1     M         1.480   1.506   1.593   1.731   1.762   1.896   1.594   1.636   1.773
2     L        -0.134  -0.219  -0.168  -0.299  -0.397  -0.326  -0.368  -0.459  -0.393
3     C        -1.244  -1.306  -1.329  -1.003  -1.117  -1.108  -0.965  -1.034  -0.999
4     A        -1.393  -1.283  -1.371  -1.198  -1.055  -1.146  -1.105  -1.006  -1.033
5     I        -0.337  -0.353  -0.224  -0.462  -0.461  -0.265  -0.617  -0.636  -0.465
6     K        -0.157  -0.155  -0.203  -0.303  -0.317  -0.427  -0.340  -0.348  -0.435
7     S        -0.815  -0.849  -0.720  -0.977  -1.088  -0.876  -0.893  -0.937  -0.770
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    T        -0.978  -0.875  -1.014  -0.861  -0.750  -0.893  -0.880  -0.804  -0.872
11    G        -1.409  -1.428  -1.368  -1.386  -1.418  -1.361  -1.135  -1.147  -1.032
12    Y        -1.244  -1.193  -1.320  -1.003  -0.987  -1.097  -0.965  -0.932  -0.992
13    R        -1.775  -1.766  -1.644  -1.717  -1.661  -1.468  -1.306  -1.294  -1.127
14    Y        -0.311  -0.248  -0.160  -0.360  -0.256  -0.124  -0.565  -0.494  -0.381
15    P        -0.908  -1.004  -1.017  -0.856  -1.010  -1.066  -0.781  -0.893  -0.870
16    R        -1.505  -1.474  -1.375  -1.493  -1.445  -1.293  -1.213  -1.184  -1.037
17    T        -1.531  -1.539  -1.397  -1.604  -1.619  -1.407  -1.226  -1.229  -1.052
18    G        -0.720  -0.668  -0.679  -0.935  -0.867  -0.884  -0.803  -0.762  -0.728
19    A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
20    L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
21    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
22    L        -0.337  -0.302  -0.224  -0.623  -0.563  -0.419  -0.617  -0.574  -0.465
23    L        -0.014  -0.079  -0.165   0.008  -0.094  -0.238  -0.133  -0.236  -0.380
24    R        -1.190  -1.187  -1.077  -1.269  -1.267  -1.096  -1.085  -1.079  -0.926
25    G        -0.250  -0.193  -0.189  -0.538  -0.450  -0.431  -0.521  -0.453  -0.421
26    R        -0.720  -0.744  -0.690  -0.697  -0.695  -0.561  -0.803  -0.825  -0.738
27    P         1.480   1.506   1.593   1.367   1.401   1.547   1.594   1.636   1.773
28    F        -0.811  -0.765  -0.693  -0.947  -0.880  -0.772  -0.901  -0.849  -0.740
29    N        -0.811  -0.765  -0.693  -0.844  -0.779  -0.664  -0.901  -0.849  -0.740
30    M        -0.166  -0.082  -0.133  -0.111   0.021  -0.030  -0.380  -0.264  -0.332
31    A        -1.190  -1.201  -1.084  -1.234  -1.253  -1.092  -1.085  -1.089  -0.933
32    T        -0.778  -0.730  -0.673  -0.887  -0.797  -0.714  -0.880  -0.817  -0.723
33    R         0.302   0.282  -0.074   0.406   0.373  -0.144   0.315   0.281  -0.245
34    K        -1.409  -1.356  -1.349  -1.003  -0.931  -0.982  -1.135  -1.078  -1.016
35    -        -0.815  -0.791  -0.689  -0.719  -0.708  -0.545  -0.893  -0.873  -0.736
36    -        -0.337  -0.263  -0.212  -0.437  -0.318  -0.263  -0.617  -0.530  -0.451
37    -        -1.293  -1.244  -1.092  -1.364  -1.297  -1.070  -1.170  -1.124  -0.939
38    I        -0.713  -0.672  -0.611  -0.609  -0.541  -0.466  -0.794  -0.728  -0.648
39    T        -0.978  -0.890  -1.014  -0.955  -0.892  -0.993  -0.880  -0.826  -0.871
40    T        -0.683  -0.767  -0.680  -0.811  -0.915  -0.793  -0.781  -0.857  -0.729
41    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
42    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
43    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
44    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
45    E        -0.978  -1.080  -1.036  -1.022  -1.186  -1.110  -0.880  -0.969  -0.888
46    R        -0.765  -0.948  -1.004  -0.589  -0.889  -0.950  -0.624  -0.833  -0.857
47    I        -1.509  -1.476  -1.370  -1.417  -1.362  -1.172  -1.221  -1.182  -1.033
48    P         0.302   0.285  -0.054   0.317   0.297  -0.209   0.315   0.285  -0.216
49    G        -0.778  -0.805  -0.684  -0.972  -0.978  -0.814  -0.880  -0.893  -0.734
50    P         1.480   1.506   1.593   1.371   1.409   1.551   1.594   1.636   1.773
51    P         1.480   1.506   1.593   1.371   1.409   1.551   1.594   1.636   1.773
52    K        -0.134  -0.038  -0.159  -0.320  -0.169  -0.361  -0.368  -0.225  -0.380
53    L         1.480   1.506   1.593   1.469   1.505   1.645   1.594   1.636   1.773
54    P         1.480   1.506   1.593   1.371   1.409   1.551   1.594   1.636   1.773
55    R        -0.234  -0.026  -0.126  -0.362  -0.031  -0.223  -0.453  -0.159  -0.325
56    E         0.568   0.711   0.597   0.422   0.627   0.458   0.400   0.637   0.394
57    E         0.018   0.156  -0.120   0.055   0.270  -0.187  -0.112   0.092  -0.316
58    Q         1.480   1.506   1.593   1.561   1.591   1.733   1.594   1.636   1.773
59    E         0.568   0.711   0.597   0.413   0.625   0.447   0.400   0.637   0.394
60    E         1.480   1.506   1.593   1.376   1.407   1.555   1.594   1.636   1.773
61    F         0.879   0.715   0.638   1.076   0.876   0.782   0.912   0.645   0.472
62    E         0.879   0.715   0.638   0.855   0.633   0.527   0.912   0.645   0.472
63    R         0.302   0.287  -0.081   0.403   0.377  -0.166   0.315   0.288  -0.256
64    L         1.480   1.506   1.593   1.469   1.505   1.645   1.594   1.636   1.773
65    Q         1.480   1.506   1.593   1.561   1.591   1.733   1.594   1.636   1.773
66    R        -0.713  -0.585  -0.632  -0.822  -0.600  -0.710  -0.794  -0.627  -0.673
67    I        -0.613  -0.675  -0.644  -0.619  -0.709  -0.674  -0.709  -0.766  -0.691
68    A         0.879   0.715   0.638   0.981   0.773   0.623   0.912   0.645   0.472
69    T        -1.144  -0.966  -1.034  -1.182  -0.937  -0.956  -1.050  -0.887  -0.890
70    S        -0.499  -0.575  -0.600  -0.497  -0.588  -0.640  -0.538  -0.614  -0.633
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    Q        -0.499  -0.575  -0.600  -0.338  -0.467  -0.523  -0.538  -0.614  -0.633
76    E        -1.409  -1.472  -1.374  -1.407  -1.524  -1.366  -1.135  -1.179  -1.035
77    A         0.512   0.619   0.594   0.454   0.620   0.569   0.299   0.478   0.388
78    I        -0.134  -0.161  -0.158  -0.094  -0.126  -0.111  -0.368  -0.405  -0.377
79    D        -0.499  -0.482  -0.612  -0.488  -0.438  -0.694  -0.538  -0.500  -0.646
80    Q        -0.978  -1.066  -1.016  -0.987  -1.106  -1.017  -0.880  -0.963  -0.872
81    Y        -0.499  -0.575  -0.600  -0.191  -0.276  -0.342  -0.538  -0.614  -0.633
82    N         0.831   0.639   0.618   0.995   0.709   0.659   0.839   0.514   0.434
83    A        -1.207  -1.168  -1.064  -1.270  -1.221  -1.076  -1.105  -1.062  -0.915
84    Q        -0.610  -0.595  -0.616  -0.629  -0.635  -0.661  -0.673  -0.659  -0.652
85    A        -1.094  -1.002  -1.055  -0.961  -0.846  -0.873  -0.997  -0.907  -0.908
86    T        -1.094  -0.997  -1.060  -0.964  -0.820  -0.964  -0.997  -0.905  -0.912
87    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
88    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
89    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
90    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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    -        -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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
99    G        -0.683  -0.700  -0.680  -0.804  -0.819  -0.786  -0.781  -0.792  -0.729
100   D         0.213   0.153  -0.101   0.389   0.295  -0.121   0.191   0.097  -0.286
101   R        -1.505  -1.516  -1.385  -1.346  -1.393  -1.208  -1.213  -1.214  -1.044
102   T        -1.094  -1.146  -1.066  -0.964  -1.035  -0.926  -0.997  -1.038  -0.916
103   K        -1.094  -1.079  -1.048  -1.048  -1.035  -0.984  -0.997  -0.974  -0.899
104   E        -0.683  -0.699  -0.684  -0.868  -0.888  -0.844  -0.781  -0.792  -0.734
105   S         0.341   0.367   0.464   0.048   0.081   0.234  -0.025   0.005   0.133
106   L        -0.795  -0.784  -0.676  -0.905  -0.869  -0.703  -0.889  -0.867  -0.725
107   N        -1.207  -1.187  -1.065  -1.168  -1.137  -0.946  -1.105  -1.078  -0.916
108   S        -1.094  -1.052  -1.064  -1.145  -1.100  -1.103  -0.997  -0.957  -0.915
109   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
110   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
111   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
112   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
113   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
114   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
115   P        -0.369  -0.346  -0.608  -0.399  -0.372  -0.808  -0.349  -0.332  -0.642
116   L        -1.804  -1.781  -1.654  -1.562  -1.568  -1.384  -1.321  -1.300  -1.133
117   L        -0.610  -0.595  -0.648  -0.629  -0.593  -0.700  -0.673  -0.646  -0.689
118   T        -0.720  -0.735  -0.685  -0.754  -0.775  -0.757  -0.803  -0.815  -0.732
119   K        -0.610  -0.686  -0.657  -0.554  -0.666  -0.638  -0.673  -0.749  -0.699
120   N        -1.094  -1.146  -1.066  -1.081  -1.162  -1.055  -0.997  -1.038  -0.916
121   D         0.213   0.034  -0.094   0.364   0.085  -0.166   0.191  -0.071  -0.276
122   I        -0.071  -0.080  -0.111   0.005  -0.002  -0.098  -0.241  -0.241  -0.301
123   G        -0.071  -0.080  -0.111  -0.196  -0.201  -0.282  -0.241  -0.241  -0.301
124   S        -0.795  -0.796  -0.671  -1.051  -1.052  -0.862  -0.889  -0.880  -0.719
125   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
126   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
127   F         0.831   0.731   0.618   1.006   0.871   0.727   0.839   0.670   0.434
128   S         0.512   0.471   0.479   0.438   0.370   0.390   0.299   0.207   0.164
129   P        -0.071  -0.061  -0.125  -0.279  -0.247  -0.378  -0.241  -0.214  -0.322
130   E         0.450   0.542   0.545   0.200   0.352   0.336   0.184   0.339   0.295
131   F        -0.720  -0.756  -0.690  -0.608  -0.659  -0.540  -0.803  -0.836  -0.738
132   S        -1.094  -1.080  -1.065  -1.113  -1.090  -1.035  -0.997  -0.975  -0.916
133   K         0.831   0.731   0.618   0.939   0.798   0.609   0.839   0.670   0.434
134   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
135   T        -0.610  -0.686  -0.657  -0.618  -0.728  -0.724  -0.673  -0.749  -0.699
136   I        -0.610  -0.686  -0.657  -0.524  -0.592  -0.553  -0.673  -0.749  -0.699
137   P         0.302   0.098  -0.038   0.331   0.046  -0.152   0.315   0.018  -0.193
138   E         0.568   0.452   0.477   0.422   0.212   0.247   0.400   0.171   0.160
139   F         1.480   1.506   1.593   1.566   1.599   1.737   1.594   1.636   1.773
140   E         1.480   1.506   1.593   1.376   1.407   1.555   1.594   1.636   1.773
141   G         1.480   1.506   1.593   1.443   1.481   1.619   1.594   1.636   1.773
142   D         0.568   0.564   0.483   0.540   0.512   0.312   0.400   0.379   0.172
143   V        -0.134  -0.098  -0.155  -0.160  -0.077  -0.196  -0.368  -0.296  -0.374
144   N         1.480   1.506   1.593   1.600   1.636   1.770   1.594   1.636   1.773
145   P         1.480   1.506   1.593   1.371   1.409   1.551   1.594   1.636   1.773
146   K         0.879   0.925   0.613   0.997   1.044   0.631   0.912   0.979   0.423
147   T         1.480   1.506   1.593   1.535   1.577   1.708   1.594   1.636   1.773
148   G         1.480   1.506   1.593   1.443   1.481   1.619   1.594   1.636   1.773
149   E         1.480   1.506   1.593   1.376   1.407   1.555   1.594   1.636   1.773
150   V         0.018   0.074  -0.148   0.130   0.192  -0.160  -0.112  -0.056  -0.361
151   G         1.480   1.506   1.593   1.443   1.481   1.619   1.594   1.636   1.773
152   G         1.480   1.506   1.593   1.443   1.481   1.619   1.594   1.636   1.773
153   P         1.480   1.506   1.593   1.371   1.409   1.551   1.594   1.636   1.773
154   K         1.480   1.506   1.593   1.509   1.532   1.683   1.594   1.636   1.773
155   Q         0.018  -0.017  -0.068   0.111   0.062  -0.035  -0.112  -0.145  -0.237
156   D         0.297   0.318   0.437  -0.016  -0.011   0.193  -0.112  -0.092   0.080
157   P         1.480   1.506   1.593   1.371   1.409   1.551   1.594   1.636   1.773
158   L         0.879   0.715   0.638   0.948   0.732   0.611   0.912   0.645   0.472
159   R        -0.182  -0.263  -0.159  -0.367  -0.456  -0.276  -0.453  -0.530  -0.386
160   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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   H         0.568   0.711   0.597   0.733   0.954   0.738   0.400   0.637   0.394
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   G         0.879   0.841   0.601   0.922   0.878   0.525   0.912   0.849   0.401
167   D         0.879   0.841   0.601   1.003   0.945   0.558   0.912   0.849   0.401
168   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
169   Y         0.297   0.344   0.437   0.377   0.443   0.584  -0.112  -0.041   0.079
170   S         1.480   1.506   1.593   1.447   1.487   1.624   1.594   1.636   1.773
171   F         0.384   0.397   0.484   0.360   0.371   0.503   0.059   0.065   0.174
172   N         0.879   0.715   0.638   1.059   0.827   0.681   0.912   0.645   0.472
173   G         1.480   1.506   1.593   1.443   1.481   1.619   1.594   1.636   1.773
174   R         1.480   1.506   1.593   1.447   1.478   1.624   1.594   1.636   1.773
175   V         0.879   0.844   0.617   1.123   1.091   0.791   0.912   0.854   0.431
176   T         0.879   0.841   0.601   1.022   0.985   0.631   0.912   0.849   0.401
177   D         1.480   1.506   1.593   1.544   1.572   1.716   1.594   1.636   1.773
178   F         1.480   1.506   1.593   1.566   1.599   1.737   1.594   1.636   1.773
* 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/P38345
Output conservation file - output/P38345
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
