1     M         1.013   1.017   1.030   1.222   1.228   1.237   1.046   1.049   1.062
2     A        -0.593  -0.638  -0.645  -0.519  -0.606  -0.654  -0.688  -0.752  -0.755
3     S        -0.593  -0.638  -0.645  -0.790  -0.851  -0.835  -0.688  -0.752  -0.755
4     E        -0.593  -0.638  -0.645  -0.623  -0.695  -0.686  -0.688  -0.752  -0.755
5     T         1.013   1.017   1.030   1.017   1.029   1.042   1.046   1.049   1.062
6     P         1.013   1.017   1.030   1.069   1.075   1.091   1.046   1.049   1.062
7     R         1.013   1.017   1.030   1.171   1.179   1.189   1.046   1.049   1.062
8     V        -0.593  -0.589  -0.635  -0.773  -0.765  -0.832  -0.688  -0.679  -0.741
9     D         1.013   1.017   1.030   1.051   1.060   1.075   1.046   1.049   1.062
10    P         1.013   1.017   1.030   1.069   1.075   1.091   1.046   1.049   1.062
11    T        -0.593  -0.589  -0.635  -0.790  -0.778  -0.822  -0.688  -0.679  -0.741
12    E        -0.593  -0.638  -0.645  -0.623  -0.695  -0.686  -0.688  -0.752  -0.755
13    I         1.013   1.017   1.030   0.840   0.847   0.874   1.046   1.049   1.062
14    S        -0.593  -0.512  -0.621  -0.790  -0.666  -0.803  -0.688  -0.566  -0.720
15    N        -0.593  -0.512  -0.621  -0.664  -0.518  -0.729  -0.688  -0.566  -0.720
16    V        -1.760  -1.738  -1.666  -1.691  -1.651  -1.533  -1.554  -1.523  -1.413
17    N        -1.760  -1.738  -1.666  -1.582  -1.550  -1.430  -1.554  -1.523  -1.413
18    A        -1.760  -1.738  -1.666  -1.457  -1.385  -1.311  -1.554  -1.523  -1.413
19    P        -0.593  -0.638  -0.645  -0.615  -0.704  -0.738  -0.688  -0.752  -0.755
20    V         1.013   1.017   1.030   0.876   0.885   0.908   1.046   1.049   1.062
21    F         1.013   1.017   1.030   1.154   1.164   1.173   1.046   1.049   1.062
22    R         1.013   1.017   1.030   1.171   1.179   1.189   1.046   1.049   1.062
23    I         1.013   1.017   1.030   0.840   0.847   0.874   1.046   1.049   1.062
24    I         1.013   1.017   1.030   0.840   0.847   0.874   1.046   1.049   1.062
25    A         1.013   1.017   1.030   1.171   1.182   1.189   1.046   1.049   1.062
26    Q        -0.593  -0.638  -0.645  -0.479  -0.560  -0.557  -0.688  -0.752  -0.755
27    I        -0.593  -0.589  -0.635  -0.756  -0.747  -0.823  -0.688  -0.679  -0.741
28    K        -0.593  -0.638  -0.645  -0.551  -0.639  -0.662  -0.688  -0.752  -0.755
29    S        -0.593  -0.638  -0.645  -0.773  -0.833  -0.813  -0.688  -0.752  -0.755
30    Q         1.013   1.017   1.030   1.051   1.047   1.075   1.046   1.049   1.062
31    P         1.013   1.017   1.030   1.069   1.075   1.091   1.046   1.049   1.062
32    T        -1.760  -1.738  -1.666  -1.746  -1.695  -1.586  -1.554  -1.523  -1.413
33    E        -0.593  -0.638  -0.645  -0.615  -0.680  -0.676  -0.688  -0.752  -0.755
34    S        -1.760  -1.738  -1.666  -1.724  -1.686  -1.565  -1.554  -1.523  -1.413
35    Q        -1.760  -1.738  -1.666  -1.647  -1.623  -1.492  -1.554  -1.523  -1.413
36    L         1.013   1.017   1.030   0.858   0.859   0.891   1.046   1.049   1.062
37    I         1.013   1.017   1.030   0.840   0.847   0.874   1.046   1.049   1.062
38    L         1.013   1.017   1.030   0.858   0.859   0.891   1.046   1.049   1.062
39    Q        -0.593  -0.512  -0.621  -0.440  -0.331  -0.473  -0.688  -0.566  -0.720
40    S         1.013   1.017   1.030   0.749   0.757   0.787   1.046   1.049   1.062
41    P         1.013   1.017   1.030   1.069   1.075   1.091   1.046   1.049   1.062
42    T         1.013   1.017   1.030   1.017   1.029   1.042   1.046   1.049   1.062
43    I        -0.593  -0.589  -0.635  -0.623  -0.612  -0.707  -0.688  -0.679  -0.741
44    S        -1.760  -1.738  -1.666  -1.713  -1.687  -1.554  -1.554  -1.523  -1.413
45    S        -0.593  -0.589  -0.635  -0.583  -0.582  -0.687  -0.688  -0.679  -0.741
46    K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
47    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
48    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
49    S        -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    V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
52    E         1.013   1.017   1.030   0.911   0.920   0.942   1.046   1.049   1.062
53    M         1.013   1.017   1.030   1.222   1.228   1.237   1.046   1.049   1.062
54    I         1.013   1.017   1.030   0.840   0.847   0.874   1.046   1.049   1.062
55    T         1.013   1.017   1.030   1.017   1.029   1.042   1.046   1.049   1.062
56    L         1.013   1.017   1.030   0.858   0.859   0.891   1.046   1.049   1.062
57    N        -1.760  -1.738  -1.666  -1.746  -1.728  -1.586  -1.554  -1.523  -1.413
58    N        -1.760  -1.738  -1.666  -1.746  -1.697  -1.586  -1.554  -1.523  -1.413
59    I        -0.593  -0.589  -0.635  -0.756  -0.747  -0.823  -0.688  -0.679  -0.741
60    R        -0.593  -0.638  -0.645  -0.371  -0.444  -0.464  -0.688  -0.752  -0.755
61    V        -0.593  -0.638  -0.645  -0.747  -0.825  -0.831  -0.688  -0.752  -0.755
62    S         1.013   1.017   1.030   0.749   0.757   0.787   1.046   1.049   1.062
63    M        -0.593  -0.638  -0.645  -0.340  -0.423  -0.444  -0.688  -0.752  -0.755
64    N        -0.593  -0.638  -0.645  -0.503  -0.571  -0.573  -0.688  -0.752  -0.755
65    K        -0.593  -0.638  -0.645  -0.599  -0.690  -0.724  -0.688  -0.752  -0.755
66    T        -0.593  -0.638  -0.645  -0.543  -0.608  -0.624  -0.688  -0.752  -0.755
67    F        -0.593  -0.638  -0.645  -0.495  -0.579  -0.617  -0.688  -0.752  -0.755
68    E        -0.593  -0.512  -0.621  -0.623  -0.500  -0.651  -0.688  -0.566  -0.720
69    I        -0.593  -0.589  -0.635  -0.756  -0.747  -0.823  -0.688  -0.679  -0.741
70    D        -0.593  -0.638  -0.645  -0.472  -0.541  -0.547  -0.688  -0.752  -0.755
71    S         1.013   1.017   1.030   0.749   0.757   0.787   1.046   1.049   1.062
72    W         1.013   1.017   1.030   1.322   1.327   1.332   1.046   1.049   1.062
73    Y         1.013   1.017   1.030   1.256   1.261   1.269   1.046   1.049   1.062
74    E         1.013   1.017   1.030   0.911   0.920   0.942   1.046   1.049   1.062
75    F         1.013   1.017   1.030   1.154   1.164   1.173   1.046   1.049   1.062
76    V         1.013   1.017   1.030   0.876   0.885   0.908   1.046   1.049   1.062
77    C         1.013   1.017   1.030   1.256   1.261   1.269   1.046   1.049   1.062
78    R         1.013   1.017   1.030   1.171   1.179   1.189   1.046   1.049   1.062
79    N        -0.593  -0.512  -0.621  -0.664  -0.518  -0.729  -0.688  -0.566  -0.720
80    N        -1.760  -1.738  -1.666  -1.861  -1.812  -1.695  -1.554  -1.523  -1.413
81    D         1.013   1.017   1.030   1.051   1.060   1.075   1.046   1.049   1.062
82    D        -1.760  -1.738  -1.666  -1.582  -1.543  -1.430  -1.554  -1.523  -1.413
83    G         1.013   1.017   1.030   1.103   1.104   1.124   1.046   1.049   1.062
84    E        -0.593  -0.589  -0.635  -0.559  -0.550  -0.639  -0.688  -0.679  -0.741
85    L        -1.760  -1.738  -1.666  -1.908  -1.877  -1.740  -1.554  -1.523  -1.413
86    G         1.013   1.017   1.030   1.103   1.104   1.124   1.046   1.049   1.062
87    F        -0.593  -0.638  -0.645  -0.487  -0.573  -0.607  -0.688  -0.752  -0.755
88    L        -0.593  -0.638  -0.645  -0.591  -0.652  -0.625  -0.688  -0.752  -0.755
89    I        -0.593  -0.589  -0.635  -0.756  -0.747  -0.823  -0.688  -0.679  -0.741
90    L         1.013   1.017   1.030   0.858   0.859   0.891   1.046   1.049   1.062
91    D         1.013   1.017   1.030   1.051   1.060   1.075   1.046   1.049   1.062
92    A        -0.593  -0.638  -0.645  -0.519  -0.606  -0.654  -0.688  -0.752  -0.755
93    V         1.013   1.017   1.030   0.876   0.885   0.908   1.046   1.049   1.062
94    L        -0.593  -0.589  -0.635  -0.551  -0.550  -0.641  -0.688  -0.679  -0.741
95    C         1.013   1.017   1.030   1.256   1.261   1.269   1.046   1.049   1.062
96    K        -1.760  -1.738  -1.666  -1.713  -1.675  -1.554  -1.554  -1.523  -1.413
97    F        -0.593  -0.589  -0.635  -0.623  -0.619  -0.654  -0.688  -0.679  -0.741
98    K        -0.593  -0.512  -0.621  -0.479  -0.353  -0.528  -0.688  -0.566  -0.720
99    E         1.013   1.017   1.030   0.911   0.920   0.942   1.046   1.049   1.062
100   N        -0.593  -0.638  -0.645  -0.503  -0.571  -0.573  -0.688  -0.752  -0.755
101   E         1.013   1.017   1.030   0.911   0.920   0.942   1.046   1.049   1.062
102   D        -0.593  -0.589  -0.635  -0.623  -0.614  -0.672  -0.688  -0.679  -0.741
103   L        -0.593  -0.589  -0.635  -0.781  -0.777  -0.843  -0.688  -0.679  -0.741
104   S         1.013   1.017   1.030   0.749   0.757   0.787   1.046   1.049   1.062
105   L        -0.593  -0.589  -0.635  -0.747  -0.741  -0.813  -0.688  -0.679  -0.741
106   N        -0.593  -0.638  -0.645  -0.664  -0.749  -0.780  -0.688  -0.752  -0.755
107   G         1.013   1.017   1.030   1.103   1.104   1.124   1.046   1.049   1.062
108   V        -0.593  -0.589  -0.635  -0.773  -0.765  -0.832  -0.688  -0.679  -0.741
109   V        -0.593  -0.512  -0.621  -0.756  -0.619  -0.798  -0.688  -0.566  -0.720
110   A         1.013   1.017   1.030   1.171   1.182   1.189   1.046   1.049   1.062
111   L         1.013   1.017   1.030   0.858   0.859   0.891   1.046   1.049   1.062
112   Q         1.013   1.017   1.030   1.051   1.047   1.075   1.046   1.049   1.062
113   R        -0.593  -0.589  -0.635  -0.440  -0.443  -0.493  -0.688  -0.679  -0.741
114   L         1.013   1.017   1.030   0.858   0.859   0.891   1.046   1.049   1.062
115   C        -1.760  -1.738  -1.666  -1.615  -1.594  -1.461  -1.554  -1.523  -1.413
116   K        -0.593  -0.638  -0.645  -0.440  -0.515  -0.520  -0.688  -0.752  -0.755
117   K         1.013   1.017   1.030   1.086   1.090   1.108   1.046   1.049   1.062
118   Y        -0.593  -0.589  -0.635  -0.310  -0.301  -0.366  -0.688  -0.679  -0.741
119   P         1.013   1.017   1.030   1.069   1.075   1.091   1.046   1.049   1.062
120   E        -0.593  -0.638  -0.645  -0.623  -0.688  -0.686  -0.688  -0.752  -0.755
121   I        -0.593  -0.638  -0.645  -0.781  -0.860  -0.860  -0.688  -0.752  -0.755
122   Y         1.013   1.017   1.030   1.256   1.261   1.269   1.046   1.049   1.062
* 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/P26755
Output conservation file - output/P26755
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
