1     M         1.886   1.896   1.953   2.141   2.160   2.246   2.079   2.093   2.177
2     D        -1.334  -1.327  -1.288  -1.608  -1.600  -1.533  -1.105  -1.094  -1.028
3     H        -1.334  -1.327  -1.288  -1.009  -1.012  -0.930  -1.105  -1.094  -1.028
4     S         0.580   0.520   0.489   0.485   0.376   0.297   0.487   0.385   0.319
5     E        -0.529  -0.503  -0.525  -0.521  -0.467  -0.531  -0.574  -0.538  -0.556
6     S         0.580   0.520   0.489   0.614   0.522   0.473   0.487   0.385   0.319
7     L         0.580   0.582   0.509   0.393   0.393   0.302   0.487   0.489   0.355
8     T        -0.529  -0.542  -0.538  -0.299  -0.334  -0.304  -0.574  -0.590  -0.574
9     F         0.580   0.520   0.489   0.695   0.609   0.554   0.487   0.385   0.319
10    N        -0.529  -0.503  -0.534  -0.513  -0.463  -0.540  -0.574  -0.538  -0.568
11    Q         0.580   0.626   0.514   0.800   0.868   0.706   0.487   0.561   0.364
12    L        -0.529  -0.568  -0.555  -0.810  -0.875  -0.842  -0.574  -0.623  -0.595
13    T         1.886   1.896   1.953   2.018   2.032   2.121   2.079   2.093   2.177
14    Q         1.886   1.896   1.953   2.037   2.054   2.141   2.079   2.093   2.177
15    D        -0.666  -0.661  -0.615  -0.876  -0.884  -0.796  -0.751  -0.742  -0.672
16    Y         0.408   0.418   0.402   0.597   0.613   0.599   0.192   0.209   0.167
17    I         1.886   1.896   1.953   2.041   2.062   2.145   2.079   2.093   2.177
18    N         0.408   0.387   0.394   0.436   0.398   0.387   0.192   0.153   0.151
19    K         1.886   1.896   1.953   1.873   1.890   1.976   2.079   2.093   2.177
20    L         0.580   0.582   0.509   0.403   0.405   0.315   0.487   0.489   0.355
21    K        -0.529  -0.568  -0.555  -0.454  -0.507  -0.472  -0.574  -0.623  -0.595
22    D        -0.529  -0.568  -0.555  -0.714  -0.767  -0.756  -0.574  -0.623  -0.595
23    A         1.886   1.896   1.953   2.018   2.032   2.121   2.079   2.093   2.177
24    F         1.886   1.896   1.953   1.960   1.980   2.063   2.079   2.093   2.177
25    Q         0.580   0.520   0.489   0.763   0.670   0.617   0.487   0.385   0.319
26    M         0.580   0.626   0.518   0.403   0.465   0.327   0.487   0.561   0.370
27    L         0.580   0.626   0.518   0.610   0.686   0.479   0.487   0.561   0.370
28    D         1.886   1.896   1.953   1.742   1.756   1.843   2.079   2.093   2.177
29    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
30    E         0.580   0.582   0.509   0.366   0.376   0.234   0.487   0.489   0.355
31    D         0.580   0.520   0.489   0.433   0.335   0.280   0.487   0.385   0.319
32    E        -0.529  -0.542  -0.546  -0.429  -0.433  -0.464  -0.574  -0.590  -0.583
33    D         1.886   1.896   1.953   1.742   1.756   1.843   2.079   2.093   2.177
34    G         0.580   0.520   0.489   0.701   0.605   0.540   0.487   0.385   0.319
35    L        -1.334  -1.327  -1.288  -1.143  -1.116  -1.064  -1.105  -1.094  -1.028
36    I         1.886   1.896   1.953   2.008   2.023   2.112   2.079   2.093   2.177
37    S        -0.529  -0.542  -0.538  -0.470  -0.491  -0.477  -0.574  -0.590  -0.574
38    R        -0.529  -0.568  -0.555  -0.458  -0.537  -0.539  -0.574  -0.623  -0.595
39    G        -0.529  -0.542  -0.546  -0.462  -0.480  -0.478  -0.574  -0.590  -0.583
40    D         0.580   0.582   0.509   0.485   0.487   0.383   0.487   0.489   0.355
41    L         0.580   0.626   0.514   0.403   0.465   0.321   0.487   0.561   0.364
42    T        -1.334  -1.327  -1.288  -1.019  -1.019  -0.940  -1.105  -1.094  -1.028
43    K         0.580   0.520   0.489   0.572   0.479   0.435   0.487   0.385   0.319
44    I        -0.529  -0.542  -0.546  -0.416  -0.460  -0.472  -0.574  -0.590  -0.583
45    Y         0.276   0.283   0.333   0.134   0.154   0.233  -0.044  -0.034   0.041
46    A        -0.529  -0.568  -0.555  -0.384  -0.459  -0.428  -0.574  -0.623  -0.595
47    T        -0.529  -0.503  -0.534  -0.412  -0.369  -0.425  -0.574  -0.538  -0.568
48    L         1.886   1.896   1.953   1.619   1.633   1.720   2.079   2.093   2.177
49    G         1.886   1.896   1.953   2.018   2.037   2.121   2.079   2.093   2.177
50    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
51    K         0.580   0.626   0.514   0.572   0.635   0.475   0.487   0.561   0.364
52    T        -1.334  -1.327  -1.288  -1.024  -1.007  -0.945  -1.105  -1.094  -1.028
53    L        -1.334  -1.327  -1.288  -1.283  -1.255  -1.205  -1.105  -1.094  -1.028
54    T         0.580   0.582   0.509   0.751   0.753   0.641   0.487   0.489   0.355
55    D        -0.529  -0.503  -0.534  -0.674  -0.643  -0.678  -0.574  -0.538  -0.568
56    E        -0.529  -0.542  -0.538  -0.820  -0.838  -0.846  -0.574  -0.590  -0.574
57    E        -0.529  -0.542  -0.546  -0.714  -0.723  -0.741  -0.574  -0.590  -0.583
58    W        -0.529  -0.542  -0.546  -0.311  -0.364  -0.345  -0.574  -0.590  -0.583
59    S        -1.334  -1.327  -1.288  -1.460  -1.460  -1.385  -1.105  -1.094  -1.028
60    K        -0.529  -0.568  -0.555  -0.564  -0.632  -0.600  -0.574  -0.623  -0.595
61    M         1.886   1.896   1.953   2.141   2.160   2.246   2.079   2.093   2.177
62    V        -0.529  -0.474  -0.528  -0.678  -0.607  -0.658  -0.574  -0.499  -0.559
63    P        -1.334  -1.327  -1.288  -1.148  -1.140  -1.070  -1.105  -1.094  -1.028
64    D        -1.334  -1.327  -1.288  -1.558  -1.522  -1.483  -1.105  -1.094  -1.028
65    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
66    D        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
67    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
68    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
69    T        -0.666  -0.658  -0.615  -0.900  -0.887  -0.819  -0.751  -0.738  -0.672
70    A        -0.666  -0.658  -0.615  -0.540  -0.535  -0.457  -0.751  -0.738  -0.672
71    E        -0.666  -0.658  -0.615  -1.057  -1.039  -0.978  -0.751  -0.738  -0.672
72    V        -1.334  -1.327  -1.288  -1.272  -1.269  -1.194  -1.105  -1.094  -1.028
73    G        -1.334  -1.327  -1.288  -1.122  -1.120  -1.043  -1.105  -1.094  -1.028
74    E         0.276   0.283   0.333  -0.192  -0.179  -0.105  -0.044  -0.034   0.041
75    E        -0.529  -0.542  -0.538  -0.691  -0.716  -0.701  -0.574  -0.590  -0.574
76    G        -1.334  -1.327  -1.288  -1.004  -1.011  -0.925  -1.105  -1.094  -1.028
77    V        -0.529  -0.503  -0.525  -0.487  -0.454  -0.490  -0.574  -0.538  -0.556
78    S        -0.529  -0.568  -0.555  -0.462  -0.519  -0.491  -0.574  -0.623  -0.595
79    F         1.886   1.896   1.953   1.960   1.980   2.063   2.079   2.093   2.177
80    P         0.580   0.520   0.489   0.899   0.807   0.748   0.487   0.385   0.319
81    I        -1.334  -1.327  -1.288  -1.217  -1.194  -1.139  -1.105  -1.094  -1.028
82    F         0.580   0.582   0.509   0.769   0.777   0.683   0.487   0.489   0.355
83    L         1.886   1.896   1.953   1.619   1.633   1.720   2.079   2.093   2.177
84    S        -0.529  -0.542  -0.538  -0.462  -0.481  -0.467  -0.574  -0.590  -0.574
85    I         0.276   0.283   0.333  -0.063  -0.049   0.031  -0.044  -0.034   0.041
86    M         1.886   1.896   1.953   2.141   2.160   2.246   2.079   2.093   2.177
87    G        -0.529  -0.542  -0.546  -0.470  -0.491  -0.488  -0.574  -0.590  -0.583
88    K         0.276   0.283   0.333  -0.123  -0.110  -0.034  -0.044  -0.034   0.041
89    N        -1.334  -1.327  -1.288  -1.137  -1.133  -1.059  -1.105  -1.094  -1.028
90    L        -0.529  -0.503  -0.534  -0.643  -0.610  -0.626  -0.574  -0.538  -0.568
91    S        -1.334  -1.327  -1.288  -1.201  -1.218  -1.123  -1.105  -1.094  -1.028
92    Q         0.276   0.283   0.333   0.033   0.055   0.126  -0.044  -0.034   0.041
93    F         0.580   0.582   0.509   0.729   0.738   0.632   0.487   0.489   0.355
94    P         0.580   0.520   0.489   0.809   0.708   0.625   0.487   0.385   0.319
95    E        -0.529  -0.474  -0.528  -0.714  -0.625  -0.713  -0.574  -0.499  -0.559
96    R        -0.529  -0.503  -0.534  -0.311  -0.255  -0.327  -0.574  -0.538  -0.568
97    E        -0.529  -0.503  -0.534  -0.732  -0.683  -0.741  -0.574  -0.538  -0.568
98    E         0.580   0.520   0.489   0.459   0.377   0.323   0.487   0.385   0.319
99    L         0.276   0.286   0.335  -0.063  -0.032   0.043  -0.044  -0.028   0.045
100   E        -1.334  -1.327  -1.288  -1.122  -1.080  -1.043  -1.105  -1.094  -1.028
101   E         0.580   0.520   0.489   0.465   0.386   0.332   0.487   0.385   0.319
102   S        -0.529  -0.474  -0.528  -0.299  -0.217  -0.288  -0.574  -0.499  -0.559
103   L         0.580   0.626   0.514   0.339   0.406   0.240   0.487   0.561   0.364
104   K         0.580   0.626   0.514   0.566   0.629   0.467   0.487   0.561   0.364
105   A        -0.529  -0.542  -0.538  -0.319  -0.340  -0.327  -0.574  -0.590  -0.574
106   I         0.276   0.286   0.335   0.183   0.199   0.276  -0.044  -0.028   0.045
107   G         0.580   0.626   0.518   0.614   0.683   0.520   0.487   0.561   0.370
108   R        -0.529  -0.474  -0.528  -0.530  -0.458  -0.509  -0.574  -0.499  -0.559
109   G        -0.529  -0.542  -0.546  -0.454  -0.489  -0.496  -0.574  -0.590  -0.583
110   H        -0.529  -0.503  -0.525  -0.521  -0.492  -0.507  -0.574  -0.538  -0.556
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   D         0.580   0.582   0.509   0.379   0.382   0.245   0.487   0.489   0.355
115   L         1.886   1.896   1.953   1.619   1.633   1.720   2.079   2.093   2.177
116   N        -1.334  -1.327  -1.288  -1.425  -1.410  -1.349  -1.105  -1.094  -1.028
117   V        -1.334  -1.327  -1.288  -1.080  -1.064  -1.002  -1.105  -1.094  -1.028
118   P         0.276   0.286   0.335   0.155   0.153   0.234  -0.044  -0.028   0.045
119   L        -1.334  -1.327  -1.288  -1.299  -1.275  -1.222  -1.105  -1.094  -1.028
120   N        -1.334  -1.327  -1.288  -1.367  -1.364  -1.291  -1.105  -1.094  -1.028
121   E        -0.529  -0.542  -0.538  -0.691  -0.702  -0.701  -0.574  -0.590  -0.574
122   V         0.580   0.626   0.518   0.393   0.453   0.314   0.487   0.561   0.370
123   I        -0.529  -0.568  -0.555  -0.568  -0.646  -0.642  -0.574  -0.623  -0.595
124   D        -1.334  -1.327  -1.288  -1.478  -1.470  -1.403  -1.105  -1.094  -1.028
125   S        -1.334  -1.327  -1.288  -1.201  -1.174  -1.123  -1.105  -1.094  -1.028
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   L         1.886   1.896   1.953   1.619   1.633   1.720   2.079   2.093   2.177
132   K        -0.529  -0.542  -0.538  -0.643  -0.655  -0.663  -0.574  -0.590  -0.574
133   E         0.580   0.582   0.509   0.366   0.376   0.234   0.487   0.489   0.355
134   A        -0.529  -0.568  -0.555  -0.319  -0.385  -0.352  -0.574  -0.623  -0.595
135   G         1.886   1.896   1.953   2.018   2.037   2.121   2.079   2.093   2.177
136   F        -0.529  -0.568  -0.555  -0.634  -0.705  -0.709  -0.574  -0.623  -0.595
137   E        -0.529  -0.542  -0.538  -0.691  -0.699  -0.701  -0.574  -0.590  -0.574
138   N         0.276   0.286   0.335   0.048   0.050   0.131  -0.044  -0.028   0.045
139   P         0.580   0.520   0.489   0.981   0.903   0.860   0.487   0.385   0.319
140   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
141   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
142   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
143   E         0.408   0.370   0.394   0.276   0.232   0.264   0.192   0.124   0.151
144   E         0.276   0.286   0.335   0.019   0.051   0.122  -0.044  -0.028   0.045
145   E        -0.529  -0.568  -0.555  -0.691  -0.743  -0.725  -0.574  -0.623  -0.595
146   F         0.580   0.582   0.509   0.563   0.568   0.414   0.487   0.489   0.355
147   A        -0.529  -0.474  -0.528  -0.674  -0.594  -0.668  -0.574  -0.499  -0.559
148   K         0.276   0.283   0.333   0.183   0.184   0.269  -0.044  -0.034   0.041
149   L        -0.529  -0.503  -0.534  -0.656  -0.626  -0.641  -0.574  -0.538  -0.568
150   F        -0.529  -0.542  -0.546  -0.678  -0.690  -0.678  -0.574  -0.590  -0.583
151   K        -0.529  -0.542  -0.546  -0.551  -0.589  -0.604  -0.574  -0.590  -0.583
152   L        -1.334  -1.327  -1.288  -1.127  -1.104  -1.048  -1.105  -1.094  -1.028
153   F         1.886   1.896   1.953   1.960   1.980   2.063   2.079   2.093   2.177
154   T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
155   T        -1.334  -1.327  -1.288  -1.085  -1.075  -1.007  -1.105  -1.094  -1.028
156   N        -0.529  -0.568  -0.555  -0.416  -0.492  -0.470  -0.574  -0.623  -0.595
157   Q        -0.529  -0.568  -0.555  -0.542  -0.624  -0.618  -0.574  -0.623  -0.595
158   Q         1.886   1.896   1.953   2.037   2.054   2.141   2.079   2.093   2.177
159   A        -0.529  -0.474  -0.528  -0.437  -0.339  -0.452  -0.574  -0.499  -0.559
160   T        -0.529  -0.503  -0.525  -0.651  -0.618  -0.639  -0.574  -0.538  -0.556
161   E         0.580   0.626   0.518   0.651   0.732   0.529   0.487   0.561   0.370
162   E        -0.529  -0.474  -0.528  -0.437  -0.328  -0.455  -0.574  -0.499  -0.559
163   R         0.580   0.520   0.489   0.797   0.694   0.626   0.487   0.385   0.319
164   T        -1.334  -1.327  -1.288  -1.009  -1.004  -0.930  -1.105  -1.094  -1.028
165   F         1.886   1.896   1.953   1.960   1.980   2.063   2.079   2.093   2.177
166   R        -0.529  -0.542  -0.546  -0.634  -0.682  -0.666  -0.574  -0.590  -0.583
167   G        -0.529  -0.542  -0.538  -0.412  -0.431  -0.432  -0.574  -0.590  -0.574
168   K        -1.334  -1.327  -1.288  -1.396  -1.387  -1.320  -1.105  -1.094  -1.028
169   L        -0.529  -0.474  -0.528  -0.678  -0.589  -0.684  -0.574  -0.499  -0.559
170   F         0.580   0.520   0.489   0.784   0.710   0.674   0.487   0.385   0.319
171   L        -0.529  -0.503  -0.525  -0.487  -0.440  -0.490  -0.574  -0.538  -0.556
172   D         0.580   0.582   0.509   0.485   0.486   0.383   0.487   0.489   0.355
173   S         0.580   0.520   0.489   0.614   0.522   0.473   0.487   0.385   0.319
174   I        -0.529  -0.542  -0.538  -0.420  -0.424  -0.440  -0.574  -0.590  -0.574
175   T        -1.334  -1.327  -1.288  -1.132  -1.125  -1.054  -1.105  -1.094  -1.028
176   D         0.580   0.582   0.509   0.379   0.382   0.245   0.487   0.489   0.355
* 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/Q06580
Output conservation file - output/Q06580
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
