1     M         0.593   0.629   0.657   0.949   0.964   0.953   0.609   0.655   0.693
2     S        -1.778  -1.717  -1.659  -2.066  -1.993  -1.760  -1.943  -1.828  -1.654
3     S        -1.524  -1.437  -1.652  -1.106  -1.155  -1.652  -1.565  -1.487  -1.646
4     A        -0.328  -0.209  -0.779  -0.672  -0.515  -1.308  -0.325  -0.167  -1.023
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    A         0.593   0.629   0.657   0.158   0.254   0.349   0.609   0.655   0.693
14    E        -1.890  -1.989  -2.267  -1.095  -1.281  -1.711  -1.660  -1.770  -1.950
15    K         0.593   0.629   0.657   0.082   0.174   0.290   0.609   0.655   0.693
16    K        -0.728  -0.801  -0.809  -1.186  -1.320  -1.354  -0.903  -1.027  -1.072
17    P         0.593   0.629   0.657   0.804   0.839   0.843   0.609   0.655   0.693
18    A         0.593   0.629   0.657   0.158   0.254   0.349   0.609   0.655   0.693
19    S        -0.265  -0.573  -0.782  -0.296  -0.586  -0.816  -0.242  -0.674  -1.027
20    K         0.593   0.629   0.657   0.082   0.174   0.290   0.609   0.655   0.693
21    A         0.593   0.629   0.657   0.158   0.254   0.349   0.609   0.655   0.693
22    P         0.593   0.629   0.657   0.804   0.839   0.843   0.609   0.655   0.693
23    A         0.593   0.629   0.657   0.158   0.254   0.349   0.609   0.655   0.693
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    E        -0.265  -0.575  -0.775   0.117  -0.241  -0.548  -0.242  -0.676  -1.016
31    K         0.593   0.629   0.657   0.082   0.174   0.290   0.609   0.655   0.693
32    K        -0.265  -0.575  -0.775  -0.592  -0.964  -1.290  -0.242  -0.676  -1.016
33    P        -1.094  -1.397  -1.652  -0.375  -0.777  -1.157  -0.998  -1.368  -1.645
34    A         0.593   0.629   0.657   0.152   0.248   0.344   0.609   0.655   0.693
35    A        -0.805  -1.020  -0.813  -1.017  -1.273  -0.890  -1.025  -1.392  -1.079
36    K        -0.265  -0.575  -0.775  -0.517  -0.823  -0.983  -0.242  -0.676  -1.016
37    K        -0.265  -0.575  -0.775  -0.499  -0.788  -0.911  -0.242  -0.676  -1.016
38    T         0.593   0.629   0.657   0.516   0.542   0.622   0.609   0.655   0.693
39    S        -2.491  -2.651  -2.276  -2.599  -2.679  -2.128  -2.416  -2.432  -1.958
40    T        -2.491  -2.568  -2.269  -2.582  -2.819  -2.494  -2.416  -2.380  -1.953
41    S        -2.034  -1.739  -1.661  -2.307  -1.968  -1.893  -2.192  -1.809  -1.656
42    V        -3.884  -3.480  -3.133  -3.082  -2.879  -2.426  -3.172  -2.719  -2.254
43    D        -1.237  -1.063  -0.812  -0.926  -0.784  -0.477  -1.754  -1.466  -1.078
44    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
45    G        -3.581  -3.037  -2.751  -3.901  -3.221  -2.720  -3.125  -2.533  -2.138
46    K         0.593   0.629   0.657   0.082   0.174   0.290   0.609   0.655   0.693
47    K         0.593   0.629   0.657   0.082   0.174   0.290   0.609   0.655   0.693
48    R         0.593   0.629   0.657   0.775   0.796   0.820   0.609   0.655   0.693
49    S        -1.778  -1.734  -1.652  -1.711  -1.595  -1.523  -1.943  -1.778  -1.646
50    K         0.593   0.629   0.657   0.082   0.174   0.290   0.609   0.655   0.693
51    V        -2.282  -2.092  -2.260  -2.113  -1.877  -1.927  -2.132  -1.875  -1.944
52    R         0.593   0.629   0.657   0.775   0.796   0.820   0.609   0.655   0.693
53    K         0.593   0.629   0.657   0.082   0.174   0.290   0.609   0.655   0.693
54    E         0.593   0.629   0.657   0.706   0.749   0.768   0.609   0.655   0.693
55    T         0.593   0.629   0.657   0.516   0.542   0.622   0.609   0.655   0.693
56    Y         0.593   0.629   0.657   0.834   0.859   0.865   0.609   0.655   0.693
57    S         0.593   0.629   0.657   0.292   0.396   0.451   0.609   0.655   0.693
58    S         0.593   0.629   0.657   0.292   0.396   0.451   0.609   0.655   0.693
59    Y         0.593   0.629   0.657   0.834   0.859   0.865   0.609   0.655   0.693
60    I         0.593   0.629   0.657   0.697   0.737   0.760   0.609   0.655   0.693
61    Y         0.593   0.629   0.657   0.834   0.859   0.865   0.609   0.655   0.693
62    K         0.593   0.629   0.657   0.082   0.174   0.290   0.609   0.655   0.693
63    V         0.593   0.629   0.657   0.804   0.829   0.843   0.609   0.655   0.693
64    L         0.593   0.629   0.657   0.809   0.835   0.846   0.609   0.655   0.693
65    K         0.593   0.629   0.657   0.082   0.174   0.290   0.609   0.655   0.693
66    Q         0.593   0.629   0.657   0.920   0.944   0.931   0.609   0.655   0.693
67    T        -0.728  -0.892  -0.806  -0.582  -0.866  -0.725  -0.903  -1.175  -1.067
68    H         0.593   0.629   0.657   0.977   0.993   0.975   0.609   0.655   0.693
69    P         0.593   0.629   0.657   0.804   0.839   0.843   0.609   0.655   0.693
70    D         0.593   0.629   0.657   0.920   0.927   0.931   0.609   0.655   0.693
71    T         0.593   0.629   0.657   0.516   0.542   0.622   0.609   0.655   0.693
72    G         0.593   0.629   0.657   0.853   0.856   0.880   0.609   0.655   0.693
73    I         0.593   0.629   0.657   0.697   0.737   0.760   0.609   0.655   0.693
74    S         0.593   0.629   0.657   0.292   0.396   0.451   0.609   0.655   0.693
75    Q        -1.524  -1.893  -1.666  -0.768  -1.370  -1.193  -1.565  -1.991  -1.661
76    K        -1.524  -1.893  -1.664  -1.559  -1.936  -1.487  -1.565  -1.991  -1.660
77    S        -1.020  -0.678  -0.789  -1.527  -0.996  -1.194  -1.376  -0.834  -1.039
78    M         0.593   0.629   0.657   0.949   0.964   0.953   0.609   0.655   0.693
79    S        -0.265  -0.575  -0.775  -0.306  -0.603  -0.847  -0.242  -0.676  -1.016
80    I         0.593   0.629   0.657   0.697   0.737   0.760   0.609   0.655   0.693
81    L        -1.237  -1.063  -0.812  -0.936  -0.783  -0.488  -1.754  -1.466  -1.078
82    N         0.593   0.629   0.657   0.901   0.917   0.916   0.609   0.655   0.693
83    S         0.593   0.629   0.657   0.292   0.396   0.451   0.609   0.655   0.693
84    F         0.593   0.629   0.657   0.973   0.985   0.971   0.609   0.655   0.693
85    V         0.593   0.629   0.657   0.804   0.829   0.843   0.609   0.655   0.693
86    N         0.593   0.629   0.657   0.901   0.917   0.916   0.609   0.655   0.693
87    D         0.593   0.629   0.657   0.920   0.927   0.931   0.609   0.655   0.693
88    I         0.593   0.629   0.657   0.697   0.737   0.760   0.609   0.655   0.693
89    F         0.593   0.629   0.657   0.973   0.985   0.971   0.609   0.655   0.693
90    E         0.593   0.629   0.657   0.706   0.749   0.768   0.609   0.655   0.693
91    R         0.593   0.629   0.657   0.775   0.796   0.820   0.609   0.655   0.693
92    I        -0.728  -0.891  -0.810  -0.405  -0.685  -0.625  -0.903  -1.174  -1.075
93    A         0.593   0.629   0.657   0.158   0.254   0.349   0.609   0.655   0.693
94    T        -1.524  -0.931  -1.630  -1.201  -0.601  -1.475  -1.565  -0.812  -1.620
95    E         0.593   0.629   0.657   0.706   0.749   0.768   0.609   0.655   0.693
96    A        -0.728  -0.372  -0.775  -1.072  -0.584  -1.170  -0.903  -0.384  -1.015
97    S         0.593   0.629   0.657   0.292   0.396   0.451   0.609   0.655   0.693
98    K         0.593   0.629   0.657   0.082   0.174   0.290   0.609   0.655   0.693
99    L         0.593   0.629   0.657   0.809   0.835   0.846   0.609   0.655   0.693
100   A         0.593   0.629   0.657   0.158   0.254   0.349   0.609   0.655   0.693
101   A        -0.265  -0.573  -0.782  -0.472  -0.808  -1.069  -0.242  -0.674  -1.027
102   Y         0.593   0.629   0.657   0.834   0.859   0.865   0.609   0.655   0.693
103   N        -0.265  -0.573  -0.782   0.275  -0.147  -0.582  -0.242  -0.674  -1.027
104   K         0.593   0.629   0.657   0.082   0.174   0.290   0.609   0.655   0.693
105   K         0.593   0.629   0.657   0.082   0.174   0.290   0.609   0.655   0.693
106   S         0.593   0.629   0.657   0.292   0.396   0.451   0.609   0.655   0.693
107   T         0.593   0.629   0.657   0.516   0.542   0.622   0.609   0.655   0.693
108   I         0.593   0.629   0.657   0.697   0.737   0.760   0.609   0.655   0.693
109   S        -0.265  -0.573  -0.782  -0.336  -0.665  -0.980  -0.242  -0.674  -1.027
110   A        -1.020  -1.070  -0.809  -1.527  -1.638  -1.217  -1.376  -1.477  -1.073
111   R         0.593   0.629   0.657   0.775   0.796   0.820   0.609   0.655   0.693
112   E         0.593   0.629   0.657   0.706   0.749   0.768   0.609   0.655   0.693
113   I         0.593   0.629   0.657   0.697   0.737   0.760   0.609   0.655   0.693
114   Q         0.593   0.629   0.657   0.920   0.944   0.931   0.609   0.655   0.693
115   T         0.593   0.629   0.657   0.516   0.542   0.622   0.609   0.655   0.693
116   A        -0.265  -0.261  -0.773  -0.498  -0.454  -1.166  -0.242  -0.234  -1.012
117   V         0.593   0.629   0.657   0.804   0.829   0.843   0.609   0.655   0.693
118   R         0.593   0.629   0.657   0.775   0.796   0.820   0.609   0.655   0.693
119   L         0.593   0.629   0.657   0.809   0.835   0.846   0.609   0.655   0.693
120   I         0.593   0.629   0.657   0.697   0.737   0.760   0.609   0.655   0.693
121   L         0.593   0.629   0.657   0.809   0.835   0.846   0.609   0.655   0.693
122   P         0.593   0.629   0.657   0.804   0.839   0.843   0.609   0.655   0.693
123   G         0.593   0.629   0.657   0.853   0.856   0.880   0.609   0.655   0.693
124   E         0.593   0.629   0.657   0.706   0.749   0.768   0.609   0.655   0.693
125   L         0.593   0.629   0.657   0.809   0.835   0.846   0.609   0.655   0.693
126   A         0.593   0.629   0.657   0.158   0.254   0.349   0.609   0.655   0.693
127   K         0.593   0.629   0.657   0.082   0.174   0.290   0.609   0.655   0.693
128   H         0.593   0.629   0.657   0.977   0.993   0.975   0.609   0.655   0.693
129   A         0.593   0.629   0.657   0.158   0.254   0.349   0.609   0.655   0.693
130   V        -0.265  -0.573  -0.782   0.178  -0.233  -0.645  -0.242  -0.674  -1.027
131   S        -1.094  -1.663  -1.651  -0.919  -1.581  -1.539  -0.998  -1.686  -1.644
132   E        -0.265  -0.573  -0.782   0.125  -0.222  -0.527  -0.242  -0.674  -1.027
133   G         0.593   0.629   0.657   0.853   0.856   0.880   0.609   0.655   0.693
134   T         0.593   0.629   0.657   0.516   0.542   0.622   0.609   0.655   0.693
135   R        -0.728  -0.892  -0.806  -0.498  -0.897  -0.930  -0.903  -1.175  -1.067
136   A        -0.265  -0.575  -0.775  -0.498  -0.847  -1.170  -0.242  -0.676  -1.016
137   V         0.593   0.629   0.657   0.804   0.829   0.843   0.609   0.655   0.693
138   T        -0.265  -0.573  -0.782  -0.150  -0.586  -0.998  -0.242  -0.674  -1.027
139   K         0.593   0.629   0.657   0.082   0.174   0.290   0.609   0.655   0.693
140   Y         0.593   0.629   0.657   0.834   0.859   0.865   0.609   0.655   0.693
141   S         0.593   0.629   0.657   0.292   0.396   0.451   0.609   0.655   0.693
142   S        -0.265  -0.573  -0.782  -0.336  -0.665  -0.980  -0.242  -0.674  -1.027
143   S        -1.898  -1.834  -1.658  -2.226  -1.922  -1.656  -2.132  -1.911  -1.653
144   T        -2.786  -2.604  -2.274  -2.837  -2.585  -2.126  -2.699  -2.407  -1.957
145   Q        -2.558  -2.219  -2.271  -1.878  -1.584  -1.883  -2.510  -2.110  -1.955
146   A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
* 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/P02294
Output conservation file - output/P02294
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
