1     M         1.405   1.423   1.527   1.588   1.614   1.770   1.535   1.563   1.728
2     N        -1.810  -1.760  -1.691  -1.580  -1.524  -1.433  -1.354  -1.313  -1.184
3     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
4     -        -0.842  -0.834  -0.743  -1.014  -1.012  -0.880  -0.931  -0.918  -0.790
5     N        -0.933  -0.905  -0.775  -0.935  -0.888  -0.704  -1.033  -0.999  -0.826
6     K        -1.225  -1.175  -1.121  -1.233  -1.165  -1.066  -1.140  -1.091  -0.977
7     L         0.164   0.190  -0.101  -0.014   0.015  -0.339   0.144   0.174  -0.252
8     I        -1.115  -1.179  -1.103  -1.049  -1.145  -1.031  -1.033  -1.087  -0.961
9     Y        -0.541  -0.590  -0.679  -0.411  -0.497  -0.613  -0.562  -0.623  -0.715
10    R        -1.209  -1.195  -1.123  -1.434  -1.369  -1.226  -1.121  -1.100  -0.977
11    S        -0.374  -0.333  -0.270  -0.384  -0.338  -0.219  -0.657  -0.606  -0.505
12    V        -0.842  -0.860  -0.765  -0.840  -0.881  -0.762  -0.931  -0.950  -0.814
13    R        -0.842  -0.867  -0.765  -0.908  -0.945  -0.800  -0.931  -0.957  -0.814
14    F        -0.842  -0.817  -0.743  -0.702  -0.669  -0.578  -0.931  -0.900  -0.790
15    A         0.270   0.280   0.383   0.188   0.193   0.348  -0.109  -0.098   0.042
16    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
17    T        -0.415  -0.377  -0.278  -0.419  -0.361  -0.225  -0.701  -0.650  -0.515
18    H        -0.875  -0.849  -0.758  -1.013  -0.957  -0.829  -0.981  -0.949  -0.810
19    N        -0.749  -0.764  -0.734  -0.654  -0.670  -0.618  -0.841  -0.854  -0.782
20    -        -0.198  -0.261  -0.238  -0.315  -0.432  -0.424  -0.383  -0.477  -0.455
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    -        -1.227  -1.272  -1.149  -1.085  -1.135  -0.951  -1.129  -1.166  -1.000
27    -        -0.838  -0.860  -0.755  -0.932  -0.942  -0.778  -0.938  -0.952  -0.804
28    -        -0.749  -0.716  -0.711  -0.906  -0.827  -0.830  -0.841  -0.786  -0.754
29    -        -1.209  -1.141  -1.115  -1.214  -1.109  -1.073  -1.121  -1.059  -0.971
30    S        -1.810  -1.840  -1.711  -1.485  -1.551  -1.363  -1.354  -1.368  -1.197
31    Q        -1.810  -1.840  -1.711  -1.662  -1.722  -1.546  -1.354  -1.368  -1.197
32    L        -0.933  -1.008  -1.060  -0.758  -0.862  -0.991  -0.819  -0.897  -0.915
33    L         0.457   0.576   0.491   0.083   0.259   0.136   0.251   0.461   0.259
34    L         0.164   0.048  -0.120  -0.019  -0.166  -0.376   0.144  -0.021  -0.280
35    P         0.770   0.711   0.571   0.901   0.836   0.621   0.786   0.691   0.411
36    P         1.405   1.423   1.527   1.458   1.492   1.642   1.535   1.563   1.728
37    L         0.770   0.711   0.573   0.515   0.444   0.262   0.786   0.691   0.415
38    V        -1.407  -1.349  -1.384  -1.154  -1.050  -1.124  -1.140  -1.082  -1.060
39    L         1.405   1.423   1.527   1.069   1.093   1.259   1.535   1.563   1.728
40    Y         1.405   1.423   1.527   1.556   1.578   1.738   1.535   1.563   1.728
41    R         0.770   0.873   0.589   0.815   0.943   0.536   0.786   0.943   0.445
42    R        -0.113  -0.075  -0.177  -0.132  -0.064  -0.231  -0.284  -0.206  -0.367
43    I        -0.238  -0.280  -0.229  -0.480  -0.556  -0.475  -0.498  -0.546  -0.457
44    L         1.405   1.423   1.527   1.069   1.093   1.259   1.535   1.563   1.728
45    R         1.405   1.423   1.527   1.396   1.417   1.581   1.535   1.563   1.728
46    Q         0.164   0.231  -0.091   0.370   0.453  -0.035   0.144   0.239  -0.236
47    H         1.405   1.423   1.527   1.565   1.597   1.747   1.535   1.563   1.728
48    -        -0.198  -0.052  -0.213  -0.238  -0.026  -0.269  -0.383  -0.167  -0.418
49    K        -0.641  -0.560  -0.667  -0.672  -0.542  -0.677  -0.712  -0.604  -0.707
50    L        -1.225  -1.206  -1.130  -1.375  -1.301  -1.164  -1.140  -1.114  -0.984
51    L         1.405   1.423   1.527   1.069   1.093   1.259   1.535   1.563   1.728
52    P         0.164   0.048  -0.120   0.348   0.201  -0.071   0.144  -0.021  -0.280
53    G        -1.810  -1.760  -1.688  -1.540  -1.480  -1.363  -1.354  -1.312  -1.182
54    P        -0.641  -0.655  -0.696  -0.601  -0.610  -0.661  -0.712  -0.717  -0.740
55    Q        -1.115  -1.181  -1.117  -1.282  -1.333  -1.264  -1.033  -1.079  -0.971
56    R         0.770   0.797   0.586   0.815   0.850   0.532   0.786   0.829   0.440
57    E        -1.407  -1.416  -1.421  -1.351  -1.400  -1.395  -1.140  -1.148  -1.090
58    M         0.457   0.482   0.465   0.105   0.140   0.127   0.251   0.292   0.207
59    G         1.405   1.423   1.527   1.472   1.501   1.656   1.535   1.563   1.728
60    D         1.405   1.423   1.527   1.500   1.524   1.683   1.535   1.563   1.728
61    Q        -0.641  -0.713  -0.713  -0.652  -0.776  -0.773  -0.712  -0.802  -0.760
62    Y         1.405   1.423   1.527   1.556   1.578   1.738   1.535   1.563   1.728
63    V         0.770   0.711   0.571   1.001   0.935   0.719   0.786   0.691   0.411
64    R         0.770   0.792   0.586   0.761   0.797   0.491   0.786   0.821   0.439
65    N        -0.823  -0.760  -0.738  -0.781  -0.702  -0.666  -0.926  -0.864  -0.789
66    E         1.405   1.423   1.527   1.363   1.390   1.548   1.535   1.563   1.728
67    F         1.405   1.423   1.527   1.643   1.667   1.824   1.535   1.563   1.728
68    K        -0.238  -0.233  -0.235  -0.487  -0.484  -0.472  -0.498  -0.499  -0.463
69    L        -0.641  -0.614  -0.695  -0.924  -0.903  -0.952  -0.712  -0.682  -0.740
70    H         1.405   1.423   1.527   1.565   1.597   1.747   1.535   1.563   1.728
71    K         0.289   0.274   0.380  -0.011  -0.048   0.108  -0.070  -0.110   0.036
72    D        -1.225  -1.176  -1.115  -1.086  -1.018  -0.922  -1.140  -1.096  -0.973
73    I        -0.113  -0.122  -0.202   0.035   0.004  -0.096  -0.284  -0.322  -0.409
74    D         0.164   0.048  -0.120   0.394   0.236  -0.024   0.144  -0.021  -0.280
75    N         0.770   0.711   0.571   1.029   0.957   0.740   0.786   0.691   0.411
76    P         1.405   1.423   1.527   1.458   1.492   1.642   1.535   1.563   1.728
77    L         0.770   0.711   0.573   0.512   0.437   0.255   0.786   0.691   0.415
78    H         0.164   0.155  -0.106   0.456   0.444   0.053   0.144   0.128  -0.259
79    I         0.457   0.396   0.430   0.385   0.249   0.218   0.251   0.130   0.139
80    V         0.770   0.711   0.573   1.001   0.935   0.723   0.786   0.691   0.415
81    G         1.405   1.423   1.527   1.472   1.501   1.656   1.535   1.563   1.728
82    F         1.405   1.423   1.527   1.643   1.667   1.824   1.535   1.563   1.728
83    L         1.405   1.423   1.527   1.069   1.093   1.259   1.535   1.563   1.728
84    A        -0.349  -0.379  -0.289  -0.345  -0.409  -0.273  -0.605  -0.650  -0.529
85    S        -0.349  -0.334  -0.287  -0.472  -0.450  -0.423  -0.605  -0.584  -0.526
86    W         1.405   1.423   1.527   1.665   1.692   1.846   1.535   1.563   1.728
87    Q         0.770   0.717   0.579   0.852   0.781   0.561   0.786   0.700   0.427
88    D        -0.406  -0.566  -0.664  -0.272  -0.543  -0.793  -0.391  -0.590  -0.697
89    Y         1.405   1.423   1.527   1.556   1.578   1.738   1.535   1.563   1.728
90    L         0.457   0.396   0.430   0.076  -0.026   0.035   0.251   0.130   0.139
91    H        -1.115  -1.181  -1.117  -1.034  -1.105  -1.053  -1.033  -1.079  -0.971
92    M        -1.115  -1.111  -1.092  -0.958  -0.948  -0.942  -1.033  -1.021  -0.950
93    I         0.770   0.717   0.579   0.912   0.839   0.564   0.786   0.700   0.427
94    S        -1.225  -1.221  -1.131  -1.195  -1.206  -1.062  -1.140  -1.125  -0.985
95    N        -0.238  -0.197  -0.226  -0.246  -0.192  -0.219  -0.498  -0.455  -0.450
96    G        -0.406  -0.566  -0.664  -0.175  -0.400  -0.570  -0.391  -0.590  -0.697
97    K        -0.823  -0.815  -0.739  -0.927  -0.882  -0.787  -0.926  -0.904  -0.789
98    W         1.405   1.423   1.527   1.665   1.692   1.846   1.535   1.563   1.728
99    K        -1.407  -1.349  -1.404  -1.303  -1.220  -1.291  -1.140  -1.087  -1.076
100   D        -1.518  -1.456  -1.427  -1.379  -1.307  -1.214  -1.247  -1.194  -1.096
101   A        -0.238  -0.236  -0.234  -0.361  -0.379  -0.341  -0.498  -0.502  -0.462
102   T        -0.113  -0.063  -0.181  -0.154  -0.075  -0.240  -0.284  -0.207  -0.376
103   L         0.770   0.717   0.579   0.519   0.454   0.282   0.786   0.700   0.427
104   S         0.457   0.393   0.414   0.487   0.372   0.371   0.251   0.124   0.106
105   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
106   S        -1.518  -1.493  -1.422  -1.528  -1.511  -1.404  -1.247  -1.223  -1.092
107   E        -1.407  -1.418  -1.394  -1.174  -1.198  -1.181  -1.140  -1.148  -1.067
108   T        -1.225  -1.227  -1.120  -1.352  -1.363  -1.192  -1.140  -1.132  -0.976
109   L         0.770   0.711   0.573   0.519   0.449   0.273   0.786   0.691   0.415
110   E         0.164   0.190  -0.100   0.246   0.274  -0.138   0.144   0.174  -0.249
111   K         0.770   0.717   0.579   0.776   0.716   0.513   0.786   0.700   0.427
112   L         0.457   0.436   0.436   0.445   0.393   0.289   0.251   0.207   0.150
113   S         0.770   0.717   0.579   0.950   0.888   0.697   0.786   0.700   0.427
114   P         0.289   0.261   0.375   0.155   0.098   0.265  -0.070  -0.136   0.026
115   E         0.770   0.717   0.579   0.795   0.730   0.519   0.786   0.700   0.427
116   Q         1.405   1.423   1.527   1.430   1.452   1.614   1.535   1.563   1.728
117   T        -0.113  -0.065  -0.184   0.035   0.117  -0.066  -0.284  -0.209  -0.381
118   V        -0.113  -0.091  -0.201  -0.017   0.004  -0.141  -0.284  -0.269  -0.410
119   Q         1.405   1.423   1.527   1.430   1.452   1.614   1.535   1.563   1.728
120   L         1.405   1.423   1.527   1.069   1.093   1.259   1.535   1.563   1.728
121   Y         0.457   0.576   0.491   0.565   0.745   0.597   0.251   0.461   0.259
122   E         1.405   1.423   1.527   1.363   1.390   1.548   1.535   1.563   1.728
123   L         1.405   1.423   1.527   1.069   1.093   1.259   1.535   1.563   1.728
124   M         0.770   0.717   0.579   1.029   0.964   0.753   0.786   0.700   0.427
125   K        -0.349  -0.318  -0.269  -0.614  -0.562  -0.508  -0.605  -0.568  -0.501
126   E         0.236   0.257   0.376  -0.007   0.032   0.215  -0.177  -0.143   0.028
127   T        -0.712  -0.777  -0.706  -0.679  -0.785  -0.695  -0.819  -0.874  -0.756
128   Q        -0.349  -0.239  -0.241  -0.572  -0.370  -0.429  -0.605  -0.445  -0.460
129   K        -0.406  -0.469  -0.640  -0.343  -0.433  -0.708  -0.391  -0.472  -0.668
130   L        -1.810  -1.801  -1.704  -1.906  -1.911  -1.682  -1.354  -1.344  -1.192
131   H        -0.712  -0.687  -0.705  -0.750  -0.714  -0.692  -0.819  -0.787  -0.755
132   Q        -1.518  -1.462  -1.420  -1.439  -1.359  -1.286  -1.247  -1.201  -1.091
133   D        -0.301  -0.231  -0.242  -0.449  -0.333  -0.357  -0.558  -0.454  -0.466
134   N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
135   E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
136   I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
137   E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
138   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
139   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
140   K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
141   D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
142   V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
143   K        -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   R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
146   N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
147   N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
148   K        -0.238  -0.198  -0.226  -0.367  -0.321  -0.342  -0.498  -0.456  -0.452
149   D        -1.115  -1.160  -1.090  -1.086  -1.150  -1.039  -1.033  -1.064  -0.948
* 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/Q04401
Output conservation file - output/Q04401
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
