1     M         1.751   1.783   1.870   1.981   2.027   2.162   1.949   2.000   2.140
2     P         0.840   0.702   0.668   0.999   0.805   0.741   0.847   0.609   0.520
3     S        -0.293  -0.349  -0.277  -0.334  -0.422  -0.306  -0.476  -0.531  -0.432
4     V        -0.293  -0.251  -0.278  -0.319  -0.282  -0.264  -0.476  -0.435  -0.439
5     D        -0.760  -0.769  -0.830  -0.673  -0.685  -0.785  -0.697  -0.709  -0.750
6     I         1.751   1.783   1.870   1.669   1.717   1.850   1.949   2.000   2.140
7     D        -0.760  -0.819  -0.844  -0.610  -0.692  -0.722  -0.697  -0.765  -0.766
8     A        -1.404  -1.406  -1.344  -1.040  -1.110  -0.954  -1.138  -1.132  -1.028
9     S        -0.293  -0.303  -0.287  -0.358  -0.386  -0.341  -0.476  -0.493  -0.449
10    Q        -1.404  -1.375  -1.349  -1.192  -1.132  -1.110  -1.138  -1.105  -1.033
11    W        -0.293  -0.213  -0.256  -0.399  -0.288  -0.290  -0.476  -0.359  -0.402
12    Q        -1.404  -1.409  -1.345  -1.179  -1.196  -1.087  -1.138  -1.135  -1.029
13    K        -1.404  -1.393  -1.339  -1.341  -1.312  -1.234  -1.138  -1.120  -1.024
14    L         0.391   0.413   0.483  -0.108  -0.077   0.012   0.044   0.076   0.168
15    T        -0.170  -0.203  -0.261  -0.362  -0.404  -0.466  -0.273  -0.319  -0.404
16    Q        -0.942  -0.957  -0.911  -0.765  -0.776  -0.705  -0.908  -0.918  -0.840
17    -        -0.350  -0.305  -0.292  -0.585  -0.501  -0.505  -0.531  -0.466  -0.447
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    -         0.614   0.654   0.577   0.590   0.667   0.514   0.461   0.525   0.349
22    -         0.614   0.672   0.597   0.554   0.648   0.482   0.461   0.556   0.387
23    -        -0.350  -0.346  -0.298  -0.299  -0.280  -0.218  -0.531  -0.528  -0.455
24    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
25    S        -0.942  -0.971  -0.903  -1.101  -1.167  -1.071  -0.908  -0.935  -0.831
26    R        -0.942  -0.949  -0.892  -0.860  -0.912  -0.796  -0.908  -0.912  -0.819
27    E        -0.942  -0.929  -0.882  -0.983  -0.975  -0.885  -0.908  -0.890  -0.809
28    K        -1.502  -1.472  -1.387  -1.457  -1.414  -1.270  -1.226  -1.188  -1.066
29    Q        -0.942  -0.861  -0.876  -0.803  -0.686  -0.693  -0.908  -0.809  -0.802
30    T        -1.871  -1.834  -1.756  -1.672  -1.593  -1.485  -1.358  -1.317  -1.200
31    T        -0.760  -0.769  -0.830  -0.662  -0.654  -0.817  -0.697  -0.709  -0.750
32    V         0.464   0.500   0.506   0.186   0.236   0.227   0.185   0.241   0.213
33    I        -1.404  -1.382  -1.338  -1.288  -1.253  -1.182  -1.138  -1.110  -1.024
34    T         1.751   1.783   1.870   1.896   1.948   2.076   1.949   2.000   2.140
35    P         0.840   0.859   0.674   0.986   1.018   0.728   0.847   0.875   0.531
36    L        -0.293  -0.349  -0.277  -0.459  -0.527  -0.409  -0.476  -0.531  -0.432
37    G         1.751   1.783   1.870   1.846   1.892   2.026   1.949   2.000   2.140
38    M        -0.937  -0.890  -0.879  -0.926  -0.816  -0.766  -0.917  -0.858  -0.809
39    M        -1.404  -1.409  -1.345  -1.187  -1.188  -1.105  -1.138  -1.135  -1.029
40    M        -0.293  -0.251  -0.278  -0.395  -0.358  -0.427  -0.476  -0.435  -0.439
41    L        -0.293  -0.303  -0.287  -0.696  -0.710  -0.676  -0.476  -0.493  -0.449
42    E         1.751   1.783   1.870   1.758   1.801   1.939   1.949   2.000   2.140
43    I         1.751   1.783   1.870   1.669   1.717   1.850   1.949   2.000   2.140
44    Q         1.751   1.783   1.870   1.932   1.975   2.112   1.949   2.000   2.140
45    G         1.751   1.783   1.870   1.846   1.892   2.026   1.949   2.000   2.140
46    E        -0.003   0.057  -0.162   0.061   0.143  -0.193  -0.035   0.051  -0.261
47    L         0.840   0.702   0.668   0.661   0.464   0.393   0.847   0.609   0.520
48    E        -0.937  -0.980  -0.902  -0.931  -1.007  -0.860  -0.917  -0.949  -0.832
49    L        -0.003  -0.125  -0.207  -0.086  -0.257  -0.345  -0.035  -0.213  -0.326
50    P         0.840   0.702   0.668   0.959   0.746   0.666   0.847   0.609   0.520
51    K        -1.404  -1.382  -1.338  -1.143  -1.096  -1.037  -1.138  -1.110  -1.024
52    D        -1.404  -1.406  -1.344  -1.291  -1.270  -1.193  -1.138  -1.132  -1.028
53    F        -0.760  -0.819  -0.844  -0.648  -0.783  -0.857  -0.697  -0.765  -0.766
54    A        -0.942  -0.979  -0.911  -0.890  -0.948  -0.842  -0.908  -0.944  -0.840
55    S        -0.350  -0.383  -0.326  -0.419  -0.503  -0.415  -0.531  -0.576  -0.494
56    L        -0.350  -0.306  -0.287  -0.410  -0.344  -0.324  -0.531  -0.466  -0.439
57    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
58    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
59    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
60    A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
61    R        -0.170  -0.133  -0.226  -0.102  -0.049  -0.182  -0.273  -0.219  -0.354
62    R        -0.170  -0.203  -0.261  -0.115  -0.165  -0.255  -0.273  -0.319  -0.404
63    D        -0.170  -0.178  -0.253  -0.091  -0.101  -0.208  -0.273  -0.285  -0.392
64    S        -0.381  -0.390  -0.325  -0.413  -0.451  -0.367  -0.591  -0.594  -0.496
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    P        -0.170  -0.203  -0.261  -0.177  -0.233  -0.345  -0.273  -0.319  -0.404
68    N        -0.942  -0.957  -0.911  -0.859  -0.894  -0.869  -0.908  -0.918  -0.840
69    E        -0.942  -0.957  -0.911  -1.246  -1.267  -1.166  -0.908  -0.918  -0.840
70    G        -1.502  -1.483  -1.387  -1.510  -1.479  -1.324  -1.226  -1.197  -1.066
71    R        -0.381  -0.358  -0.319  -0.407  -0.362  -0.319  -0.591  -0.555  -0.488
72    F         1.751   1.783   1.870   1.949   1.999   2.130   1.949   2.000   2.140
73    S        -0.350  -0.324  -0.293  -0.463  -0.424  -0.361  -0.531  -0.493  -0.448
74    E        -0.350  -0.313  -0.304  -0.420  -0.359  -0.339  -0.531  -0.476  -0.464
75    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
76    Q        -0.350  -0.346  -0.326  -0.311  -0.297  -0.251  -0.531  -0.524  -0.494
77    D         0.391   0.410   0.476   0.151   0.175   0.269   0.044   0.070   0.153
78    G         0.391   0.440   0.496   0.146   0.235   0.302   0.044   0.127   0.193
79    E        -1.502  -1.483  -1.387  -1.288  -1.258  -1.102  -1.226  -1.197  -1.066
80    T        -1.502  -1.483  -1.387  -1.317  -1.298  -1.131  -1.226  -1.197  -1.066
81    L        -0.293  -0.371  -0.293  -0.362  -0.483  -0.397  -0.476  -0.565  -0.456
82    I        -0.003  -0.092  -0.186   0.071  -0.073  -0.221  -0.035  -0.169  -0.296
83    R         0.350   0.385   0.473   0.137   0.210   0.347  -0.035   0.020   0.147
84    F         0.840   0.702   0.668   1.087   0.877   0.802   0.847   0.609   0.520
85    G         1.751   1.783   1.870   1.846   1.892   2.026   1.949   2.000   2.140
86    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
87    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
88    S        -0.003   0.125  -0.149   0.190   0.370  -0.018  -0.035   0.148  -0.243
89    L        -0.003  -0.125  -0.207  -0.128  -0.311  -0.414  -0.035  -0.213  -0.326
90    Q        -1.404  -1.317  -1.328  -1.323  -1.199  -1.194  -1.138  -1.043  -1.014
91    I        -0.293  -0.255  -0.281  -0.413  -0.327  -0.433  -0.476  -0.414  -0.437
92    D         0.350   0.383   0.471   0.057   0.103   0.248  -0.035   0.016   0.144
93    G        -1.404  -1.331  -1.334  -1.326  -1.217  -1.206  -1.138  -1.057  -1.020
94    E         0.840   0.900   0.690   0.818   0.907   0.582   0.847   0.941   0.561
95    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
96    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
97    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
98    R        -0.760  -0.692  -0.810  -0.621  -0.523  -0.653  -0.697  -0.608  -0.727
99    A         0.350   0.379   0.469   0.226   0.276   0.420  -0.035   0.008   0.139
100   T         0.840   0.919   0.693   1.023   1.137   0.786   0.847   0.971   0.566
101   L         1.751   1.783   1.870   1.533   1.595   1.714   1.949   2.000   2.140
102   F        -0.293  -0.371  -0.293  -0.100  -0.229  -0.117  -0.476  -0.565  -0.456
103   V         0.464   0.527   0.526   0.186   0.286   0.265   0.185   0.293   0.251
104   G         0.840   0.702   0.668   0.977   0.767   0.701   0.847   0.609   0.520
105   K        -0.003  -0.125  -0.207   0.026  -0.156  -0.277  -0.035  -0.213  -0.326
106   K         0.464   0.545   0.544   0.238   0.374   0.354   0.185   0.326   0.287
107   Q         1.751   1.783   1.870   1.932   1.975   2.112   1.949   2.000   2.140
108   R         1.751   1.783   1.870   1.960   2.003   2.140   1.949   2.000   2.140
109   L         0.840   0.702   0.668   0.707   0.532   0.479   0.847   0.609   0.520
110   L        -0.003  -0.125  -0.207  -0.077  -0.235  -0.329  -0.035  -0.213  -0.326
111   G         1.751   1.783   1.870   1.846   1.892   2.026   1.949   2.000   2.140
112   K        -0.293  -0.195  -0.251  -0.411  -0.251  -0.325  -0.476  -0.342  -0.396
113   V        -0.293  -0.275  -0.286  -0.455  -0.475  -0.433  -0.476  -0.464  -0.449
114   T        -0.003  -0.092  -0.186   0.061  -0.108  -0.239  -0.035  -0.169  -0.296
115   K         0.840   0.914   0.696   0.846   0.955   0.642   0.847   0.964   0.572
116   L         0.840   0.859   0.674   0.641   0.683   0.366   0.847   0.875   0.531
117   D        -0.470  -0.439  -0.351  -0.702  -0.660  -0.515  -0.697  -0.653  -0.529
118   V        -0.760  -0.830  -0.852  -0.628  -0.769  -0.812  -0.697  -0.778  -0.775
119   P         1.751   1.783   1.870   1.846   1.896   2.026   1.949   2.000   2.140
120   M         0.840   0.900   0.690   0.707   0.803   0.512   0.847   0.941   0.561
121   G         0.464   0.545   0.544   0.461   0.589   0.582   0.185   0.326   0.287
122   I        -0.470  -0.434  -0.348  -0.966  -0.926  -0.783  -0.697  -0.646  -0.524
123   M         0.840   0.900   0.690   0.707   0.803   0.512   0.847   0.941   0.561
124   H        -0.293  -0.213  -0.256  -0.325  -0.217  -0.229  -0.476  -0.359  -0.402
125   F        -0.293  -0.349  -0.277  -0.289  -0.340  -0.243  -0.476  -0.531  -0.432
126   N        -0.937  -0.853  -0.881  -0.966  -0.840  -0.880  -0.917  -0.823  -0.812
127   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
128   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
129   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
130   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
131   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
132   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
133   -        -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   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
138   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
139   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
140   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
141   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
142   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
143   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
144   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
145   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
146   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
147   S        -1.502  -1.464  -1.387  -1.463  -1.424  -1.276  -1.226  -1.181  -1.066
148   K        -0.937  -0.980  -0.882  -0.999  -1.038  -0.878  -0.917  -0.949  -0.813
149   D        -0.760  -0.766  -0.807  -0.648  -0.657  -0.716  -0.697  -0.706  -0.724
150   N        -1.404  -1.415  -1.366  -1.271  -1.256  -1.185  -1.138  -1.140  -1.048
151   K        -1.871  -1.834  -1.756  -1.801  -1.698  -1.614  -1.358  -1.317  -1.200
152   V         0.464   0.545   0.544   0.231   0.365   0.337   0.185   0.326   0.287
153   E        -0.937  -0.980  -0.902  -1.103  -1.166  -1.026  -0.917  -0.949  -0.832
154   L        -0.003   0.105  -0.139  -0.153   0.016  -0.351  -0.035   0.120  -0.229
155   V        -0.760  -0.819  -0.844  -0.793  -0.918  -0.964  -0.697  -0.765  -0.766
156   D         0.840   0.702   0.668   0.914   0.703   0.635   0.847   0.609   0.520
157   V         0.464   0.500   0.506   0.186   0.236   0.227   0.185   0.241   0.213
158   M        -0.760  -0.689  -0.832  -0.786  -0.683  -0.932  -0.697  -0.605  -0.752
159   K        -0.003  -0.077  -0.178   0.004  -0.106  -0.265  -0.035  -0.149  -0.284
160   Y        -0.760  -0.769  -0.830  -0.330  -0.334  -0.444  -0.697  -0.709  -0.750
161   K         1.751   1.783   1.870   1.692   1.743   1.873   1.949   2.000   2.140
162   V         0.464   0.506   0.500   0.231   0.289   0.242   0.185   0.253   0.201
163   I         0.840   0.702   0.668   0.811   0.608   0.550   0.847   0.609   0.520
164   F         1.751   1.783   1.870   1.960   2.013   2.140   1.949   2.000   2.140
165   K        -0.003  -0.077  -0.178   0.023  -0.088  -0.236  -0.035  -0.149  -0.284
166   D        -0.293  -0.243  -0.265  -0.313  -0.232  -0.250  -0.476  -0.396  -0.415
167   R         0.840   0.702   0.668   1.068   0.843   0.768   0.847   0.609   0.520
168   P         1.751   1.783   1.870   1.846   1.896   2.026   1.949   2.000   2.140
169   L         0.840   0.702   0.668   0.659   0.464   0.390   0.847   0.609   0.520
170   P         1.751   1.783   1.870   1.846   1.896   2.026   1.949   2.000   2.140
171   I         0.840   0.702   0.668   0.797   0.586   0.524   0.847   0.609   0.520
172   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
173   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
174   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
175   M         0.840   0.702   0.668   1.106   0.890   0.820   0.847   0.609   0.520
* 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/P38877
Output conservation file - output/P38877
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
