1     M         1.408   1.422   1.481   1.712   1.725   1.818   1.525   1.542   1.627
2     P        -1.636  -1.607  -1.531  -1.347  -1.300  -1.187  -1.275  -1.241  -1.130
3     L        -0.359  -0.306  -0.316  -0.628  -0.510  -0.600  -0.575  -0.497  -0.509
4     F        -0.948  -0.927  -0.849  -0.958  -0.920  -0.804  -0.995  -0.965  -0.854
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        -0.384  -0.335  -0.331  -0.904  -0.844  -0.782  -0.625  -0.560  -0.534
14    R        -0.207  -0.137  -0.261  -0.259  -0.134  -0.446  -0.356  -0.255  -0.432
15    L        -0.207  -0.153  -0.262  -0.246  -0.164  -0.297  -0.356  -0.277  -0.434
16    C         0.558   0.632   0.468   0.523   0.630   0.416   0.450   0.572   0.263
17    Q        -0.066  -0.063  -0.223   0.097   0.115  -0.188  -0.155  -0.155  -0.378
18    P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
19    Q        -0.703  -0.789  -0.780  -0.485  -0.627  -0.608  -0.715  -0.811  -0.779
20    S        -0.066  -0.104  -0.214  -0.150  -0.195  -0.347  -0.155  -0.211  -0.365
21    R        -1.636  -1.607  -1.531  -1.785  -1.640  -1.616  -1.275  -1.241  -1.130
22    R         0.558   0.480   0.438   0.292   0.162   0.095   0.450   0.311   0.208
23    M        -0.856  -0.809  -0.812  -0.703  -0.654  -0.622  -0.894  -0.834  -0.815
24    F        -0.384  -0.412  -0.338  -0.577  -0.599  -0.483  -0.625  -0.651  -0.543
25    S        -0.856  -0.866  -0.824  -1.177  -1.228  -1.114  -0.894  -0.900  -0.828
26    S        -0.384  -0.365  -0.335  -0.492  -0.450  -0.372  -0.625  -0.595  -0.540
27    I        -0.384  -0.366  -0.329  -0.442  -0.405  -0.369  -0.625  -0.597  -0.532
28    S         0.264   0.294   0.334  -0.084  -0.028   0.033  -0.088  -0.036   0.010
29    S        -0.207  -0.257  -0.282  -0.375  -0.431  -0.473  -0.356  -0.428  -0.461
30    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
31    F        -1.244  -1.246  -1.200  -1.069  -1.103  -0.998  -1.088  -1.082  -0.998
32    S        -0.066  -0.104  -0.214  -0.169  -0.214  -0.376  -0.155  -0.211  -0.365
33    A        -1.244  -1.225  -1.191  -1.059  -1.019  -0.986  -1.088  -1.064  -0.990
34    L        -0.703  -0.740  -0.774  -0.880  -0.917  -1.017  -0.715  -0.757  -0.772
35    S        -0.851  -0.871  -0.814  -1.148  -1.164  -1.102  -0.901  -0.911  -0.819
36    V        -0.851  -0.766  -0.803  -0.777  -0.666  -0.704  -0.901  -0.812  -0.809
37    L        -0.703  -0.740  -0.774  -0.711  -0.750  -0.787  -0.715  -0.757  -0.772
38    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
39    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
40    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
41    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
42    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
43    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
44    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
45    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
46    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
47    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
48    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
49    R        -1.244  -1.175  -1.185  -1.127  -1.032  -1.054  -1.088  -1.015  -0.985
50    P        -0.066  -0.088  -0.209   0.157   0.115  -0.096  -0.155  -0.186  -0.359
51    Q        -1.636  -1.607  -1.531  -1.228  -1.199  -1.070  -1.275  -1.241  -1.130
52    T        -1.636  -1.607  -1.531  -1.390  -1.332  -1.229  -1.275  -1.241  -1.130
53    G        -0.384  -0.414  -0.334  -0.495  -0.577  -0.443  -0.625  -0.653  -0.539
54    M        -0.948  -0.927  -0.849  -1.024  -1.006  -0.869  -0.995  -0.965  -0.854
55    L         1.408   1.422   1.481   1.314   1.342   1.427   1.525   1.542   1.627
56    L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
57    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
58    S        -1.244  -1.257  -1.203  -1.250  -1.261  -1.134  -1.088  -1.093  -1.001
59    S        -1.636  -1.607  -1.531  -1.383  -1.335  -1.222  -1.275  -1.241  -1.130
60    P        -1.244  -1.276  -1.199  -1.096  -1.169  -1.043  -1.088  -1.108  -0.998
61    L        -0.311  -0.310  -0.301  -0.664  -0.657  -0.631  -0.528  -0.526  -0.496
62    K        -1.636  -1.607  -1.531  -1.285  -1.245  -1.126  -1.275  -1.241  -1.130
63    T        -0.703  -0.789  -0.780  -0.644  -0.816  -0.812  -0.715  -0.811  -0.779
64    P        -0.703  -0.665  -0.752  -0.787  -0.733  -0.828  -0.715  -0.666  -0.748
65    S         0.326   0.282   0.332  -0.093  -0.174  -0.120   0.032  -0.058   0.005
66    F        -0.703  -0.621  -0.743  -0.435  -0.315  -0.502  -0.715  -0.610  -0.737
67    T        -0.311  -0.251  -0.301  -0.382  -0.285  -0.390  -0.528  -0.454  -0.498
68    P        -1.244  -1.257  -1.199  -1.124  -1.164  -1.064  -1.088  -1.092  -0.997
69    L        -1.244  -1.257  -1.203  -1.322  -1.304  -1.232  -1.088  -1.093  -1.001
70    G        -1.636  -1.607  -1.531  -1.365  -1.329  -1.204  -1.275  -1.241  -1.130
71    F         0.642   0.731   0.513   0.861   0.982   0.678   0.592   0.731   0.347
72    G        -0.066  -0.113  -0.215   0.040  -0.047  -0.206  -0.155  -0.221  -0.366
73    L        -0.703  -0.771  -0.772  -0.779  -0.878  -0.876  -0.715  -0.791  -0.770
74    I        -1.244  -1.214  -1.192  -0.871  -0.848  -0.794  -1.088  -1.051  -0.991
75    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
76    Q         1.408   1.422   1.481   1.594   1.613   1.701   1.525   1.542   1.627
77    R        -0.066  -0.063  -0.223  -0.231  -0.232  -0.423  -0.155  -0.155  -0.378
78    R         1.408   1.422   1.481   1.167   1.181   1.282   1.525   1.542   1.627
79    W        -0.311  -0.315  -0.299  -0.078  -0.062  -0.054  -0.528  -0.518  -0.493
80    K         1.408   1.422   1.481   1.518   1.543   1.627   1.525   1.542   1.627
81    S        -0.066  -0.181  -0.236  -0.145  -0.299  -0.370  -0.155  -0.317  -0.396
82    R         0.642   0.569   0.490   0.470   0.366   0.281   0.592   0.466   0.303
83    G         1.408   1.422   1.481   1.505   1.521   1.614   1.525   1.542   1.627
84    N         0.642   0.589   0.499   0.942   0.859   0.723   0.592   0.500   0.321
85    T        -0.703  -0.771  -0.772  -0.487  -0.567  -0.586  -0.715  -0.791  -0.770
86    Y         0.642   0.652   0.507   1.028   1.036   0.799   0.592   0.605   0.335
87    Q         1.408   1.422   1.481   1.594   1.613   1.701   1.525   1.542   1.627
88    P         1.408   1.422   1.481   1.633   1.652   1.741   1.525   1.542   1.627
89    S         1.408   1.422   1.481   1.262   1.297   1.376   1.525   1.542   1.627
90    T        -0.066  -0.181  -0.236   0.169  -0.006  -0.076  -0.155  -0.317  -0.396
91    L         0.230   0.247   0.318  -0.366  -0.344  -0.224  -0.155  -0.126  -0.022
92    K         1.408   1.422   1.481   1.529   1.555   1.638   1.525   1.542   1.627
93    R         1.408   1.422   1.481   1.167   1.181   1.282   1.525   1.542   1.627
94    K         1.408   1.422   1.481   1.529   1.555   1.638   1.525   1.542   1.627
95    R         1.408   1.422   1.481   1.167   1.181   1.282   1.525   1.542   1.627
96    T        -0.851  -0.864  -0.813  -1.095  -1.134  -1.086  -0.901  -0.903  -0.818
97    F        -0.851  -0.871  -0.814  -0.829  -0.835  -0.726  -0.901  -0.911  -0.819
98    G         1.408   1.422   1.481   1.505   1.521   1.614   1.525   1.542   1.627
99    F         1.408   1.422   1.481   1.570   1.595   1.678   1.525   1.542   1.627
100   L         1.408   1.422   1.481   1.339   1.372   1.452   1.525   1.542   1.627
101   A         0.642   0.569   0.490   0.855   0.726   0.555   0.592   0.466   0.303
102   R         1.408   1.422   1.481   1.167   1.181   1.282   1.525   1.542   1.627
103   A        -0.851  -0.895  -0.816  -0.975  -1.037  -0.922  -0.901  -0.934  -0.821
104   K         0.642   0.731   0.522   0.415   0.533   0.235   0.592   0.732   0.361
105   S         1.408   1.422   1.481   1.262   1.297   1.376   1.525   1.542   1.627
106   K        -0.851  -0.834  -0.812  -1.013  -1.008  -0.910  -0.901  -0.876  -0.817
107   Q        -1.244  -1.190  -1.181  -1.172  -1.090  -1.094  -1.088  -1.029  -0.981
108   G         1.408   1.422   1.481   1.505   1.521   1.614   1.525   1.542   1.627
109   S        -0.066   0.009  -0.191  -0.362  -0.244  -0.576  -0.155  -0.047  -0.333
110   K        -0.066  -0.129  -0.230  -0.018  -0.140  -0.343  -0.155  -0.245  -0.388
111   I         0.642   0.569   0.490   0.970   0.863   0.742   0.592   0.466   0.303
112   L         0.642   0.589   0.499   0.621   0.558   0.420   0.592   0.500   0.321
113   K        -0.703  -0.678  -0.761  -0.718  -0.715  -0.862  -0.715  -0.684  -0.758
114   R         0.642   0.569   0.490   0.482   0.383   0.303   0.592   0.466   0.303
115   R         1.408   1.422   1.481   1.167   1.181   1.282   1.525   1.542   1.627
116   K        -0.311  -0.346  -0.312  -0.576  -0.647  -0.601  -0.528  -0.567  -0.511
117   L        -0.851  -0.871  -0.811  -0.867  -0.904  -0.787  -0.901  -0.911  -0.817
118   K         1.408   1.422   1.481   1.529   1.555   1.638   1.525   1.542   1.627
119   G         1.408   1.422   1.481   1.505   1.521   1.614   1.525   1.542   1.627
120   R         1.408   1.422   1.481   1.167   1.181   1.282   1.525   1.542   1.627
121   W         0.642   0.569   0.490   1.070   0.963   0.831   0.592   0.466   0.303
122   F         0.230   0.246   0.318   0.259   0.288   0.403  -0.155  -0.130  -0.023
123   L         1.408   1.422   1.481   1.339   1.372   1.452   1.525   1.542   1.627
124   S         0.326   0.310   0.347   0.017  -0.004   0.048   0.032  -0.004   0.035
125   H         0.642   0.652   0.507   1.089   1.098   0.887   0.592   0.605   0.335
* 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/Q04598
Output conservation file - output/Q04598
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
