1     M         0.690   0.709   0.739   1.039   1.029   1.047   0.723   0.749   0.788
2     S        -0.802  -1.043  -1.194  -0.531  -0.841  -1.147  -0.815  -1.134  -1.306
3     -        -0.325  -0.433  -0.477  -0.465  -0.628  -0.659  -0.488  -0.674  -0.769
4     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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     -        -0.325  -0.331  -0.470  -0.663  -0.649  -0.906  -0.488  -0.503  -0.757
9     G         0.690   0.709   0.739   0.530   0.546   0.624   0.723   0.749   0.788
10    K         0.690   0.709   0.739   0.423   0.475   0.535   0.723   0.749   0.788
11    A        -2.693  -2.683  -2.467  -2.341  -2.348  -2.083  -2.234  -2.186  -1.882
12    H        -1.488  -1.754  -1.731  -1.037  -1.483  -1.592  -1.406  -1.696  -1.604
13    G         0.690   0.709   0.739   0.530   0.546   0.624   0.723   0.749   0.788
14    G         0.690   0.709   0.739   0.530   0.546   0.624   0.723   0.749   0.788
15    K         0.690   0.709   0.739   0.423   0.475   0.535   0.723   0.749   0.788
16    G        -0.074  -0.115  -0.438  -0.127  -0.178  -0.621  -0.105  -0.166  -0.701
17    K        -0.802  -1.043  -1.194  -0.925  -1.259  -1.475  -0.815  -1.134  -1.306
18    S        -0.451  -0.504  -0.489  -0.488  -0.602  -0.660  -0.696  -0.797  -0.791
19    G        -1.136  -1.125  -1.194  -1.326  -1.326  -1.447  -1.288  -1.238  -1.307
20    A        -1.990  -1.955  -1.738  -2.305  -2.238  -1.840  -1.997  -1.913  -1.612
21    K        -2.341  -2.306  -2.137  -2.496  -2.499  -2.154  -2.116  -2.046  -1.772
22    D        -0.675  -0.648  -0.502  -0.670  -0.660  -0.464  -1.094  -1.055  -0.813
23    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
28    S        -2.474  -2.267  -2.134  -2.452  -2.039  -1.920  -2.234  -1.995  -1.770
29    L        -2.341  -2.321  -2.137  -2.615  -2.543  -2.167  -2.116  -2.046  -1.772
30    R        -2.474  -2.426  -2.138  -2.747  -2.735  -2.288  -2.234  -2.127  -1.773
31    S        -1.857  -1.562  -1.722  -1.687  -1.245  -1.522  -1.879  -1.535  -1.597
32    Q        -1.136  -1.125  -1.194  -0.779  -0.752  -0.878  -1.288  -1.238  -1.307
33    S         0.690   0.709   0.739   0.780   0.815   0.831   0.723   0.749   0.788
34    S        -0.451  -0.298  -0.462  -0.229  -0.006  -0.347  -0.696  -0.450  -0.744
35    S         0.690   0.709   0.739   0.780   0.815   0.831   0.723   0.749   0.788
36    A        -0.074  -0.158  -0.441  -0.195  -0.282  -0.676  -0.105  -0.230  -0.707
37    R         0.690   0.709   0.739   0.732   0.747   0.791   0.723   0.749   0.788
38    A         0.690   0.709   0.739   0.463   0.498   0.568   0.723   0.749   0.788
39    G         0.690   0.709   0.739   0.530   0.546   0.624   0.723   0.749   0.788
40    L         0.690   0.709   0.739   0.468   0.517   0.573   0.723   0.749   0.788
41    Q         0.690   0.709   0.739   0.942   0.936   0.966   0.723   0.749   0.788
42    F         0.690   0.709   0.739   1.064   1.061   1.067   0.723   0.749   0.788
43    P         0.690   0.709   0.739   0.993   0.994   1.009   0.723   0.749   0.788
44    V        -0.074  -0.115  -0.438   0.172   0.120  -0.291  -0.105  -0.166  -0.701
45    G         0.690   0.709   0.739   0.530   0.546   0.624   0.723   0.749   0.788
46    R         0.690   0.709   0.739   0.732   0.747   0.791   0.723   0.749   0.788
47    I        -0.716  -0.644  -0.502  -0.855  -0.751  -0.526  -1.169  -1.047  -0.814
48    K        -0.074  -0.294  -0.451  -0.242  -0.509  -0.743  -0.105  -0.444  -0.723
49    R         0.690   0.709   0.739   0.732   0.747   0.791   0.723   0.749   0.788
50    Y        -0.451  -0.568  -0.497  -0.111  -0.320  -0.253  -0.696  -0.910  -0.806
51    L        -0.074  -0.158  -0.441  -0.149  -0.218  -0.551  -0.105  -0.230  -0.707
52    K         0.690   0.709   0.739   0.423   0.475   0.535   0.723   0.749   0.788
53    R        -1.488  -1.754  -1.731  -1.299  -1.774  -1.794  -1.406  -1.696  -1.604
54    H        -2.341  -2.220  -2.130  -1.960  -1.914  -1.741  -2.116  -1.983  -1.767
55    A        -1.136  -1.278  -1.216  -1.273  -1.436  -1.275  -1.288  -1.472  -1.335
56    T        -1.488  -1.134  -1.700  -1.033  -0.591  -1.478  -1.406  -0.987  -1.574
57    G        -0.652  -0.489  -0.477  -0.711  -0.407  -0.485  -1.051  -0.770  -0.770
58    R        -1.136  -1.148  -1.192  -1.336  -1.271  -1.286  -1.288  -1.269  -1.304
59    T        -2.474  -2.289  -2.136  -2.155  -1.860  -1.756  -2.234  -2.015  -1.771
60    R         0.690   0.709   0.739   0.732   0.747   0.791   0.723   0.749   0.788
61    V         0.690   0.709   0.739   0.780   0.791   0.831   0.723   0.749   0.788
62    G         0.690   0.709   0.739   0.530   0.546   0.624   0.723   0.749   0.788
63    S        -0.652  -0.647  -0.501  -0.929  -0.993  -0.752  -1.051  -1.054  -0.811
64    K         0.690   0.709   0.739   0.423   0.475   0.535   0.723   0.749   0.788
65    A        -0.451  -0.489  -0.492  -0.717  -0.763  -0.747  -0.696  -0.770  -0.796
66    A         0.690   0.709   0.739   0.463   0.498   0.568   0.723   0.749   0.788
67    I        -0.451  -0.568  -0.497  -0.363  -0.597  -0.514  -0.696  -0.910  -0.806
68    Y         0.690   0.709   0.739   0.998   1.003   1.013   0.723   0.749   0.788
69    L        -1.488  -1.754  -1.731  -1.453  -1.790  -1.702  -1.406  -1.696  -1.604
70    T        -0.451  -0.582  -0.499  -0.395  -0.710  -0.649  -0.696  -0.936  -0.809
71    A         0.690   0.709   0.739   0.463   0.498   0.568   0.723   0.749   0.788
72    V         0.690   0.709   0.739   0.780   0.791   0.831   0.723   0.749   0.788
73    L         0.690   0.709   0.739   0.468   0.517   0.573   0.723   0.749   0.788
74    E         0.690   0.709   0.739   0.869   0.875   0.906   0.723   0.749   0.788
75    Y         0.690   0.709   0.739   0.998   1.003   1.013   0.723   0.749   0.788
76    L         0.690   0.709   0.739   0.468   0.517   0.573   0.723   0.749   0.788
77    T         0.690   0.709   0.739   0.895   0.906   0.927   0.723   0.749   0.788
78    A         0.690   0.709   0.739   0.463   0.498   0.568   0.723   0.749   0.788
79    E         0.690   0.709   0.739   0.869   0.875   0.906   0.723   0.749   0.788
80    V         0.690   0.709   0.739   0.780   0.791   0.831   0.723   0.749   0.788
81    L         0.690   0.709   0.739   0.468   0.517   0.573   0.723   0.749   0.788
82    E         0.690   0.709   0.739   0.869   0.875   0.906   0.723   0.749   0.788
83    L         0.690   0.709   0.739   0.468   0.517   0.573   0.723   0.749   0.788
84    A         0.690   0.709   0.739   0.463   0.498   0.568   0.723   0.749   0.788
85    G         0.690   0.709   0.739   0.530   0.546   0.624   0.723   0.749   0.788
86    N         0.690   0.709   0.739   0.983   0.987   1.000   0.723   0.749   0.788
87    A         0.690   0.709   0.739   0.463   0.498   0.568   0.723   0.749   0.788
88    A         0.690   0.709   0.739   0.463   0.498   0.568   0.723   0.749   0.788
89    K        -0.074  -0.158  -0.441  -0.242  -0.318  -0.728  -0.105  -0.230  -0.707
90    D         0.690   0.709   0.739   0.972   0.984   0.992   0.723   0.749   0.788
91    L         0.690   0.709   0.739   0.468   0.517   0.573   0.723   0.749   0.788
92    K         0.690   0.709   0.739   0.423   0.475   0.535   0.723   0.749   0.788
93    V         0.690   0.709   0.739   0.780   0.791   0.831   0.723   0.749   0.788
94    K         0.690   0.709   0.739   0.423   0.475   0.535   0.723   0.749   0.788
95    R         0.690   0.709   0.739   0.732   0.747   0.791   0.723   0.749   0.788
96    I         0.690   0.709   0.739   0.827   0.836   0.871   0.723   0.749   0.788
97    T         0.690   0.709   0.739   0.895   0.906   0.927   0.723   0.749   0.788
98    P         0.690   0.709   0.739   0.993   0.994   1.009   0.723   0.749   0.788
99    R         0.690   0.709   0.739   0.732   0.747   0.791   0.723   0.749   0.788
100   H         0.690   0.709   0.739   0.967   0.975   0.987   0.723   0.749   0.788
101   L         0.690   0.709   0.739   0.468   0.517   0.573   0.723   0.749   0.788
102   Q         0.690   0.709   0.739   0.942   0.936   0.966   0.723   0.749   0.788
103   L         0.690   0.709   0.739   0.468   0.517   0.573   0.723   0.749   0.788
104   A         0.690   0.709   0.739   0.463   0.498   0.568   0.723   0.749   0.788
105   I         0.690   0.709   0.739   0.827   0.836   0.871   0.723   0.749   0.788
106   R         0.690   0.709   0.739   0.732   0.747   0.791   0.723   0.749   0.788
107   G         0.690   0.709   0.739   0.530   0.546   0.624   0.723   0.749   0.788
108   D         0.690   0.709   0.739   0.972   0.984   0.992   0.723   0.749   0.788
109   D        -0.652  -0.489  -0.477  -0.585  -0.341  -0.352  -1.051  -0.770  -0.770
110   E         0.690   0.709   0.739   0.869   0.875   0.906   0.723   0.749   0.788
111   L         0.690   0.709   0.739   0.468   0.517   0.573   0.723   0.749   0.788
112   D         0.690   0.709   0.739   0.972   0.984   0.992   0.723   0.749   0.788
113   S        -1.505  -1.270  -1.211  -1.429  -1.070  -1.004  -1.761  -1.445  -1.328
114   L         0.690   0.709   0.739   0.468   0.517   0.573   0.723   0.749   0.788
115   I         0.690   0.709   0.739   0.827   0.836   0.871   0.723   0.749   0.788
116   R        -1.136  -1.012  -1.186  -1.166  -0.912  -1.229  -1.288  -1.086  -1.297
117   A         0.690   0.709   0.739   0.463   0.498   0.568   0.723   0.749   0.788
118   T         0.690   0.709   0.739   0.895   0.906   0.927   0.723   0.749   0.788
119   I         0.690   0.709   0.739   0.827   0.836   0.871   0.723   0.749   0.788
120   A         0.690   0.709   0.739   0.463   0.498   0.568   0.723   0.749   0.788
121   S        -1.990  -1.989  -1.738  -1.739  -1.768  -1.419  -1.997  -1.944  -1.612
122   G         0.690   0.709   0.739   0.530   0.546   0.624   0.723   0.749   0.788
123   G         0.690   0.709   0.739   0.530   0.546   0.624   0.723   0.749   0.788
124   V         0.690   0.709   0.739   0.780   0.791   0.831   0.723   0.749   0.788
125   L        -0.074  -0.158  -0.441  -0.149  -0.218  -0.551  -0.105  -0.230  -0.707
126   P         0.690   0.709   0.739   0.993   0.994   1.009   0.723   0.749   0.788
127   H         0.690   0.709   0.739   0.967   0.975   0.987   0.723   0.749   0.788
128   I         0.690   0.709   0.739   0.827   0.836   0.871   0.723   0.749   0.788
129   N         0.690   0.709   0.739   0.983   0.987   1.000   0.723   0.749   0.788
130   K        -0.074  -0.115  -0.438  -0.242  -0.262  -0.723  -0.105  -0.166  -0.701
131   A        -0.074  -0.294  -0.451  -0.170  -0.434  -0.613  -0.105  -0.444  -0.723
132   L         0.690   0.709   0.739   0.468   0.517   0.573   0.723   0.749   0.788
133   L         0.690   0.709   0.739   0.468   0.517   0.573   0.723   0.749   0.788
134   L        -0.074  -0.294  -0.451  -0.182  -0.443  -0.663  -0.105  -0.444  -0.723
135   K        -0.074  -0.294  -0.451  -0.242  -0.509  -0.743  -0.105  -0.444  -0.723
136   V        -0.074  -0.294  -0.451   0.139  -0.155  -0.408  -0.105  -0.444  -0.723
137   E        -0.074  -0.294  -0.451   0.163  -0.182  -0.548  -0.105  -0.444  -0.723
138   K        -1.771  -1.841  -1.735  -1.755  -1.785  -1.505  -1.761  -1.818  -1.609
139   K        -0.802  -0.800  -1.180  -0.890  -0.848  -1.366  -0.815  -0.813  -1.288
140   G        -0.925  -1.002  -1.188  -1.052  -1.110  -1.367  -0.976  -1.088  -1.298
141   S        -2.012  -1.882  -1.734  -2.226  -1.971  -1.751  -2.002  -1.840  -1.607
142   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
143   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
144   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
145   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
146   K        -2.825  -2.682  -2.464  -2.556  -2.411  -2.035  -2.352  -2.188  -1.880
147   K        -1.488  -1.623  -1.722  -1.521  -1.704  -1.769  -1.406  -1.560  -1.596
* 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/Q12692
Output conservation file - output/Q12692
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
