1     M         0.577   0.621   0.645   0.949   0.965   0.950   0.592   0.648   0.681
2     S        -1.899  -1.758  -1.692  -2.278  -2.055  -1.808  -2.129  -1.880  -1.688
3     A        -1.194  -1.027  -0.834  -1.251  -1.089  -0.916  -1.649  -1.385  -1.099
4     K         0.577   0.621   0.645   0.043   0.141   0.265   0.592   0.648   0.681
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         0.577   0.621   0.645   0.133   0.241   0.333   0.592   0.648   0.681
14    E        -1.816  -1.961  -2.306  -0.995  -1.237  -1.755  -1.569  -1.739  -1.988
15    K         0.577   0.621   0.645   0.052   0.161   0.271   0.592   0.648   0.681
16    K        -0.704  -0.801  -0.835  -1.145  -1.311  -1.398  -0.849  -1.012  -1.102
17    P         0.577   0.621   0.645   0.797   0.836   0.835   0.592   0.648   0.681
18    A         0.577   0.621   0.645   0.133   0.241   0.333   0.592   0.648   0.681
19    S        -0.246  -0.589  -0.808  -0.283  -0.596  -0.849  -0.208  -0.685  -1.057
20    K         0.577   0.621   0.645   0.052   0.161   0.271   0.592   0.648   0.681
21    A         0.577   0.621   0.645   0.133   0.241   0.333   0.592   0.648   0.681
22    P         0.577   0.621   0.645   0.797   0.836   0.835   0.592   0.648   0.681
23    A         0.577   0.621   0.645   0.133   0.241   0.333   0.592   0.648   0.681
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        -0.246  -0.595  -0.802   0.145  -0.255  -0.576  -0.208  -0.695  -1.047
31    K         0.577   0.621   0.645   0.052   0.161   0.271   0.592   0.648   0.681
32    K        -0.246  -0.595  -0.802  -0.579  -0.991  -1.336  -0.208  -0.695  -1.047
33    P        -1.044  -1.403  -1.686  -0.310  -0.772  -1.193  -0.929  -1.366  -1.680
34    A         0.577   0.621   0.645   0.127   0.233   0.328   0.592   0.648   0.681
35    A        -0.775  -1.046  -0.839  -0.976  -1.304  -0.917  -0.958  -1.419  -1.108
36    K        -0.246  -0.595  -0.802  -0.510  -0.847  -1.020  -0.208  -0.695  -1.047
37    K        -0.246  -0.595  -0.802  -0.493  -0.811  -0.946  -0.208  -0.695  -1.047
38    T         0.577   0.621   0.645   0.505   0.537   0.614   0.592   0.648   0.681
39    S        -2.452  -2.629  -2.311  -2.528  -2.621  -2.176  -2.369  -2.402  -1.992
40    T        -3.116  -3.010  -2.788  -2.979  -3.091  -2.742  -2.770  -2.569  -2.172
41    S        -1.991  -1.717  -1.694  -2.197  -1.921  -1.940  -2.120  -1.777  -1.690
42    T        -3.859  -3.404  -3.179  -3.133  -2.851  -2.488  -3.170  -2.666  -2.293
43    D        -1.285  -1.081  -0.838  -0.948  -0.787  -0.499  -1.809  -1.479  -1.106
44    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
45    G        -3.772  -3.109  -2.795  -3.947  -3.242  -2.770  -3.282  -2.584  -2.177
46    K         0.577   0.621   0.645   0.052   0.161   0.271   0.592   0.648   0.681
47    K         0.577   0.621   0.645   0.052   0.161   0.271   0.592   0.648   0.681
48    R         0.577   0.621   0.645   0.770   0.795   0.815   0.592   0.648   0.681
49    S        -1.747  -1.679  -1.682  -1.628  -1.485  -1.555  -1.889  -1.695  -1.676
50    K         0.577   0.621   0.645   0.052   0.161   0.271   0.592   0.648   0.681
51    A        -1.475  -1.478  -1.675  -1.500  -1.453  -1.629  -1.489  -1.452  -1.668
52    R         0.577   0.621   0.645   0.770   0.795   0.815   0.592   0.648   0.681
53    K         0.577   0.621   0.645   0.052   0.161   0.271   0.592   0.648   0.681
54    E         0.577   0.621   0.645   0.697   0.746   0.759   0.592   0.648   0.681
55    T         0.577   0.621   0.645   0.505   0.537   0.614   0.592   0.648   0.681
56    Y         0.577   0.621   0.645   0.829   0.858   0.859   0.592   0.648   0.681
57    S         0.577   0.621   0.645   0.268   0.390   0.435   0.592   0.648   0.681
58    S         0.577   0.621   0.645   0.268   0.390   0.435   0.592   0.648   0.681
59    Y         0.577   0.621   0.645   0.829   0.858   0.859   0.592   0.648   0.681
60    I         0.577   0.621   0.645   0.687   0.734   0.752   0.592   0.648   0.681
61    Y         0.577   0.621   0.645   0.829   0.858   0.859   0.592   0.648   0.681
62    K         0.577   0.621   0.645   0.052   0.161   0.271   0.592   0.648   0.681
63    V         0.577   0.621   0.645   0.811   0.836   0.845   0.592   0.648   0.681
64    L         0.577   0.621   0.645   0.802   0.833   0.839   0.592   0.648   0.681
65    K         0.577   0.621   0.645   0.052   0.161   0.271   0.592   0.648   0.681
66    Q         0.577   0.621   0.645   0.914   0.942   0.923   0.592   0.648   0.681
67    T        -0.704  -0.907  -0.832  -0.531  -0.870  -0.746  -0.849  -1.185  -1.097
68    H         0.577   0.621   0.645   0.976   0.993   0.970   0.592   0.648   0.681
69    P         0.577   0.621   0.645   0.797   0.836   0.835   0.592   0.648   0.681
70    D         0.577   0.621   0.645   0.918   0.927   0.927   0.592   0.648   0.681
71    T         0.577   0.621   0.645   0.505   0.537   0.614   0.592   0.648   0.681
72    G         0.577   0.621   0.645   0.851   0.855   0.876   0.592   0.648   0.681
73    I         0.577   0.621   0.645   0.687   0.734   0.752   0.592   0.648   0.681
74    S         0.577   0.621   0.645   0.268   0.390   0.435   0.592   0.648   0.681
75    Q        -1.475  -1.920  -1.700  -0.681  -1.383  -1.228  -1.489  -2.012  -1.696
76    K        -1.475  -1.922  -1.698  -1.507  -1.967  -1.527  -1.489  -2.014  -1.695
77    S        -1.194  -0.771  -0.816  -1.809  -1.129  -1.236  -1.649  -0.965  -1.069
78    M         0.577   0.621   0.645   0.949   0.965   0.950   0.592   0.648   0.681
79    S        -0.246  -0.595  -0.802  -0.292  -0.619  -0.882  -0.208  -0.695  -1.047
80    I         0.577   0.621   0.645   0.687   0.734   0.752   0.592   0.648   0.681
81    L        -1.285  -1.081  -0.838  -0.974  -0.792  -0.512  -1.809  -1.479  -1.106
82    N         0.577   0.621   0.645   0.901   0.918   0.913   0.592   0.648   0.681
83    S         0.577   0.621   0.645   0.268   0.390   0.435   0.592   0.648   0.681
84    F         0.577   0.621   0.645   0.972   0.985   0.967   0.592   0.648   0.681
85    V         0.577   0.621   0.645   0.811   0.836   0.845   0.592   0.648   0.681
86    N         0.577   0.621   0.645   0.901   0.918   0.913   0.592   0.648   0.681
87    D         0.577   0.621   0.645   0.918   0.927   0.927   0.592   0.648   0.681
88    I         0.577   0.621   0.645   0.687   0.734   0.752   0.592   0.648   0.681
89    F         0.577   0.621   0.645   0.972   0.985   0.967   0.592   0.648   0.681
90    E         0.577   0.621   0.645   0.697   0.746   0.759   0.592   0.648   0.681
91    R         0.577   0.621   0.645   0.770   0.795   0.815   0.592   0.648   0.681
92    I        -0.704  -0.903  -0.836  -0.352  -0.683  -0.646  -0.849  -1.179  -1.104
93    A         0.577   0.621   0.645   0.133   0.241   0.333   0.592   0.648   0.681
94    T        -1.875  -1.211  -1.674  -1.632  -0.894  -1.539  -1.969  -1.113  -1.666
95    E         0.577   0.621   0.645   0.697   0.746   0.759   0.592   0.648   0.681
96    A        -0.704  -0.337  -0.802  -1.030  -0.541  -1.213  -0.849  -0.327  -1.047
97    S         0.577   0.621   0.645   0.268   0.390   0.435   0.592   0.648   0.681
98    K         0.577   0.621   0.645   0.052   0.161   0.271   0.592   0.648   0.681
99    L         0.577   0.621   0.645   0.802   0.833   0.839   0.592   0.648   0.681
100   A         0.577   0.621   0.645   0.133   0.241   0.333   0.592   0.648   0.681
101   A        -0.246  -0.589  -0.808  -0.457  -0.825  -1.104  -0.208  -0.685  -1.057
102   Y         0.577   0.621   0.645   0.829   0.858   0.859   0.592   0.648   0.681
103   N        -0.246  -0.589  -0.808   0.314  -0.151  -0.608  -0.208  -0.685  -1.057
104   K         0.577   0.621   0.645   0.052   0.161   0.271   0.592   0.648   0.681
105   K         0.577   0.621   0.645   0.052   0.161   0.271   0.592   0.648   0.681
106   S         0.577   0.621   0.645   0.268   0.390   0.435   0.592   0.648   0.681
107   T         0.577   0.621   0.645   0.505   0.537   0.614   0.592   0.648   0.681
108   I         0.577   0.621   0.645   0.687   0.734   0.752   0.592   0.648   0.681
109   S        -0.246  -0.589  -0.808  -0.321  -0.675  -1.016  -0.208  -0.685  -1.057
110   A        -1.006  -1.097  -0.834  -1.483  -1.672  -1.255  -1.329  -1.506  -1.100
111   R         0.577   0.621   0.645   0.770   0.795   0.815   0.592   0.648   0.681
112   E         0.577   0.621   0.645   0.697   0.746   0.759   0.592   0.648   0.681
113   I         0.577   0.621   0.645   0.687   0.734   0.752   0.592   0.648   0.681
114   Q         0.577   0.621   0.645   0.914   0.942   0.923   0.592   0.648   0.681
115   T         0.577   0.621   0.645   0.505   0.537   0.614   0.592   0.648   0.681
116   A        -0.246  -0.257  -0.799  -0.482  -0.449  -1.207  -0.208  -0.220  -1.042
117   V         0.577   0.621   0.645   0.811   0.836   0.845   0.592   0.648   0.681
118   R         0.577   0.621   0.645   0.770   0.795   0.815   0.592   0.648   0.681
119   L         0.577   0.621   0.645   0.802   0.833   0.839   0.592   0.648   0.681
120   I         0.577   0.621   0.645   0.687   0.734   0.752   0.592   0.648   0.681
121   L         0.577   0.621   0.645   0.802   0.833   0.839   0.592   0.648   0.681
122   P         0.577   0.621   0.645   0.797   0.836   0.835   0.592   0.648   0.681
123   G         0.577   0.621   0.645   0.851   0.855   0.876   0.592   0.648   0.681
124   E         0.577   0.621   0.645   0.697   0.746   0.759   0.592   0.648   0.681
125   L         0.577   0.621   0.645   0.802   0.833   0.839   0.592   0.648   0.681
126   A         0.577   0.621   0.645   0.133   0.241   0.333   0.592   0.648   0.681
127   K         0.577   0.621   0.645   0.052   0.161   0.271   0.592   0.648   0.681
128   H         0.577   0.621   0.645   0.976   0.993   0.970   0.592   0.648   0.681
129   A         0.577   0.621   0.645   0.133   0.241   0.333   0.592   0.648   0.681
130   V        -0.246  -0.589  -0.808   0.225  -0.231  -0.665  -0.208  -0.685  -1.057
131   S        -1.044  -1.691  -1.686  -0.868  -1.602  -1.580  -0.929  -1.710  -1.681
132   E        -0.246  -0.589  -0.808   0.152  -0.230  -0.554  -0.208  -0.685  -1.057
133   G         0.577   0.621   0.645   0.851   0.855   0.876   0.592   0.648   0.681
134   T         0.577   0.621   0.645   0.505   0.537   0.614   0.592   0.648   0.681
135   R        -0.704  -0.907  -0.832  -0.430  -0.901  -0.967  -0.849  -1.185  -1.097
136   A        -0.246  -0.595  -0.802  -0.482  -0.871  -1.213  -0.208  -0.695  -1.047
137   V         0.577   0.621   0.645   0.811   0.836   0.845   0.592   0.648   0.681
138   T        -0.246  -0.589  -0.808  -0.118  -0.597  -1.032  -0.208  -0.685  -1.057
139   K         0.577   0.621   0.645   0.052   0.161   0.271   0.592   0.648   0.681
140   Y         0.577   0.621   0.645   0.829   0.858   0.859   0.592   0.648   0.681
141   S         0.577   0.621   0.645   0.268   0.390   0.435   0.592   0.648   0.681
142   S        -0.246  -0.589  -0.808  -0.321  -0.675  -1.016  -0.208  -0.685  -1.057
143   S        -1.899  -1.833  -1.691  -2.206  -1.890  -1.700  -2.129  -1.895  -1.686
144   T        -2.775  -2.617  -2.312  -2.747  -2.580  -2.175  -2.690  -2.420  -1.994
145   Q        -2.563  -2.224  -2.309  -1.843  -1.571  -1.928  -2.530  -2.116  -1.991
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/P02293
Output conservation file - output/P02293
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
