1     M         1.451   1.459   1.467   1.905   1.921   1.930   1.529   1.537   1.547
2     L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
3     S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
4     N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
5     A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
6     K        -0.273  -0.268  -0.252   0.279   0.289   0.309  -0.449  -0.438  -0.413
7     L        -0.133  -0.103  -0.167   0.163   0.205   0.095  -0.229  -0.183  -0.281
8     L        -0.133  -0.189  -0.195   0.127   0.058   0.055  -0.229  -0.314  -0.323
9     L        -1.282  -1.268  -1.257  -1.424  -1.345  -1.388  -1.108  -1.086  -1.067
10    S        -1.282  -1.268  -1.257  -1.301  -1.267  -1.266  -1.108  -1.086  -1.067
11    L        -0.133  -0.189  -0.195  -0.006  -0.104  -0.106  -0.229  -0.314  -0.323
12    A        -1.282  -1.268  -1.257  -1.435  -1.347  -1.400  -1.108  -1.086  -1.067
13    M        -0.133  -0.103  -0.167   0.134   0.173   0.096  -0.229  -0.183  -0.281
14    -         1.451   1.459   1.467   1.719   1.735   1.745   1.529   1.537   1.547
15    A        -1.282  -1.268  -1.257  -1.818  -1.846  -1.782  -1.108  -1.086  -1.067
16    S        -1.282  -1.268  -1.257  -1.162  -1.120  -1.128  -1.108  -1.086  -1.067
17    T        -0.133  -0.189  -0.195  -0.692  -0.758  -0.748  -0.229  -0.314  -0.323
18    A         1.451   1.459   1.467   1.375   1.384   1.402   1.529   1.537   1.547
19    L        -0.133  -0.189  -0.195   0.061  -0.022  -0.025  -0.229  -0.314  -0.323
20    G        -0.273  -0.268  -0.252  -0.215  -0.208  -0.184  -0.449  -0.438  -0.413
21    L        -0.273  -0.268  -0.252  -0.390  -0.383  -0.358  -0.449  -0.438  -0.413
22    V        -0.273  -0.268  -0.252  -0.048  -0.040  -0.017  -0.449  -0.438  -0.413
23    S        -0.273  -0.268  -0.252  -0.360  -0.353  -0.328  -0.449  -0.438  -0.413
24    N         1.451   1.459   1.467   1.745   1.761   1.770   1.529   1.537   1.547
25    S        -0.273  -0.268  -0.252  -0.375  -0.368  -0.343  -0.449  -0.438  -0.413
26    S        -0.273  -0.268  -0.252  -0.953  -0.949  -0.919  -0.449  -0.438  -0.413
27    S         1.451   1.459   1.467   1.373   1.388   1.400   1.529   1.537   1.547
28    S         1.451   1.459   1.467   1.373   1.388   1.400   1.529   1.537   1.547
29    V        -0.273  -0.268  -0.252  -0.021  -0.013   0.010  -0.449  -0.438  -0.413
30    I         1.451   1.459   1.467   1.745   1.761   1.770   1.529   1.537   1.547
31    V        -0.273  -0.268  -0.252  -0.230  -0.222  -0.198  -0.449  -0.438  -0.413
32    V         1.451   1.459   1.467   1.552   1.568   1.578   1.529   1.537   1.547
33    P         1.451   1.459   1.467   1.572   1.587   1.598   1.529   1.537   1.547
34    S        -0.273  -0.268  -0.252  -0.953  -0.949  -0.919  -0.449  -0.438  -0.413
35    S        -0.273  -0.268  -0.252  -0.230  -0.222  -0.198  -0.449  -0.438  -0.413
36    D        -0.273  -0.268  -0.252   0.151   0.160   0.182  -0.449  -0.438  -0.413
37    A        -0.273  -0.268  -0.252  -0.988  -0.984  -0.954  -0.449  -0.438  -0.413
38    T         1.451   1.459   1.467   0.797   0.810   0.826   1.529   1.537   1.547
39    I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
40    A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
41    G        -0.273  -0.268  -0.252  -0.187  -0.179  -0.155  -0.449  -0.438  -0.413
42    N        -0.273  -0.268  -0.252  -0.089  -0.081  -0.058  -0.449  -0.438  -0.413
43    D         1.451   1.459   1.467   1.857   1.874   1.882   1.529   1.537   1.547
44    T        -0.273  -0.268  -0.252  -0.782  -0.778  -0.749  -0.449  -0.438  -0.413
45    A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
46    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
47    P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
48    A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
49    P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
50    E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
51    P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
52    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
53    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
54    A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
55    A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
56    P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
57    I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
58    F        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
59    Y        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
60    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
61    S        -0.133  -0.189  -0.195  -0.253  -0.354  -0.368  -0.229  -0.314  -0.323
62    T         1.451   1.459   1.467   0.789   0.811   0.817   1.529   1.537   1.547
63    A         1.451   1.459   1.467   1.375   1.384   1.402   1.529   1.537   1.547
64    T        -1.282  -1.268  -1.257  -1.141  -1.114  -1.107  -1.108  -1.086  -1.067
65    A        -1.282  -1.268  -1.257  -0.980  -0.941  -0.946  -1.108  -1.086  -1.067
66    T         1.451   1.459   1.467   0.789   0.811   0.817   1.529   1.537   1.547
67    Q        -1.282  -1.268  -1.257  -1.070  -1.126  -1.035  -1.108  -1.086  -1.067
68    Y        -1.282  -1.268  -1.257  -0.636  -0.601  -0.603  -1.108  -1.086  -1.067
69    E        -0.133  -0.189  -0.195   0.054  -0.052  -0.079  -0.229  -0.314  -0.323
70    V        -1.282  -1.268  -1.257  -1.576  -1.507  -1.541  -1.108  -1.086  -1.067
71    V         1.451   1.459   1.467   1.541   1.559   1.567   1.529   1.537   1.547
72    S        -0.133  -0.103  -0.167  -0.820  -0.768  -0.867  -0.229  -0.183  -0.281
73    E        -0.133  -0.189  -0.195   0.263   0.188   0.175  -0.229  -0.314  -0.323
74    F        -0.133  -0.189  -0.195   0.318   0.229   0.231  -0.229  -0.314  -0.323
75    T         1.451   1.459   1.467   0.789   0.811   0.817   1.529   1.537   1.547
76    T         1.451   1.459   1.467   0.789   0.811   0.817   1.529   1.537   1.547
77    Y         1.451   1.459   1.467   1.874   1.881   1.899   1.529   1.537   1.547
78    C         1.451   1.459   1.467   1.859   1.876   1.884   1.529   1.537   1.547
79    P         1.451   1.459   1.467   1.702   1.721   1.728   1.529   1.537   1.547
80    E        -0.133  -0.189  -0.195   0.312   0.243   0.234  -0.229  -0.314  -0.323
81    P        -0.133  -0.189  -0.195   0.054  -0.052  -0.079  -0.229  -0.314  -0.323
82    T         1.451   1.459   1.467   0.789   0.811   0.817   1.529   1.537   1.547
83    T        -0.133  -0.189  -0.195  -0.639  -0.683  -0.683  -0.229  -0.314  -0.323
84    F        -0.133  -0.103  -0.167   0.134   0.157   0.084  -0.229  -0.183  -0.281
85    V        -1.282  -1.268  -1.257  -1.517  -1.568  -1.481  -1.108  -1.086  -1.067
86    T        -0.133  -0.189  -0.195  -0.728  -0.787  -0.791  -0.229  -0.314  -0.323
87    N         1.451   1.459   1.467   1.718   1.729   1.744   1.529   1.537   1.547
88    G        -1.282  -1.268  -1.257  -0.941  -0.908  -0.907  -1.108  -1.086  -1.067
89    A        -1.282  -1.268  -1.257  -1.070  -1.080  -1.035  -1.108  -1.086  -1.067
90    T        -0.133  -0.189  -0.195  -0.692  -0.758  -0.748  -0.229  -0.314  -0.323
91    F        -0.133  -0.103  -0.167   0.134   0.157   0.084  -0.229  -0.183  -0.281
92    T        -0.133  -0.073  -0.161  -0.692  -0.620  -0.715  -0.229  -0.138  -0.271
93    V        -0.133  -0.189  -0.195   0.009  -0.088  -0.092  -0.229  -0.314  -0.323
94    T         1.451   1.459   1.467   0.789   0.811   0.817   1.529   1.537   1.547
95    A        -1.282  -1.268  -1.257  -0.951  -0.922  -0.917  -1.108  -1.086  -1.067
96    P         1.451   1.459   1.467   1.702   1.721   1.728   1.529   1.537   1.547
97    T         1.451   1.459   1.467   0.789   0.811   0.817   1.529   1.537   1.547
98    T         1.451   1.459   1.467   0.789   0.811   0.817   1.529   1.537   1.547
99    L         1.451   1.459   1.467   1.525   1.540   1.551   1.529   1.537   1.547
100   T         1.451   1.459   1.467   0.789   0.811   0.817   1.529   1.537   1.547
101   I         1.451   1.459   1.467   1.606   1.604   1.632   1.529   1.537   1.547
102   T         1.451   1.459   1.467   0.789   0.811   0.817   1.529   1.537   1.547
103   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
104   N        -1.282  -1.268  -1.257  -0.707  -0.695  -0.674  -1.108  -1.086  -1.067
105   C         1.451   1.459   1.467   1.859   1.876   1.884   1.529   1.537   1.547
106   P        -0.133  -0.189  -0.195  -0.197  -0.343  -0.389  -0.229  -0.314  -0.323
107   C        -0.133  -0.189  -0.195   0.263   0.158   0.136  -0.229  -0.314  -0.323
108   T        -1.282  -1.268  -1.257  -1.345  -1.273  -1.310  -1.108  -1.086  -1.067
109   I        -0.133  -0.189  -0.195   0.192   0.098   0.113  -0.229  -0.314  -0.323
110   E        -1.282  -1.268  -1.257  -1.446  -1.380  -1.411  -1.108  -1.086  -1.067
111   K        -0.133  -0.189  -0.195   0.227   0.107   0.085  -0.229  -0.314  -0.323
112   P        -0.133  -0.103  -0.167  -0.639  -0.595  -0.662  -0.229  -0.183  -0.281
113   T        -0.133  -0.189  -0.195  -0.728  -0.787  -0.791  -0.229  -0.314  -0.323
114   S        -1.282  -1.268  -1.257  -0.990  -0.957  -0.956  -1.108  -1.086  -1.067
115   E        -0.133  -0.189  -0.195   0.054  -0.057  -0.079  -0.229  -0.314  -0.323
116   -         1.451   1.459   1.467   1.428   1.443   1.455   1.529   1.537   1.547
117   -         1.451   1.459   1.467   1.653   1.669   1.679   1.529   1.537   1.547
118   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
119   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
120   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
121   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
122   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
123   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
124   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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   -        -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   -        -0.273  -0.268  -0.252  -0.889  -0.884  -0.855  -0.449  -0.438  -0.413
142   -        -0.273  -0.268  -0.252  -0.889  -0.884  -0.855  -0.449  -0.438  -0.413
143   -        -0.273  -0.268  -0.252  -0.243  -0.236  -0.211  -0.449  -0.438  -0.413
144   -        -0.273  -0.268  -0.252  -0.210  -0.203  -0.178  -0.449  -0.438  -0.413
145   -        -0.273  -0.268  -0.252  -0.889  -0.884  -0.855  -0.449  -0.438  -0.413
146   -        -0.273  -0.268  -0.252  -0.082  -0.074  -0.051  -0.449  -0.438  -0.413
147   -        -0.273  -0.268  -0.252  -0.243  -0.236  -0.211  -0.449  -0.438  -0.413
148   -         1.451   1.459   1.467   0.742   0.754   0.771   1.529   1.537   1.547
149   -        -0.273  -0.268  -0.252  -0.276  -0.269  -0.244  -0.449  -0.438  -0.413
150   T        -1.282  -1.268  -1.257  -1.638  -1.594  -1.602  -1.108  -1.086  -1.067
151   S        -0.133  -0.189  -0.195  -0.097  -0.168  -0.178  -0.229  -0.314  -0.323
152   V        -0.133  -0.103  -0.167  -0.174  -0.125  -0.229  -0.229  -0.183  -0.281
153   S        -0.133  -0.189  -0.195  -0.089  -0.164  -0.169  -0.229  -0.314  -0.323
154   S        -0.133  -0.189  -0.195  -0.066  -0.136  -0.141  -0.229  -0.314  -0.323
155   T        -1.282  -1.268  -1.257  -1.818  -1.776  -1.782  -1.108  -1.086  -1.067
156   H         1.451   1.459   1.467   1.949   1.966   1.974   1.529   1.537   1.547
157   D        -0.273  -0.268  -0.252  -0.542  -0.536  -0.509  -0.449  -0.438  -0.413
158   V         1.451   1.459   1.467   1.552   1.568   1.578   1.529   1.537   1.547
159   E        -0.273  -0.268  -0.252   0.073   0.081   0.103  -0.449  -0.438  -0.413
160   T         1.451   1.459   1.467   0.797   0.810   0.826   1.529   1.537   1.547
161   N        -0.273  -0.268  -0.252   0.086   0.095   0.116  -0.449  -0.438  -0.413
162   S        -0.273  -0.268  -0.252  -0.145  -0.137  -0.114  -0.449  -0.438  -0.413
163   N        -1.282  -1.268  -1.257  -0.980  -0.984  -0.946  -1.108  -1.086  -1.067
164   A        -1.282  -1.268  -1.257  -0.864  -0.832  -0.831  -1.108  -1.086  -1.067
165   A        -1.282  -1.268  -1.257  -1.162  -1.158  -1.128  -1.108  -1.086  -1.067
166   N        -0.133  -0.073  -0.161   0.241   0.324   0.198  -0.229  -0.138  -0.271
167   A        -1.282  -1.268  -1.257  -1.090  -1.084  -1.056  -1.108  -1.086  -1.067
168   R        -0.133  -0.073  -0.161   0.502   0.588   0.457  -0.229  -0.138  -0.271
169   A        -1.282  -1.268  -1.257  -1.301  -1.290  -1.266  -1.108  -1.086  -1.067
170   I        -1.282  -1.268  -1.257  -1.162  -1.146  -1.128  -1.108  -1.086  -1.067
171   P        -1.282  -1.268  -1.257  -0.951  -0.962  -0.917  -1.108  -1.086  -1.067
172   G         1.451   1.459   1.467   1.765   1.781   1.791   1.529   1.537   1.547
173   A        -0.133  -0.073  -0.161  -0.074  -0.003  -0.108  -0.229  -0.138  -0.271
174   L        -1.282  -1.268  -1.257  -1.060  -1.018  -1.025  -1.108  -1.086  -1.067
175   G        -0.133  -0.189  -0.195   0.177   0.074   0.056  -0.229  -0.314  -0.323
176   L        -1.282  -1.268  -1.257  -1.204  -1.177  -1.169  -1.108  -1.086  -1.067
177   A        -0.133  -0.073  -0.161  -0.182  -0.097  -0.228  -0.229  -0.138  -0.271
178   G        -0.133  -0.103  -0.167  -0.066  -0.033  -0.107  -0.229  -0.183  -0.281
179   A        -1.282  -1.268  -1.257  -0.951  -0.955  -0.917  -1.108  -1.086  -1.067
180   V        -1.282  -1.268  -1.257  -0.970  -0.939  -0.936  -1.108  -1.086  -1.067
181   M        -1.282  -1.268  -1.257  -0.922  -0.914  -0.888  -1.108  -1.086  -1.067
182   M        -1.282  -1.268  -1.257  -0.970  -0.976  -0.936  -1.108  -1.086  -1.067
183   L        -0.133  -0.189  -0.195   0.061  -0.022  -0.025  -0.229  -0.314  -0.323
184   L        -0.133  -0.189  -0.195  -0.006  -0.104  -0.106  -0.229  -0.314  -0.323
* 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/P40092
Output conservation file - output/P40092
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
