -1.068  -1.338  -1.310  -1.176
150   A        -0.241  -0.231  -0.125  -0.569  -0.552  -0.367  -0.641  -0.625  -0.461
151   K        -0.703  -0.660  -0.705  -0.787  -0.731  -0.764  -0.940  -0.900  -0.898
152   Q        -1.556  -1.595  -1.522  -1.474  -1.569  -1.475  -1.437  -1.470  -1.334
153   V        -1.094  -1.115  -1.157  -1.129  -1.158  -1.182  -1.139  -1.166  -1.163
154   A         0.897   0.903   0.946   0.830   0.834   0.909   0.950   0.957   1.019
155   R        -1.556  -1.592  -1.506  -1.491  -1.529  -1.396  -1.437  -1.459  -1.321
156   A        -1.556  -1.617  -1.523  -1.619  -1.695  -1.537  -1.437  -1.487  -1.335
157   I         0.279   0.276  -0.009   0.433   0.431   0.039   0.254   0.249  -0.244
158   G         0.279   0.276  -0.009   0.370   0.368  -0.006   0.254   0.249  -0.244
159   A         0.897   0.903   0.946   0.830   0.834   0.909   0.950   0.957   1.019
160   K        -0.026  -0.055  -0.089  -0.096  -0.145  -0.225  -0.244  -0.298  -0.393
161   K         0.897   0.903   0.946   0.891   0.900   0.965   0.950   0.957   1.019
162   Y         0.897   0.903   0.946   1.025   1.034   1.087   0.950   0.957   1.019
163   M        -0.189  -0.168  -0.114  -0.412  -0.383  -0.268  -0.542  -0.505  -0.440
164   E         0.897   0.903   0.946   0.859   0.873   0.935   0.950   0.957   1.019
165   C        -0.026  -0.017  -0.074   0.042   0.052  -0.086  -0.244  -0.230  -0.364
166   S         0.897   0.903   0.946   0.922   0.927   0.993   0.950   0.957   1.019
167   A        -0.026  -0.055  -0.089  -0.162  -0.217  -0.284  -0.244  -0.298  -0.393
168   L         0.897   0.903   0.946   0.752   0.759   0.838   0.950   0.957   1.019
169   T         0.279   0.276  -0.009   0.394   0.393  -0.017   0.254   0.249  -0.244
170   G         0.897   0.903   0.946   0.888   0.894   0.962   0.950   0.957   1.019
171   E        -0.311  -0.440  -0.657  -0.212  -0.377  -0.706  -0.343  -0.519  -0.826
172   G         0.279   0.347  -0.007   0.357   0.438  -0.038   0.254   0.354  -0.240
173   V         0.897   0.903   0.946   0.772   0.777   0.856   0.950   0.957   1.019
174   D         0.897   0.903   0.946   0.897   0.906   0.970   0.950   0.957   1.019
175   D         0.897   0.903   0.946   0.897   0.906   0.970   0.950   0.957   1.019
176   V        -0.026  -0.017  -0.074  -0.208  -0.197  -0.288  -0.244  -0.230  -0.364
177   F         0.897   0.903   0.946   1.022   1.031   1.085   0.950   0.957   1.019
178   E         0.897   0.903   0.946   0.859   0.873   0.935   0.950   0.957   1.019
179   V        -1.271  -1.251  -1.177  -1.509  -1.487  -1.358  -1.338  -1.319  -1.183
180   A         0.897   0.903   0.946   0.830   0.834   0.909   0.950   0.957   1.019
181   T         0.279   0.297  -0.008   0.358   0.383  -0.111   0.254   0.281  -0.243
182   R         0.897   0.903   0.946   0.944   0.952   1.014   0.950   0.957   1.019
183   T        -0.703  -0.682  -0.716  -0.868  -0.864  -0.862  -0.940  -0.925  -0.911
184   S        -0.026  -0.055  -0.089  -0.102  -0.161  -0.258  -0.244  -0.298  -0.393
185   L         0.897   0.903   0.946   0.752   0.759   0.838   0.950   0.957   1.019
186   L         0.279   0.219  -0.017   0.203   0.126  -0.220   0.254   0.161  -0.260
187   M        -1.094  -1.036  -1.138  -1.121  -1.042  -1.159  -1.139  -1.061  -1.141
188   K        -2.232  -2.233  -2.050  -1.822  -1.836  -1.586  -1.736  -1.731  -1.512
189   K        -1.199  -1.249  -1.176  -1.321  -1.406  -1.298  -1.259  -1.310  -1.182
190   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
191   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
192   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
193   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
194   E        -1.094  -1.061  -1.150  -1.074  -1.010  -1.113  -1.139  -1.093  -1.154
195   P        -1.271  -1.308  -1.186  -1.360  -1.427  -1.240  -1.338  -1.368  -1.192
196   G        -1.271  -1.261  -1.177  -1.320  -1.316  -1.169  -1.338  -1.331  -1.183
197   A        -1.948  -1.939  -1.807  -1.713  -1.715  -1.540  -1.636  -1.624  -1.437
198   N        -1.379  -1.350  -1.484  -1.191  -1.163  -1.342  -1.238  -1.209  -1.300
199   C         0.897   0.903   0.946   1.041   1.047   1.101   0.950   0.957   1.019
200   C         0.897   0.903   0.946   1.041   1.047   1.101   0.950   0.957   1.019
201   I        -1.271  -1.222  -1.167  -1.402  -1.320  -1.237  -1.338  -1.284  -1.173
202   I         0.279   0.201  -0.012   0.383   0.276  -0.097   0.254   0.133  -0.250
203   L        -1.094  -1.110  -1.147  -1.190  -1.223  -1.208  -1.139  -1.159  -1.152
* 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/P06781
Output conservation file - output/P06781
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
