1     M         1.704   1.727   1.751   2.029   2.059   2.098   1.826   1.854   1.889
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     G        -0.671  -0.718  -0.693  -0.421  -0.490  -0.448  -0.672  -0.725  -0.685
5     K        -0.671  -0.703  -0.689  -0.724  -0.729  -0.743  -0.672  -0.707  -0.680
6     K        -1.462  -1.421  -1.397  -1.276  -1.170  -1.164  -1.171  -1.116  -1.076
7     T        -0.671  -0.688  -0.687  -0.841  -0.899  -0.875  -0.672  -0.690  -0.677
8     F        -0.805  -0.778  -0.744  -0.751  -0.710  -0.646  -0.838  -0.795  -0.746
9     R        -1.462  -1.421  -1.397  -1.276  -1.237  -1.164  -1.171  -1.116  -1.076
10    E         1.704   1.727   1.751   1.650   1.692   1.723   1.826   1.854   1.889
11    W         1.704   1.727   1.751   1.993   2.030   2.063   1.826   1.854   1.889
12    Q        -0.671  -0.718  -0.693  -0.538  -0.646  -0.587  -0.672  -0.725  -0.685
13    Y         1.704   1.727   1.751   1.946   1.976   2.015   1.826   1.854   1.889
14    F         0.420   0.287   0.296   0.550   0.306   0.325   0.327   0.110   0.117
15    K        -0.671  -0.703  -0.689  -0.904  -0.950  -0.952  -0.672  -0.707  -0.680
16    L         1.704   1.727   1.751   1.470   1.487   1.546   1.826   1.854   1.889
17    S        -0.671  -0.718  -0.693  -0.858  -0.933  -0.897  -0.672  -0.725  -0.685
18    I         0.121   0.153   0.185  -0.126  -0.063  -0.008  -0.172  -0.118  -0.073
19    T        -0.671  -0.703  -0.689  -0.553  -0.612  -0.576  -0.672  -0.707  -0.680
20    S        -0.671  -0.703  -0.689  -0.675  -0.712  -0.679  -0.672  -0.707  -0.680
21    F        -0.805  -0.779  -0.744  -0.617  -0.573  -0.513  -0.838  -0.796  -0.746
22    D        -0.671  -0.703  -0.689  -0.774  -0.803  -0.797  -0.672  -0.707  -0.680
23    Q        -0.671  -0.688  -0.687  -0.681  -0.706  -0.683  -0.672  -0.690  -0.677
24    D        -0.671  -0.718  -0.693  -0.670  -0.701  -0.684  -0.672  -0.725  -0.685
25    V        -0.671  -0.718  -0.693  -0.746  -0.829  -0.793  -0.672  -0.725  -0.685
26    D         1.704   1.727   1.751   1.662   1.695   1.736   1.826   1.854   1.889
27    D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
28    A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
29    H        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
30    A        -1.462  -1.421  -1.397  -1.223  -1.177  -1.112  -1.171  -1.116  -1.076
31    I         0.420   0.474   0.348   0.382   0.460   0.268   0.327   0.413   0.203
32    D         1.704   1.727   1.751   1.662   1.695   1.736   1.826   1.854   1.889
33    Q        -1.462  -1.421  -1.397  -1.488  -1.407  -1.373  -1.171  -1.116  -1.076
34    M        -0.671  -0.688  -0.687  -0.590  -0.648  -0.602  -0.672  -0.690  -0.677
35    T         0.420   0.287   0.296   0.479   0.245   0.252   0.327   0.110   0.117
36    W         0.420   0.287   0.296   0.605   0.344   0.345   0.327   0.110   0.117
37    R        -0.671  -0.589  -0.659  -0.681  -0.517  -0.680  -0.672  -0.559  -0.643
38    Q         0.420   0.287   0.296   0.682   0.484   0.496   0.327   0.110   0.117
39    W        -1.462  -1.421  -1.397  -1.243  -1.242  -1.131  -1.171  -1.116  -1.076
40    L        -0.671  -0.703  -0.689  -0.963  -1.027  -0.973  -0.672  -0.707  -0.680
41    N        -0.671  -0.703  -0.689  -0.543  -0.592  -0.590  -0.672  -0.707  -0.680
42    N        -0.671  -0.718  -0.693  -0.611  -0.743  -0.678  -0.672  -0.725  -0.685
43    A         1.704   1.727   1.751   1.836   1.878   1.908   1.826   1.854   1.889
44    L         1.704   1.727   1.751   1.470   1.487   1.546   1.826   1.854   1.889
45    K        -0.671  -0.703  -0.689  -0.590  -0.601  -0.589  -0.672  -0.707  -0.680
46    R        -0.671  -0.703  -0.689  -0.497  -0.527  -0.534  -0.672  -0.707  -0.680
47    S         1.704   1.727   1.751   1.637   1.661   1.711   1.826   1.854   1.889
48    Y        -0.671  -0.688  -0.687  -0.351  -0.403  -0.376  -0.672  -0.690  -0.677
49    G         1.704   1.727   1.751   1.897   1.920   1.968   1.826   1.854   1.889
50    I        -0.671  -0.589  -0.659  -0.870  -0.727  -0.855  -0.672  -0.559  -0.643
51    F         1.704   1.727   1.751   1.873   1.897   1.944   1.826   1.854   1.889
52    G         1.704   1.727   1.751   1.897   1.920   1.968   1.826   1.854   1.889
53    E         0.420   0.287   0.296   0.320   0.098   0.104   0.327   0.110   0.117
54    G        -0.671  -0.550  -0.643  -0.476  -0.278  -0.423  -0.672  -0.510  -0.622
55    V         0.420   0.528   0.368   0.382   0.541   0.302   0.327   0.496   0.236
56    E         0.420   0.287   0.296   0.455   0.279   0.296   0.327   0.110   0.117
57    Y        -0.671  -0.703  -0.689  -0.659  -0.740  -0.727  -0.672  -0.707  -0.680
58    S        -1.462  -1.421  -1.397  -1.488  -1.421  -1.373  -1.171  -1.116  -1.076
59    F        -0.671  -0.589  -0.659  -0.585  -0.451  -0.570  -0.672  -0.559  -0.643
60    L         1.704   1.727   1.751   1.470   1.487   1.546   1.826   1.854   1.889
61    H        -0.671  -0.589  -0.659  -0.431  -0.289  -0.416  -0.672  -0.559  -0.643
62    V        -0.671  -0.703  -0.689  -0.638  -0.668  -0.660  -0.672  -0.707  -0.680
63    D         0.420   0.287   0.296   0.423   0.231   0.244   0.327   0.110   0.117
64    D        -0.671  -0.688  -0.687  -0.606  -0.656  -0.659  -0.672  -0.690  -0.677
65    K         0.420   0.474   0.348   0.291   0.401   0.152   0.327   0.413   0.203
66    L        -1.462  -1.421  -1.397  -1.467  -1.368  -1.352  -1.171  -1.116  -1.076
67    A        -0.671  -0.718  -0.693  -0.697  -0.820  -0.756  -0.672  -0.725  -0.685
68    Y         0.121   0.144   0.179   0.019   0.069   0.128  -0.172  -0.133  -0.083
69    I        -0.671  -0.718  -0.693  -0.830  -0.958  -0.873  -0.672  -0.725  -0.685
70    R         0.121   0.144   0.179   0.001   0.070   0.110  -0.172  -0.133  -0.083
71    V         0.121   0.148   0.181   0.167   0.268   0.283  -0.172  -0.127  -0.080
72    N        -1.462  -1.421  -1.397  -1.185  -1.108  -1.074  -1.171  -1.116  -1.076
73    H        -1.462  -1.421  -1.397  -1.276  -1.229  -1.164  -1.171  -1.116  -1.076
74    A        -0.671  -0.718  -0.693  -0.569  -0.654  -0.607  -0.672  -0.725  -0.685
75    D         1.704   1.727   1.751   1.662   1.695   1.736   1.826   1.854   1.889
76    K         0.420   0.474   0.348   0.402   0.509   0.294   0.327   0.413   0.203
77    D         0.420   0.287   0.296   0.345   0.131   0.133   0.327   0.110   0.117
78    T        -0.671  -0.688  -0.687  -0.752  -0.788  -0.772  -0.672  -0.690  -0.677
79    F        -0.671  -0.703  -0.689  -0.691  -0.754  -0.749  -0.672  -0.707  -0.680
80    S        -1.462  -1.421  -1.397  -1.666  -1.621  -1.549  -1.171  -1.116  -1.076
81    S        -0.671  -0.688  -0.687  -0.675  -0.701  -0.713  -0.672  -0.690  -0.677
82    S         0.420   0.528   0.368   0.503   0.686   0.409   0.327   0.496   0.236
83    I         0.121   0.148   0.181  -0.336  -0.317  -0.236  -0.172  -0.127  -0.080
84    S        -0.671  -0.703  -0.689  -0.675  -0.712  -0.679  -0.672  -0.707  -0.680
85    T         0.420   0.287   0.296   0.479   0.245   0.252   0.327   0.110   0.117
86    Y         1.704   1.727   1.751   1.946   1.976   2.015   1.826   1.854   1.889
87    I         0.420   0.287   0.296   0.382   0.158   0.180   0.327   0.110   0.117
88    S         0.250   0.260   0.229   0.103   0.112   0.073   0.050   0.065   0.002
89    T         0.250   0.283   0.234   0.074   0.119   0.047   0.050   0.103   0.012
90    D         0.250   0.260   0.233   0.074   0.081   0.044   0.050   0.065   0.009
91    E         1.704   1.727   1.751   1.616   1.653   1.690   1.826   1.854   1.889
92    L         1.704   1.727   1.751   1.503   1.537   1.578   1.826   1.854   1.889
93    V         1.704   1.727   1.751   1.759   1.783   1.831   1.826   1.854   1.889
94    G         1.704   1.727   1.751   1.914   1.942   1.984   1.826   1.854   1.889
95    S         0.250   0.260   0.229   0.074   0.081   0.037   0.050   0.065   0.002
96    P         0.250   0.260   0.229   0.422   0.434   0.344   0.050   0.065   0.002
97    L         1.704   1.727   1.751   1.503   1.537   1.578   1.826   1.854   1.889
98    T        -0.805  -0.792  -0.744  -0.913  -0.888  -0.805  -0.838  -0.811  -0.746
99    V         0.250   0.283   0.234   0.140   0.200   0.107   0.050   0.103   0.012
100   S        -0.805  -0.792  -0.744  -0.874  -0.852  -0.767  -0.838  -0.811  -0.746
101   I        -0.805  -0.792  -0.744  -0.751  -0.718  -0.645  -0.838  -0.811  -0.746
102   L         0.250   0.260   0.233  -0.124  -0.100  -0.160   0.050   0.065   0.009
103   Q        -0.671  -0.718  -0.693  -0.512  -0.568  -0.557  -0.672  -0.725  -0.685
104   E         0.420   0.474   0.348   0.410   0.507   0.312   0.327   0.413   0.203
105   S        -0.671  -0.703  -0.689  -0.611  -0.630  -0.606  -0.672  -0.707  -0.680
106   S        -0.671  -0.718  -0.693  -0.741  -0.824  -0.760  -0.672  -0.725  -0.685
107   S        -0.671  -0.571  -0.652  -0.512  -0.326  -0.483  -0.672  -0.536  -0.634
108   L         0.420   0.287   0.296   0.156  -0.080  -0.044   0.327   0.110   0.117
109   R        -0.671  -0.589  -0.659  -0.502  -0.361  -0.486  -0.672  -0.559  -0.643
110   L        -0.671  -0.589  -0.659  -0.774  -0.671  -0.726  -0.672  -0.559  -0.643
111   L         0.420   0.287   0.296   0.279   0.092   0.132   0.327   0.110   0.117
112   E        -0.805  -0.792  -0.744  -0.893  -0.863  -0.786  -0.838  -0.811  -0.746
113   V         0.250   0.260   0.233   0.066   0.077   0.005   0.050   0.065   0.009
114   T        -0.805  -0.792  -0.744  -0.535  -0.504  -0.432  -0.838  -0.811  -0.746
115   D         0.250   0.283   0.234  -0.008   0.051  -0.046   0.050   0.103   0.012
116   D         1.704   1.727   1.751   1.632   1.656   1.706   1.826   1.854   1.889
117   D         1.704   1.727   1.751   1.632   1.656   1.706   1.826   1.854   1.889
118   R         0.250   0.260   0.233   0.318   0.357   0.258   0.050   0.065   0.009
119   L         0.250   0.260   0.229  -0.077  -0.052  -0.111   0.050   0.065   0.002
120   W         1.704   1.727   1.751   1.975   2.004   2.044   1.826   1.854   1.889
121   L         0.250   0.283   0.234   0.183   0.243   0.119   0.050   0.103   0.012
122   K         0.250   0.260   0.233   0.147   0.183   0.128   0.050   0.065   0.009
123   K         1.704   1.727   1.751   1.648   1.701   1.722   1.826   1.854   1.889
124   V        -0.671  -0.589  -0.659  -0.835  -0.683  -0.827  -0.672  -0.559  -0.643
125   M        -0.671  -0.688  -0.687  -0.675  -0.763  -0.700  -0.672  -0.690  -0.677
126   E         0.420   0.287   0.296   0.435   0.251   0.268   0.327   0.110   0.117
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   E        -0.671  -0.550  -0.643  -0.681  -0.449  -0.637  -0.672  -0.510  -0.622
134   E         0.420   0.287   0.296   0.320   0.098   0.104   0.327   0.110   0.117
135   E        -1.462  -1.421  -1.397  -1.496  -1.425  -1.381  -1.171  -1.116  -1.076
136   Q        -1.462  -1.421  -1.397  -1.236  -1.156  -1.125  -1.171  -1.116  -1.076
137   D        -0.671  -0.718  -0.693  -0.670  -0.701  -0.684  -0.672  -0.725  -0.685
138   C         0.250   0.293   0.261   0.443   0.521   0.442   0.050   0.119   0.057
139   K        -0.805  -0.779  -0.744  -0.893  -0.818  -0.786  -0.838  -0.796  -0.746
140   C        -0.805  -0.779  -0.744  -0.560  -0.530  -0.458  -0.838  -0.796  -0.746
141   I        -0.805  -0.779  -0.744  -1.140  -1.090  -1.030  -0.838  -0.796  -0.746
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     *
* 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/P38208
Output conservation file - output/P38208
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
