1     M         1.326   1.327   1.342   1.517   1.518   1.541   1.379   1.380   1.398
2     S        -0.065  -0.052  -0.107  -0.013   0.006  -0.077  -0.205  -0.186  -0.270
3     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
4     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
5     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
6     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
7     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
8     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
17    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
18    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
27    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
28    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
29    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
33    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
34    Q        -0.065  -0.052  -0.106  -0.119  -0.095  -0.199  -0.205  -0.186  -0.269
35    F         1.326   1.327   1.342   1.501   1.503   1.525   1.379   1.380   1.398
36    E        -0.065  -0.085  -0.115  -0.196  -0.234  -0.290  -0.205  -0.237  -0.284
37    K        -1.074  -1.073  -1.054  -1.018  -1.008  -0.982  -0.997  -0.994  -0.961
38    Q        -0.065  -0.052  -0.106   0.017   0.041  -0.069  -0.205  -0.186  -0.269
39    K         1.326   1.327   1.342   1.205   1.205   1.230   1.379   1.380   1.398
40    E        -1.074  -1.073  -1.054  -0.998  -0.994  -0.962  -0.997  -0.994  -0.961
41    Q        -1.074  -1.073  -1.054  -1.152  -1.141  -1.116  -0.997  -0.994  -0.961
42    G         1.326   1.327   1.342   1.420   1.423   1.445   1.379   1.380   1.398
43    N         1.326   1.327   1.342   1.338   1.342   1.363   1.379   1.380   1.398
44    S        -1.074  -1.073  -1.054  -1.028  -1.030  -0.992  -0.997  -0.994  -0.961
45    L        -1.074  -1.073  -1.054  -1.058  -1.047  -1.023  -0.997  -0.994  -0.961
46    F        -0.065  -0.052  -0.107   0.068   0.090  -0.012  -0.205  -0.186  -0.270
47    K         1.326   1.327   1.342   1.205   1.205   1.230   1.379   1.380   1.398
48    Q        -0.065  -0.085  -0.115  -0.251  -0.285  -0.345  -0.205  -0.237  -0.284
49    G        -0.065  -0.052  -0.107  -0.006   0.017  -0.082  -0.205  -0.186  -0.270
50    L        -1.074  -1.073  -1.054  -1.216  -1.215  -1.180  -0.997  -0.994  -0.961
51    Y        -0.065  -0.052  -0.107  -0.006   0.014  -0.066  -0.205  -0.186  -0.270
52    R        -1.074  -1.073  -1.054  -0.909  -0.907  -0.874  -0.997  -0.994  -0.961
53    E        -1.074  -1.073  -1.054  -1.173  -1.179  -1.137  -0.997  -0.994  -0.961
54    A         1.326   1.327   1.342   1.272   1.273   1.297   1.379   1.380   1.398
55    V        -0.065  -0.085  -0.115   0.002  -0.028  -0.081  -0.205  -0.237  -0.284
56    H        -1.074  -1.073  -1.054  -0.938  -0.941  -0.903  -0.997  -0.994  -0.961
57    C        -1.074  -1.073  -1.054  -0.909  -0.912  -0.874  -0.997  -0.994  -0.961
58    Y         1.326   1.327   1.342   1.338   1.341   1.363   1.379   1.380   1.398
59    D        -1.074  -1.073  -1.054  -1.038  -1.033  -1.003  -0.997  -0.994  -0.961
60    Q        -0.065  -0.052  -0.106  -0.259  -0.237  -0.333  -0.205  -0.186  -0.269
61    L        -1.074  -1.073  -1.054  -1.100  -1.090  -1.064  -0.997  -0.994  -0.961
62    I         1.326   1.327   1.342   1.420   1.422   1.445   1.379   1.380   1.398
63    T        -0.065  -0.085  -0.115   0.002  -0.034  -0.088  -0.205  -0.237  -0.284
64    A        -1.074  -1.073  -1.054  -1.216  -1.219  -1.180  -0.997  -0.994  -0.961
65    Q        -1.074  -1.073  -1.054  -1.120  -1.118  -1.085  -0.997  -0.994  -0.961
66    P         1.326   1.327   1.342   1.453   1.453   1.477   1.379   1.380   1.398
67    Q        -0.065  -0.052  -0.106  -0.058  -0.035  -0.141  -0.205  -0.186  -0.269
68    N         1.326   1.327   1.342   1.338   1.342   1.363   1.379   1.380   1.398
69    P        -0.065  -0.085  -0.115  -0.006  -0.044  -0.105  -0.205  -0.237  -0.284
70    V         1.326   1.327   1.342   1.388   1.393   1.413   1.379   1.380   1.398
71    G         1.326   1.327   1.342   1.420   1.423   1.445   1.379   1.380   1.398
72    Y         1.326   1.327   1.342   1.338   1.341   1.363   1.379   1.380   1.398
73    S         1.326   1.327   1.342   1.355   1.357   1.380   1.379   1.380   1.398
74    N         1.326   1.327   1.342   1.338   1.342   1.363   1.379   1.380   1.398
75    K        -1.074  -1.073  -1.054  -1.141  -1.148  -1.106  -0.997  -0.994  -0.961
76    A         1.326   1.327   1.342   1.272   1.273   1.297   1.379   1.380   1.398
77    M         1.326   1.327   1.342   1.517   1.518   1.541   1.379   1.380   1.398
78    A         1.326   1.327   1.342   1.272   1.273   1.297   1.379   1.380   1.398
79    L        -0.065  -0.085  -0.115  -0.267  -0.301  -0.343  -0.205  -0.237  -0.284
80    I        -0.065  -0.085  -0.115  -0.096  -0.138  -0.205  -0.205  -0.237  -0.284
81    K         1.326   1.327   1.342   1.205   1.205   1.230   1.379   1.380   1.398
82    L        -0.065  -0.085  -0.115  -0.267  -0.301  -0.343  -0.205  -0.237  -0.284
83    G        -1.074  -1.073  -1.054  -0.948  -0.944  -0.913  -0.997  -0.994  -0.961
84    E        -1.074  -1.073  -1.054  -0.978  -0.970  -0.943  -0.997  -0.994  -0.961
85    Y        -0.065  -0.085  -0.115  -0.028  -0.059  -0.105  -0.205  -0.237  -0.284
86    T        -1.074  -1.073  -1.054  -0.998  -0.993  -0.962  -0.997  -0.994  -0.961
87    Q        -1.074  -1.073  -1.054  -1.120  -1.118  -1.085  -0.997  -0.994  -0.961
88    A         1.326   1.327   1.342   1.272   1.273   1.297   1.379   1.380   1.398
89    I        -1.074  -1.073  -1.054  -1.069  -1.071  -1.033  -0.997  -0.994  -0.961
90    Q        -0.065  -0.085  -0.115  -0.149  -0.178  -0.223  -0.205  -0.237  -0.284
91    M        -0.065  -0.085  -0.115   0.053   0.015  -0.049  -0.205  -0.237  -0.284
92    C         1.326   1.327   1.342   1.517   1.517   1.541   1.379   1.380   1.398
93    Q        -0.065  -0.085  -0.115  -0.220  -0.253  -0.307  -0.205  -0.237  -0.284
94    Q        -1.074  -1.073  -1.054  -0.958  -0.949  -0.923  -0.997  -0.994  -0.961
95    G         1.326   1.327   1.342   1.420   1.423   1.445   1.379   1.380   1.398
96    L         1.326   1.327   1.342   1.136   1.135   1.162   1.379   1.380   1.398
97    R        -1.074  -1.073  -1.054  -0.890  -0.890  -0.855  -0.997  -0.994  -0.961
98    Y         1.326   1.327   1.342   1.338   1.341   1.363   1.379   1.380   1.398
99    T        -1.074  -1.073  -1.054  -0.861  -0.854  -0.826  -0.997  -0.994  -0.961
100   S        -1.074  -1.073  -1.054  -1.120  -1.120  -1.085  -0.997  -0.994  -0.961
101   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
102   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
103   T         1.326   1.327   1.342   1.450   1.451   1.474   1.379   1.380   1.398
104   A        -0.188  -0.188  -0.170  -0.311  -0.310  -0.279  -0.403  -0.402  -0.371
105   E        -0.188  -0.188  -0.170  -0.329  -0.328  -0.297  -0.403  -0.402  -0.371
106   H        -0.065  -0.052  -0.106   0.090   0.109   0.034  -0.205  -0.186  -0.269
107   V        -1.074  -1.073  -1.054  -0.968  -0.960  -0.933  -0.997  -0.994  -0.961
108   A        -0.065  -0.052  -0.106  -0.235  -0.216  -0.305  -0.205  -0.186  -0.269
109   I        -1.074  -1.073  -1.054  -1.089  -1.093  -1.054  -0.997  -0.994  -0.961
110   R         1.326   1.327   1.342   1.420   1.420   1.445   1.379   1.380   1.398
111   S        -1.074  -1.073  -1.054  -1.195  -1.191  -1.159  -0.997  -0.994  -0.961
112   K         1.326   1.327   1.342   1.205   1.205   1.230   1.379   1.380   1.398
113   L         1.326   1.327   1.342   1.136   1.135   1.162   1.379   1.380   1.398
114   Q         1.326   1.327   1.342   1.222   1.226   1.247   1.379   1.380   1.398
115   Y        -0.065  -0.052  -0.107   0.061   0.078   0.012  -0.205  -0.186  -0.270
116   R         1.326   1.327   1.342   1.420   1.420   1.445   1.379   1.380   1.398
117   L         1.326   1.327   1.342   1.136   1.135   1.162   1.379   1.380   1.398
118   E        -0.065  -0.052  -0.107  -0.142  -0.124  -0.211  -0.205  -0.186  -0.270
119   L        -0.065  -0.052  -0.107  -0.243  -0.225  -0.302  -0.205  -0.186  -0.270
120   A        -0.065  -0.052  -0.107  -0.058  -0.041  -0.113  -0.205  -0.186  -0.270
121   Q        -1.074  -1.073  -1.054  -1.058  -1.050  -1.023  -0.997  -0.994  -0.961
122   G        -1.074  -1.073  -1.054  -0.988  -0.985  -0.952  -0.997  -0.994  -0.961
123   A        -1.074  -1.073  -1.054  -1.163  -1.154  -1.127  -0.997  -0.994  -0.961
124   V        -1.074  -1.073  -1.054  -1.227  -1.225  -1.191  -0.997  -0.994  -0.961
125   G        -1.074  -1.073  -1.054  -1.028  -1.023  -0.992  -0.997  -0.994  -0.961
126   S        -1.074  -1.073  -1.054  -0.928  -0.923  -0.893  -0.997  -0.994  -0.961
127   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
128   -        -0.188  -0.188  -0.170  -0.234  -0.233  -0.202  -0.403  -0.402  -0.371
129   -         1.326   1.327   1.342   1.131   1.133   1.157   1.379   1.380   1.398
130   V        -1.074  -1.073  -1.054  -1.038  -1.035  -1.003  -0.997  -0.994  -0.961
131   Q        -0.065  -0.052  -0.107  -0.180  -0.158  -0.246  -0.205  -0.186  -0.270
132   I        -1.074  -1.073  -1.054  -1.089  -1.093  -1.054  -0.997  -0.994  -0.961
133   P        -1.074  -1.073  -1.054  -1.089  -1.089  -1.054  -0.997  -0.994  -0.961
134   V        -0.065  -0.052  -0.106   0.017   0.039  -0.054  -0.205  -0.186  -0.269
135   V        -1.074  -1.073  -1.054  -0.823  -0.821  -0.788  -0.997  -0.994  -0.961
136   E         1.326   1.327   1.342   1.272   1.270   1.297   1.379   1.380   1.398
137   V         1.326   1.327   1.342   1.388   1.393   1.413   1.379   1.380   1.398
138   D        -0.065  -0.085  -0.115  -0.050  -0.088  -0.147  -0.205  -0.237  -0.284
139   E        -1.074  -1.073  -1.054  -1.120  -1.116  -1.085  -0.997  -0.994  -0.961
140   L        -0.065  -0.085  -0.115  -0.227  -0.260  -0.296  -0.205  -0.237  -0.284
141   P         1.326   1.327   1.342   1.453   1.453   1.477   1.379   1.380   1.398
142   E        -1.074  -1.073  -1.054  -1.008  -1.003  -0.972  -0.997  -0.994  -0.961
143   G        -1.074  -1.073  -1.054  -1.120  -1.120  -1.085  -0.997  -0.994  -0.961
144   Y        -0.065  -0.085  -0.115  -0.173  -0.213  -0.278  -0.205  -0.237  -0.284
145   D        -1.074  -1.073  -1.054  -1.120  -1.116  -1.085  -0.997  -0.994  -0.961
146   R        -1.074  -1.073  -1.054  -0.948  -0.947  -0.913  -0.997  -0.994  -0.961
147   S        -0.065  -0.052  -0.106  -0.259  -0.242  -0.319  -0.205  -0.186  -0.269
* 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/P25638
Output conservation file - output/P25638
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
