1     M         1.396   1.397   1.415   1.783   1.787   1.805   1.464   1.464   1.485
2     P         1.396   1.397   1.415   1.536   1.541   1.563   1.464   1.464   1.485
3     S        -1.462  -1.459  -1.416  -1.198  -1.187  -1.124  -1.255  -1.250  -1.183
4     K        -0.407  -0.407  -0.371  -0.543  -0.542  -0.481  -0.575  -0.574  -0.516
5     D         1.396   1.397   1.415   1.335   1.339   1.365   1.464   1.464   1.485
6     P        -0.407  -0.407  -0.371  -0.285  -0.284  -0.227  -0.575  -0.574  -0.516
7     E         1.396   1.397   1.415   1.071   1.074   1.105   1.464   1.464   1.485
8     S        -0.407  -0.407  -0.371  -0.375  -0.374  -0.316  -0.575  -0.574  -0.516
9     V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
10    I        -0.260  -0.241  -0.299  -0.598  -0.580  -0.634  -0.349  -0.320  -0.405
11    D        -0.260  -0.241  -0.299  -0.589  -0.557  -0.640  -0.349  -0.320  -0.405
12    K        -0.260  -0.300  -0.308  -0.220  -0.278  -0.278  -0.349  -0.410  -0.418
13    E         1.396   1.397   1.415   1.070   1.074   1.104   1.464   1.464   1.485
14    I        -1.462  -1.459  -1.416  -0.936  -0.917  -0.867  -1.255  -1.250  -1.183
15    R        -0.260  -0.300  -0.308  -0.103  -0.175  -0.204  -0.349  -0.410  -0.418
16    K         1.396   1.397   1.415   1.336   1.338   1.365   1.464   1.464   1.485
17    I        -0.260  -0.241  -0.299  -0.598  -0.580  -0.634  -0.349  -0.320  -0.405
18    S        -1.462  -1.459  -1.416  -1.603  -1.624  -1.523  -1.255  -1.250  -1.183
19    A        -0.260  -0.300  -0.308   0.097   0.044   0.025  -0.349  -0.410  -0.418
20    R         1.396   1.397   1.415   1.608   1.614   1.633   1.464   1.464   1.485
21    N        -0.260  -0.300  -0.308   0.113   0.052   0.028  -0.349  -0.410  -0.418
22    D        -0.260  -0.300  -0.308  -0.445  -0.522  -0.554  -0.349  -0.410  -0.418
23    E        -0.260  -0.232  -0.298  -0.589  -0.543  -0.638  -0.349  -0.306  -0.403
24    L        -0.260  -0.232  -0.298  -0.598  -0.567  -0.632  -0.349  -0.306  -0.403
25    I        -0.260  -0.300  -0.308  -0.357  -0.444  -0.481  -0.349  -0.410  -0.418
26    K        -0.260  -0.232  -0.298  -0.228  -0.187  -0.275  -0.349  -0.306  -0.403
27    Q         1.396   1.397   1.415   1.661   1.664   1.685   1.464   1.464   1.485
28    D        -0.260  -0.232  -0.298  -0.445  -0.386  -0.533  -0.349  -0.306  -0.403
29    G        -1.462  -1.459  -1.416  -0.916  -0.911  -0.847  -1.255  -1.250  -1.183
30    T        -0.260  -0.300  -0.308  -0.170  -0.232  -0.257  -0.349  -0.410  -0.418
31    L        -0.260  -0.232  -0.298  -0.645  -0.614  -0.686  -0.349  -0.306  -0.403
32    K        -0.260  -0.300  -0.308  -0.228  -0.285  -0.288  -0.349  -0.410  -0.418
33    R        -0.260  -0.241  -0.299  -0.228  -0.201  -0.277  -0.349  -0.320  -0.405
34    E        -0.260  -0.300  -0.308  -0.589  -0.649  -0.652  -0.349  -0.410  -0.418
35    Y         1.396   1.397   1.415   1.661   1.665   1.685   1.464   1.464   1.485
36    T        -1.462  -1.459  -1.416  -1.198  -1.193  -1.124  -1.255  -1.250  -1.183
37    T        -0.260  -0.300  -0.308  -0.128  -0.184  -0.208  -0.349  -0.410  -0.418
38    L        -0.260  -0.232  -0.298  -0.445  -0.423  -0.456  -0.349  -0.306  -0.403
39    L        -0.260  -0.232  -0.298  -0.645  -0.614  -0.686  -0.349  -0.306  -0.403
40    R         1.396   1.397   1.415   1.608   1.614   1.633   1.464   1.464   1.485
41    K         1.396   1.397   1.415   1.336   1.338   1.365   1.464   1.464   1.485
42    V        -1.462  -1.459  -1.416  -1.411  -1.394  -1.334  -1.255  -1.250  -1.183
43    S        -0.260  -0.241  -0.299  -0.170  -0.131  -0.243  -0.349  -0.320  -0.405
44    S         1.396   1.397   1.415   1.409   1.414   1.438   1.464   1.464   1.485
45    V        -0.260  -0.232  -0.298  -0.014   0.033  -0.085  -0.349  -0.306  -0.403
46    I        -0.260  -0.300  -0.308   0.042  -0.004  -0.008  -0.349  -0.410  -0.418
47    T        -0.260  -0.300  -0.308  -0.055  -0.107  -0.121  -0.349  -0.410  -0.418
48    V        -0.260  -0.232  -0.298  -0.237  -0.185  -0.344  -0.349  -0.306  -0.403
49    L         1.396   1.397   1.415   0.991   0.983   1.027   1.464   1.464   1.485
50    N        -1.462  -1.459  -1.416  -1.253  -1.273  -1.178  -1.255  -1.250  -1.183
51    S         1.396   1.397   1.415   1.409   1.414   1.438   1.464   1.464   1.485
52    I        -0.260  -0.241  -0.299  -0.598  -0.580  -0.634  -0.349  -0.320  -0.405
53    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
54    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
55    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
56    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
57    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
58    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
59    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
60    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
61    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
62    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
63    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
64    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
65    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
66    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
67    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
68    D        -1.462  -1.459  -1.416  -1.470  -1.441  -1.392  -1.255  -1.250  -1.183
69    D        -0.260  -0.241  -0.299  -0.153  -0.118  -0.231  -0.349  -0.320  -0.405
70    A        -1.462  -1.459  -1.416  -1.220  -1.213  -1.146  -1.255  -1.250  -1.183
71    -        -0.407  -0.407  -0.371  -0.679  -0.678  -0.615  -0.575  -0.574  -0.516
72    -         1.396   1.397   1.415   1.610   1.614   1.635   1.464   1.464   1.485
73    D        -0.260  -0.300  -0.308  -0.322  -0.389  -0.408  -0.349  -0.410  -0.418
74    T        -1.462  -1.459  -1.416  -0.886  -0.871  -0.818  -1.255  -1.250  -1.183
75    G        -1.462  -1.459  -1.416  -0.966  -0.980  -0.897  -1.255  -1.250  -1.183
76    S        -1.462  -1.459  -1.416  -1.641  -1.624  -1.560  -1.255  -1.250  -1.183
77    A        -1.462  -1.459  -1.416  -1.231  -1.202  -1.157  -1.255  -1.250  -1.183
78    E        -1.462  -1.459  -1.416  -1.691  -1.676  -1.610  -1.255  -1.250  -1.183
79    T        -1.462  -1.459  -1.416  -1.018  -1.003  -0.947  -1.255  -1.250  -1.183
80    E        -1.462  -1.459  -1.416  -1.679  -1.702  -1.597  -1.255  -1.250  -1.183
81    L        -1.462  -1.459  -1.416  -1.743  -1.716  -1.660  -1.255  -1.250  -1.183
82    P         1.396   1.397   1.415   1.536   1.541   1.563   1.464   1.464   1.485
83    R        -0.260  -0.300  -0.308  -0.254  -0.345  -0.384  -0.349  -0.410  -0.418
84    L         1.396   1.397   1.415   0.991   0.983   1.027   1.464   1.464   1.485
85    I        -0.260  -0.300  -0.308  -0.203  -0.270  -0.297  -0.349  -0.410  -0.418
86    S         1.396   1.397   1.415   1.409   1.414   1.438   1.464   1.464   1.485
87    Q        -1.462  -1.459  -1.416  -1.717  -1.736  -1.635  -1.255  -1.250  -1.183
88    A        -0.260  -0.241  -0.299  -0.453  -0.425  -0.483  -0.349  -0.320  -0.405
89    T        -0.260  -0.300  -0.308  -0.322  -0.398  -0.439  -0.349  -0.410  -0.418
90    V        -0.260  -0.232  -0.298  -0.014   0.033  -0.085  -0.349  -0.306  -0.403
91    E        -1.462  -1.459  -1.416  -1.264  -1.240  -1.189  -1.255  -1.250  -1.183
92    K        -0.260  -0.300  -0.308  -0.322  -0.388  -0.399  -0.349  -0.410  -0.418
93    V        -0.260  -0.300  -0.308  -0.237  -0.333  -0.368  -0.349  -0.410  -0.418
94    P         1.396   1.397   1.415   1.536   1.541   1.563   1.464   1.464   1.485
95    E        -0.407  -0.407  -0.371  -0.505  -0.504  -0.443  -0.575  -0.574  -0.516
96    L         1.396   1.397   1.415   1.125   1.128   1.158   1.464   1.464   1.485
97    K        -0.407  -0.407  -0.371  -0.562  -0.561  -0.499  -0.575  -0.574  -0.516
98    W         1.396   1.397   1.415   1.832   1.836   1.853   1.464   1.464   1.485
99    Y         1.396   1.397   1.415   1.662   1.667   1.687   1.464   1.464   1.485
100   N         1.396   1.397   1.415   1.687   1.691   1.711   1.464   1.464   1.485
101   D        -0.407  -0.407  -0.371  -0.818  -0.818  -0.752  -0.575  -0.574  -0.516
102   Q         1.396   1.397   1.415   1.687   1.691   1.711   1.464   1.464   1.485
103   I         1.396   1.397   1.415   1.438   1.442   1.466   1.464   1.464   1.485
104   S        -0.407  -0.407  -0.371  -0.562  -0.561  -0.499  -0.575  -0.574  -0.516
105   L         1.396   1.397   1.415   1.125   1.128   1.158   1.464   1.464   1.485
106   I        -0.407  -0.407  -0.371  -0.321  -0.319  -0.262  -0.575  -0.574  -0.516
107   T        -0.407  -0.407  -0.371  -0.303  -0.301  -0.245  -0.575  -0.574  -0.516
108   E         1.396   1.397   1.415   1.071   1.074   1.105   1.464   1.464   1.485
109   K        -0.407  -0.407  -0.371  -0.562  -0.561  -0.499  -0.575  -0.574  -0.516
110   L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
111   E        -0.407  -0.407  -0.371  -0.505  -0.504  -0.443  -0.575  -0.574  -0.516
112   D         1.396   1.397   1.415   1.335   1.339   1.365   1.464   1.464   1.485
113   D        -1.462  -1.459  -1.416  -1.743  -1.762  -1.660  -1.255  -1.250  -1.183
114   E        -0.260  -0.241  -0.299  -0.445  -0.404  -0.537  -0.349  -0.320  -0.405
115   D        -0.260  -0.300  -0.308  -0.445  -0.522  -0.554  -0.349  -0.410  -0.418
116   I        -0.260  -0.232  -0.298   0.010   0.053  -0.033  -0.349  -0.306  -0.403
117   E        -0.260  -0.232  -0.298  -0.589  -0.543  -0.638  -0.349  -0.306  -0.403
118   V        -0.260  -0.300  -0.308  -0.014  -0.081  -0.102  -0.349  -0.410  -0.418
119   P         1.396   1.397   1.415   1.536   1.541   1.563   1.464   1.464   1.485
120   E        -0.260  -0.232  -0.298  -0.507  -0.466  -0.543  -0.349  -0.306  -0.403
121   E        -0.260  -0.300  -0.308  -0.453  -0.499  -0.492  -0.349  -0.410  -0.418
122   L         1.396   1.397   1.415   0.991   0.983   1.027   1.464   1.464   1.485
123   M        -1.462  -1.459  -1.416  -0.906  -0.901  -0.837  -1.255  -1.250  -1.183
124   D        -0.260  -0.241  -0.299  -0.589  -0.557  -0.640  -0.349  -0.320  -0.405
125   A        -0.260  -0.241  -0.299  -0.145  -0.114  -0.195  -0.349  -0.320  -0.405
126   Y         1.396   1.397   1.415   1.661   1.665   1.685   1.464   1.464   1.485
127   T        -0.260  -0.241  -0.299  -0.525  -0.494  -0.566  -0.349  -0.320  -0.405
128   L         1.396   1.397   1.415   0.991   0.983   1.027   1.464   1.464   1.485
129   Y        -0.260  -0.241  -0.299   0.213   0.244   0.141  -0.349  -0.320  -0.405
130   K         1.396   1.397   1.415   1.336   1.338   1.365   1.464   1.464   1.485
131   E        -1.462  -1.459  -1.416  -1.144  -1.123  -1.071  -1.255  -1.250  -1.183
132   T        -0.260  -0.232  -0.298  -0.357  -0.297  -0.458  -0.349  -0.306  -0.403
133   P        -0.260  -0.232  -0.298  -0.030   0.015  -0.086  -0.349  -0.306  -0.403
134   L         1.396   1.397   1.415   0.991   0.983   1.027   1.464   1.464   1.485
135   L         1.396   1.397   1.415   0.991   0.983   1.027   1.464   1.464   1.485
136   Y        -0.260  -0.232  -0.298   0.034   0.081  -0.037  -0.349  -0.306  -0.403
137   N        -0.260  -0.241  -0.299  -0.178  -0.152  -0.219  -0.349  -0.320  -0.405
138   D         1.396   1.397   1.415   1.373   1.379   1.402   1.464   1.464   1.485
139   -         1.396   1.397   1.415   1.711   1.715   1.734   1.464   1.464   1.485
140   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
141   T        -0.407  -0.407  -0.371  -0.505  -0.504  -0.443  -0.575  -0.574  -0.516
142   H        -0.407  -0.407  -0.371  -0.393  -0.392  -0.334  -0.575  -0.574  -0.516
143   T        -0.260  -0.241  -0.299  -0.211  -0.178  -0.272  -0.349  -0.320  -0.405
144   P        -0.260  -0.241  -0.299  -0.507  -0.480  -0.545  -0.349  -0.320  -0.405
* 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/P40060
Output conservation file - output/P40060
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
