1     M         1.315   1.320   1.342   1.496   1.506   1.533   1.389   1.394   1.422
2     L         0.013   0.019  -0.015  -0.112  -0.104  -0.156  -0.179  -0.169  -0.232
3     F        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
4     Y        -0.933  -0.925  -0.875  -0.888  -0.870  -0.791  -0.964  -0.949  -0.877
5     K         0.013   0.007  -0.016  -0.055  -0.057  -0.138  -0.179  -0.188  -0.233
6     P         0.013   0.007  -0.016  -0.017  -0.029  -0.069  -0.179  -0.188  -0.233
7     V         0.013   0.007  -0.016  -0.203  -0.213  -0.260  -0.179  -0.188  -0.233
8     M        -0.933  -0.925  -0.875  -0.904  -0.891  -0.806  -0.964  -0.949  -0.877
9     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
10    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
11    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
12    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
13    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
14    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
15    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
16    R         1.315   1.320   1.342   1.434   1.440   1.472   1.389   1.394   1.422
17    M        -0.933  -0.925  -0.875  -0.904  -0.889  -0.806  -0.964  -0.949  -0.877
18    A         1.315   1.320   1.342   1.228   1.235   1.272   1.389   1.394   1.422
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    -        -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    V         0.013   0.032  -0.013  -0.138  -0.107  -0.175  -0.179  -0.148  -0.227
27    R         0.013   0.032  -0.013  -0.011   0.024  -0.076  -0.179  -0.148  -0.227
28    P         1.315   1.320   1.342   1.380   1.385   1.420   1.389   1.394   1.422
29    L         0.013   0.032  -0.013  -0.118  -0.088  -0.159  -0.179  -0.148  -0.227
30    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
31    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
32    K        -0.933  -0.925  -0.875  -1.099  -1.072  -0.997  -0.964  -0.949  -0.877
33    S        -0.933  -0.925  -0.875  -0.954  -0.937  -0.855  -0.964  -0.949  -0.877
34    I        -0.933  -0.925  -0.875  -0.962  -0.951  -0.863  -0.964  -0.949  -0.877
35    R         1.315   1.320   1.342   1.434   1.440   1.472   1.389   1.394   1.422
36    F         1.315   1.320   1.342   1.339   1.346   1.380   1.389   1.394   1.422
37    Q         1.315   1.320   1.342   1.501   1.506   1.537   1.389   1.394   1.422
38    S         1.315   1.320   1.342   1.353   1.359   1.393   1.389   1.394   1.422
39    S         0.013   0.019  -0.015  -0.030  -0.019  -0.083  -0.179  -0.169  -0.232
40    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
41    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
42    Y         0.013   0.019  -0.015   0.111   0.122   0.048  -0.179  -0.169  -0.232
43    T        -0.933  -0.925  -0.875  -0.954  -0.939  -0.855  -0.964  -0.949  -0.877
44    S        -0.103  -0.094  -0.057  -0.210  -0.191  -0.131  -0.376  -0.359  -0.302
45    I         0.164   0.074   0.040   0.183   0.025  -0.038   0.066  -0.079  -0.139
46    T        -0.813  -0.842  -0.836  -0.857  -0.859  -0.855  -0.817  -0.851  -0.830
47    K        -1.522  -1.501  -1.456  -1.238  -1.185  -1.132  -1.258  -1.231  -1.165
48    L        -0.813  -0.844  -0.832  -0.895  -0.932  -0.924  -0.817  -0.854  -0.826
49    T        -0.813  -0.844  -0.832  -0.969  -1.045  -1.026  -0.817  -0.854  -0.826
50    N        -0.103  -0.091  -0.056  -0.141  -0.130  -0.064  -0.376  -0.355  -0.300
51    L         0.164   0.074   0.040   0.098  -0.040  -0.116   0.066  -0.079  -0.139
52    T        -1.522  -1.501  -1.456  -1.386  -1.402  -1.276  -1.258  -1.231  -1.165
53    E         1.315   1.320   1.342   1.422   1.425   1.461   1.389   1.394   1.422
54    F         0.164   0.199   0.059   0.162   0.216  -0.022   0.066   0.120  -0.108
55    R        -1.522  -1.501  -1.456  -1.334  -1.314  -1.225  -1.258  -1.231  -1.165
56    N        -1.522  -1.501  -1.456  -1.476  -1.416  -1.364  -1.258  -1.231  -1.165
57    L        -0.103  -0.094  -0.057  -0.461  -0.453  -0.376  -0.376  -0.359  -0.302
58    I        -0.103  -0.092  -0.055  -0.133  -0.119  -0.056  -0.376  -0.355  -0.300
59    K         0.164   0.074   0.040  -0.052  -0.195  -0.270   0.066  -0.079  -0.139
60    Q        -1.522  -1.501  -1.456  -1.569  -1.545  -1.455  -1.258  -1.231  -1.165
61    N        -1.522  -1.501  -1.456  -1.200  -1.145  -1.095  -1.258  -1.231  -1.165
62    D        -0.813  -0.842  -0.836  -0.640  -0.696  -0.692  -0.817  -0.851  -0.830
63    K        -0.813  -0.842  -0.836  -0.929  -0.951  -0.970  -0.817  -0.851  -0.830
64    L        -0.813  -0.842  -0.836  -0.809  -0.856  -0.866  -0.817  -0.851  -0.830
65    V         0.164   0.223   0.071   0.069   0.164  -0.082   0.066   0.157  -0.089
66    I        -0.813  -0.830  -0.835  -0.857  -0.887  -0.906  -0.817  -0.837  -0.829
67    D         1.315   1.320   1.342   1.336   1.340   1.377   1.389   1.394   1.422
68    F         0.164   0.074   0.040   0.133  -0.037  -0.098   0.066  -0.079  -0.139
69    Y        -0.103  -0.094  -0.057  -0.126  -0.114  -0.049  -0.376  -0.359  -0.302
70    A         1.315   1.320   1.342   1.137   1.124   1.183   1.389   1.394   1.422
71    T         1.315   1.320   1.342   1.336   1.338   1.377   1.389   1.394   1.422
72    W         1.315   1.320   1.342   1.610   1.614   1.644   1.389   1.394   1.422
73    C         1.315   1.320   1.342   1.558   1.565   1.594   1.389   1.394   1.422
74    G         1.315   1.320   1.342   1.390   1.401   1.429   1.389   1.394   1.422
75    P         1.315   1.320   1.342   1.368   1.371   1.408   1.389   1.394   1.422
76    C         1.315   1.320   1.342   1.558   1.565   1.594   1.389   1.394   1.422
77    K         1.315   1.320   1.342   1.148   1.178   1.194   1.389   1.394   1.422
78    M         0.164   0.203   0.056   0.058   0.095  -0.082   0.066   0.126  -0.113
79    M        -0.813  -0.830  -0.835  -0.699  -0.729  -0.755  -0.817  -0.837  -0.829
80    Q        -0.813  -0.765  -0.827  -0.939  -0.885  -0.937  -0.817  -0.753  -0.820
81    P         1.315   1.320   1.342   1.368   1.371   1.408   1.389   1.394   1.422
82    H        -0.813  -0.844  -0.832  -0.601  -0.666  -0.653  -0.817  -0.854  -0.826
83    L        -0.103  -0.094  -0.057  -0.395  -0.368  -0.310  -0.376  -0.359  -0.302
84    T        -1.522  -1.501  -1.456  -1.422  -1.426  -1.311  -1.258  -1.231  -1.165
85    K         1.315   1.320   1.342   1.148   1.178   1.194   1.389   1.394   1.422
86    L        -0.813  -0.844  -0.832  -0.735  -0.749  -0.740  -0.817  -0.854  -0.826
87    I        -0.813  -0.765  -0.827  -0.772  -0.679  -0.806  -0.817  -0.753  -0.820
88    Q        -0.813  -0.765  -0.827  -0.649  -0.576  -0.668  -0.817  -0.753  -0.820
89    A        -1.522  -1.501  -1.456  -1.519  -1.463  -1.406  -1.258  -1.231  -1.165
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    Y         0.164   0.074   0.040   0.324   0.173   0.080   0.066  -0.079  -0.139
94    P        -1.522  -1.501  -1.456  -1.446  -1.406  -1.334  -1.258  -1.231  -1.165
95    D        -0.813  -0.830  -0.835  -0.726  -0.766  -0.748  -0.817  -0.837  -0.829
96    V         1.315   1.320   1.342   1.226   1.232   1.270   1.389   1.394   1.422
97    R        -0.813  -0.842  -0.836  -0.814  -0.816  -0.806  -0.817  -0.851  -0.830
98    F         1.315   1.320   1.342   1.336   1.341   1.377   1.389   1.394   1.422
99    V        -0.813  -0.842  -0.836  -0.763  -0.845  -0.841  -0.817  -0.851  -0.830
100   K         1.315   1.320   1.342   1.148   1.178   1.194   1.389   1.394   1.422
101   C        -0.813  -0.842  -0.836  -0.795  -0.846  -0.803  -0.817  -0.851  -0.830
102   D         1.315   1.320   1.342   1.336   1.340   1.377   1.389   1.394   1.422
103   V         1.315   1.320   1.342   1.226   1.232   1.270   1.389   1.394   1.422
104   D         1.315   1.320   1.342   1.336   1.340   1.377   1.389   1.394   1.422
105   E         0.164   0.074   0.040   0.218   0.045  -0.021   0.066  -0.079  -0.139
106   S         0.164   0.074   0.040   0.249   0.114   0.031   0.066  -0.079  -0.139
107   P         1.315   1.320   1.342   1.368   1.371   1.408   1.389   1.394   1.422
108   D         1.315   1.320   1.342   1.336   1.340   1.377   1.389   1.394   1.422
109   I        -0.813  -0.844  -0.832  -0.857  -0.912  -0.900  -0.817  -0.854  -0.826
110   A         1.315   1.320   1.342   1.137   1.124   1.183   1.389   1.394   1.422
111   K        -1.522  -1.501  -1.456  -1.380  -1.312  -1.271  -1.258  -1.231  -1.165
112   E        -0.813  -0.751  -0.817  -0.726  -0.626  -0.738  -0.817  -0.736  -0.809
113   C        -0.813  -0.765  -0.827  -0.676  -0.596  -0.668  -0.817  -0.753  -0.820
114   E         0.164   0.203   0.056   0.276   0.339   0.107   0.066   0.126  -0.113
115   V        -0.103  -0.094  -0.057  -0.329  -0.310  -0.244  -0.376  -0.359  -0.302
116   T        -0.813  -0.842  -0.836  -0.676  -0.704  -0.710  -0.817  -0.851  -0.830
117   A         0.164   0.223   0.071   0.029   0.099  -0.100   0.066   0.157  -0.089
118   M         1.315   1.320   1.342   1.496   1.506   1.533   1.389   1.394   1.422
119   P         1.315   1.320   1.342   1.368   1.371   1.408   1.389   1.394   1.422
120   T         1.315   1.320   1.342   1.336   1.338   1.377   1.389   1.394   1.422
121   F         1.315   1.320   1.342   1.336   1.341   1.377   1.389   1.394   1.422
122   V         1.315   1.320   1.342   1.226   1.232   1.270   1.389   1.394   1.422
123   L        -0.813  -0.844  -0.832  -0.847  -0.886  -0.868  -0.817  -0.854  -0.826
124   G        -0.813  -0.765  -0.827  -0.777  -0.700  -0.795  -0.817  -0.753  -0.820
125   K         1.315   1.320   1.342   1.148   1.178   1.194   1.389   1.394   1.422
126   D        -0.103  -0.094  -0.057  -0.141  -0.118  -0.060  -0.376  -0.359  -0.302
127   G         0.164   0.199   0.059   0.249   0.308   0.075   0.066   0.120  -0.108
128   Q        -0.813  -0.748  -0.815  -0.800  -0.684  -0.802  -0.817  -0.732  -0.806
129   L        -1.522  -1.501  -1.456  -1.557  -1.519  -1.442  -1.258  -1.231  -1.165
130   I        -0.813  -0.842  -0.836  -0.934  -1.001  -0.976  -0.817  -0.851  -0.830
131   G        -0.813  -0.844  -0.832  -0.654  -0.709  -0.673  -0.817  -0.854  -0.826
132   K         0.164   0.074   0.040   0.044  -0.069  -0.131   0.066  -0.079  -0.139
133   I        -0.813  -0.830  -0.835  -0.828  -0.861  -0.872  -0.817  -0.837  -0.829
134   I        -0.813  -0.765  -0.827  -0.824  -0.751  -0.825  -0.817  -0.753  -0.820
135   G         1.315   1.320   1.342   1.390   1.401   1.429   1.389   1.394   1.422
136   A         1.315   1.320   1.342   1.137   1.124   1.183   1.389   1.394   1.422
137   N         0.164   0.223   0.071   0.361   0.454   0.199   0.066   0.157  -0.089
138   P         1.315   1.320   1.342   1.368   1.371   1.408   1.389   1.394   1.422
139   T        -1.522  -1.501  -1.456  -1.464  -1.416  -1.352  -1.258  -1.231  -1.165
140   A        -0.103  -0.092  -0.055  -0.370  -0.373  -0.290  -0.376  -0.355  -0.300
141   L         0.164   0.223   0.071   0.098   0.206  -0.061   0.066   0.157  -0.089
142   E        -0.813  -0.844  -0.832  -0.838  -0.902  -0.894  -0.817  -0.854  -0.826
143   K        -0.813  -0.830  -0.835  -1.014  -1.054  -1.036  -0.817  -0.837  -0.829
144   G        -0.813  -0.842  -0.836  -0.949  -1.008  -0.959  -0.817  -0.851  -0.830
145   I         1.315   1.320   1.342   1.358   1.361   1.398   1.389   1.394   1.422
146   K        -0.813  -0.844  -0.832  -0.925  -0.956  -0.928  -0.817  -0.854  -0.826
147   D        -1.522  -1.501  -1.456  -1.380  -1.367  -1.271  -1.258  -1.231  -1.165
148   L        -0.813  -0.842  -0.836  -0.749  -0.775  -0.776  -0.817  -0.851  -0.830
149   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
150   -         0.013  -0.033  -0.016  -0.215  -0.284  -0.257  -0.179  -0.255  -0.233
* 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/P25372
Output conservation file - output/P25372
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
