1     M         0.989   0.997   1.070   1.116   1.131   1.229   1.042   1.056   1.164
2     S        -1.491  -1.525  -1.465  -1.416  -1.432  -1.338  -1.417  -1.431  -1.287
3     Q        -1.176  -1.130  -0.947  -1.106  -1.045  -0.772  -1.326  -1.283  -1.021
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     -        -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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
14    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
15    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
16    A        -0.407  -0.466  -0.867  -0.183  -0.246  -0.799  -0.324  -0.407  -0.917
17    V        -1.491  -1.352  -1.459  -1.467  -1.283  -1.428  -1.417  -1.286  -1.282
18    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
19    N        -2.001  -1.975  -1.895  -1.872  -1.853  -1.634  -1.690  -1.668  -1.471
20    A        -1.686  -1.614  -1.477  -1.983  -1.903  -1.636  -1.599  -1.537  -1.299
21    K        -0.743  -0.597  -0.888  -0.878  -0.681  -1.102  -0.779  -0.595  -0.946
22    K         0.277   0.170  -0.110   0.231   0.090  -0.315   0.314   0.163  -0.307
23    R         0.989   0.997   1.070   0.800   0.815   0.950   1.042   1.056   1.164
24    V        -1.176  -1.073  -0.954  -1.302  -1.127  -0.985  -1.326  -1.201  -1.027
25    F         0.989   0.997   1.070   1.082   1.094   1.199   1.042   1.056   1.164
26    K        -0.310  -0.315  -0.198  -0.709  -0.742  -0.559  -0.597  -0.616  -0.460
27    T        -0.743  -0.868  -0.924  -0.610  -0.843  -0.907  -0.779  -0.966  -0.993
28    H        -0.743  -0.579  -0.893  -0.479  -0.273  -0.690  -0.779  -0.574  -0.951
29    S        -0.092  -0.026  -0.113  -0.045   0.051  -0.133  -0.233  -0.134  -0.312
30    Y         0.277   0.263  -0.097   0.608   0.590   0.052   0.314   0.293  -0.285
31    R        -0.310  -0.261  -0.189  -0.722  -0.641  -0.545  -0.597  -0.521  -0.443
32    G         0.989   0.997   1.070   0.941   0.954   1.074   1.042   1.056   1.164
33    V         0.277   0.150  -0.108   0.344   0.194  -0.187   0.314   0.133  -0.303
34    D        -0.092  -0.026  -0.113   0.117   0.202   0.003  -0.233  -0.134  -0.312
35    L         0.989   0.997   1.070   0.887   0.897   1.026   1.042   1.056   1.164
36    E        -0.923  -1.027  -0.936  -1.050  -1.203  -1.012  -1.052  -1.171  -1.008
37    K        -1.686  -1.700  -1.481  -1.563  -1.567  -1.277  -1.599  -1.598  -1.302
38    L         0.989   0.997   1.070   0.887   0.897   1.026   1.042   1.056   1.164
39    L         0.277   0.263  -0.097   0.286   0.268  -0.255   0.314   0.293  -0.285
40    E        -0.310  -0.315  -0.198  -0.383  -0.400  -0.221  -0.597  -0.616  -0.460
41    M        -0.923  -1.005  -0.942  -0.915  -1.039  -0.954  -1.052  -1.144  -1.014
42    S        -0.923  -0.985  -0.921  -0.921  -0.994  -0.931  -1.052  -1.106  -0.989
43    T        -0.743  -0.799  -0.897  -0.607  -0.661  -0.869  -0.779  -0.837  -0.955
44    E        -0.092  -0.221  -0.201  -0.058  -0.253  -0.225  -0.233  -0.453  -0.465
45    D        -1.176  -1.079  -0.927  -1.106  -0.991  -0.763  -1.326  -1.205  -0.995
46    F        -0.310  -0.315  -0.198  -0.431  -0.456  -0.320  -0.597  -0.616  -0.460
47    V        -1.924  -2.009  -1.892  -1.834  -2.001  -1.864  -1.599  -1.678  -1.468
48    K        -0.923  -1.005  -0.942  -1.007  -1.123  -0.989  -1.052  -1.144  -1.014
49    L        -0.407  -0.458  -0.865  -0.284  -0.364  -0.926  -0.324  -0.400  -0.914
50    A        -2.238  -2.155  -1.903  -2.014  -1.921  -1.590  -1.872  -1.808  -1.477
51    P        -1.686  -1.708  -1.493  -1.583  -1.593  -1.326  -1.599  -1.607  -1.313
52    A         0.989   0.997   1.070   0.958   0.981   1.090   1.042   1.056   1.164
53    R         0.989   0.997   1.070   0.800   0.815   0.950   1.042   1.056   1.164
54    V        -0.413  -0.406  -0.215  -0.738  -0.725  -0.426  -0.779  -0.778  -0.491
55    R         0.989   0.997   1.070   0.800   0.815   0.950   1.042   1.056   1.164
56    R         0.989   0.997   1.070   0.800   0.815   0.950   1.042   1.056   1.164
57    R        -0.092   0.018  -0.140  -0.335  -0.166  -0.448  -0.233  -0.065  -0.358
58    F        -0.743  -0.799  -0.897  -0.527  -0.592  -0.781  -0.779  -0.837  -0.955
59    A        -1.805  -1.762  -1.487  -1.823  -1.743  -1.377  -1.690  -1.653  -1.307
60    R         0.989   0.997   1.070   0.800   0.815   0.950   1.042   1.056   1.164
61    G         0.989   0.997   1.070   0.941   0.954   1.074   1.042   1.056   1.164
62    M        -0.407  -0.271  -0.854  -0.284  -0.125  -0.909  -0.324  -0.160  -0.900
63    T        -2.434  -2.477  -2.238  -2.136  -2.214  -1.867  -1.872  -1.899  -1.587
64    S        -2.434  -2.430  -2.237  -2.263  -2.313  -2.110  -1.872  -1.870  -1.586
65    K        -0.092  -0.026  -0.113  -0.211  -0.132  -0.234  -0.233  -0.134  -0.312
66    P        -0.092  -0.026  -0.113  -0.080   0.021  -0.162  -0.233  -0.134  -0.312
67    A        -2.120  -2.059  -1.893  -1.875  -1.775  -1.568  -1.781  -1.723  -1.469
68    G        -0.743  -0.782  -0.889  -0.765  -0.798  -1.000  -0.779  -0.815  -0.945
69    F        -0.413  -0.363  -0.205  -0.690  -0.618  -0.366  -0.779  -0.701  -0.473
70    M        -0.310  -0.215  -0.176  -0.347  -0.199  -0.174  -0.597  -0.443  -0.421
71    K        -1.356  -1.357  -1.438  -1.401  -1.395  -1.468  -1.234  -1.231  -1.259
72    K         0.989   0.997   1.070   0.828   0.829   0.974   1.042   1.056   1.164
73    L         0.989   0.997   1.070   0.887   0.897   1.026   1.042   1.056   1.164
74    R         0.989   0.997   1.070   0.800   0.815   0.950   1.042   1.056   1.164
75    A        -0.413  -0.406  -0.215  -0.798  -0.808  -0.495  -0.779  -0.778  -0.491
76    A         0.989   0.997   1.070   0.958   0.981   1.090   1.042   1.056   1.164
77    K         0.277   0.263  -0.097   0.211   0.182  -0.356   0.314   0.293  -0.285
78    L        -1.671  -1.708  -1.867  -1.361  -1.408  -1.615  -1.326  -1.372  -1.448
79    A        -0.923  -0.852  -0.923  -1.014  -0.936  -0.984  -1.052  -0.993  -0.991
80    A        -0.743  -0.690  -0.900  -0.576  -0.495  -0.773  -0.779  -0.703  -0.961
81    P        -1.356  -1.519  -1.468  -1.236  -1.488  -1.499  -1.234  -1.400  -1.289
82    E        -1.176  -1.079  -0.927  -1.369  -1.200  -1.014  -1.326  -1.205  -0.995
83    N         0.989   0.997   1.070   1.160   1.170   1.267   1.042   1.056   1.164
84    E         0.989   0.997   1.070   0.967   0.983   1.098   1.042   1.056   1.164
85    K         0.277   0.263  -0.097   0.211   0.182  -0.356   0.314   0.293  -0.285
86    P         0.989   0.997   1.070   1.020   1.034   1.144   1.042   1.056   1.164
87    A         0.277   0.150  -0.108   0.396   0.257  -0.097   0.314   0.133  -0.303
88    P        -1.924  -1.893  -1.874  -1.770  -1.741  -1.730  -1.599  -1.570  -1.454
89    V         0.989   0.997   1.070   0.927   0.944   1.062   1.042   1.056   1.164
90    R        -0.092   0.012  -0.142  -0.315  -0.165  -0.444  -0.233  -0.074  -0.362
91    T         0.989   0.997   1.070   1.051   1.068   1.172   1.042   1.056   1.164
92    H         0.989   0.997   1.070   1.202   1.213   1.305   1.042   1.056   1.164
93    M         0.277   0.348  -0.095   0.311   0.390  -0.176   0.314   0.408  -0.281
94    R         0.989   0.997   1.070   0.800   0.815   0.950   1.042   1.056   1.164
95    N         0.277   0.150  -0.108   0.595   0.444   0.062   0.314   0.133  -0.303
96    M         0.989   0.997   1.070   1.116   1.131   1.229   1.042   1.056   1.164
97    I         0.277   0.170  -0.110   0.455   0.313  -0.153   0.314   0.163  -0.307
98    I        -0.310  -0.335  -0.207  -0.433  -0.500  -0.335  -0.597  -0.651  -0.476
99    V        -0.743  -0.782  -0.889  -0.746  -0.777  -0.965  -0.779  -0.815  -0.945
100   P         0.989   0.997   1.070   1.020   1.034   1.144   1.042   1.056   1.164
101   E         0.989   0.997   1.070   0.967   0.983   1.098   1.042   1.056   1.164
102   M         0.989   0.997   1.070   1.116   1.131   1.229   1.042   1.056   1.164
103   I        -0.092  -0.026  -0.113  -0.050   0.043  -0.142  -0.233  -0.134  -0.312
104   G         0.989   0.997   1.070   0.941   0.954   1.074   1.042   1.056   1.164
105   S         0.989   0.997   1.070   1.056   1.065   1.175   1.042   1.056   1.164
106   V         0.989   0.997   1.070   0.927   0.944   1.062   1.042   1.056   1.164
107   V         0.277   0.150  -0.108   0.344   0.194  -0.187   0.314   0.133  -0.303
108   G         0.989   0.997   1.070   0.941   0.954   1.074   1.042   1.056   1.164
109   I        -0.413  -0.398  -0.216  -0.650  -0.637  -0.358  -0.779  -0.763  -0.492
110   Y         0.989   0.997   1.070   1.190   1.200   1.294   1.042   1.056   1.164
111   N         0.277   0.150  -0.108   0.575   0.418  -0.002   0.314   0.133  -0.303
112   G         0.989   0.997   1.070   0.941   0.954   1.074   1.042   1.056   1.164
113   K         0.989   0.997   1.070   0.828   0.829   0.974   1.042   1.056   1.164
114   A        -1.924  -1.993  -1.892  -1.844  -1.938  -1.819  -1.599  -1.658  -1.469
115   F         0.989   0.997   1.070   1.082   1.094   1.199   1.042   1.056   1.164
116   N         0.277   0.170  -0.110   0.575   0.445  -0.007   0.314   0.163  -0.307
117   Q        -0.310  -0.329  -0.205  -0.171  -0.219  -0.101  -0.597  -0.640  -0.472
118   V         0.989   0.997   1.070   0.927   0.944   1.062   1.042   1.056   1.164
119   E         0.989   0.997   1.070   0.967   0.983   1.098   1.042   1.056   1.164
120   I         0.277   0.327  -0.094   0.460   0.513  -0.106   0.314   0.380  -0.279
121   R        -0.413  -0.406  -0.216  -0.931  -0.935  -0.598  -0.779  -0.778  -0.491
122   P         0.989   0.997   1.070   1.020   1.034   1.144   1.042   1.056   1.164
123   E         0.989   0.997   1.070   0.967   0.983   1.098   1.042   1.056   1.164
124   M         0.989   0.997   1.070   1.116   1.131   1.229   1.042   1.056   1.164
125   L        -1.176  -1.113  -0.946  -1.388  -1.296  -1.061  -1.326  -1.259  -1.019
126   G         0.989   0.997   1.070   0.941   0.954   1.074   1.042   1.056   1.164
127   H         0.277   0.170  -0.110   0.625   0.498   0.052   0.314   0.163  -0.307
128   Y         0.989   0.997   1.070   1.190   1.200   1.294   1.042   1.056   1.164
129   L         0.989   0.997   1.070   0.887   0.897   1.026   1.042   1.056   1.164
130   G         0.277   0.150  -0.108   0.344   0.189  -0.218   0.314   0.133  -0.303
131   E         0.989   0.997   1.070   0.967   0.983   1.098   1.042   1.056   1.164
132   F         0.989   0.997   1.070   1.082   1.094   1.199   1.042   1.056   1.164
133   S         0.989   0.997   1.070   1.056   1.065   1.175   1.042   1.056   1.164
134   I         0.989   0.997   1.070   1.060   1.066   1.179   1.042   1.056   1.164
135   T         0.277   0.150  -0.108   0.467   0.317  -0.089   0.314   0.133  -0.303
136   Y         0.989   0.997   1.070   1.190   1.200   1.294   1.042   1.056   1.164
137   T        -0.923  -0.889  -0.926  -1.022  -0.999  -1.038  -1.052  -1.028  -0.995
138   P         0.989   0.997   1.070   1.020   1.034   1.144   1.042   1.056   1.164
139   V        -0.310  -0.308  -0.202  -0.498  -0.496  -0.349  -0.597  -0.603  -0.467
140   R        -0.310  -0.315  -0.198  -0.722  -0.748  -0.564  -0.597  -0.616  -0.460
141   H         0.989   0.997   1.070   1.202   1.213   1.305   1.042   1.056   1.164
142   G         0.989   0.997   1.070   0.941   0.954   1.074   1.042   1.056   1.164
143   R         0.989   0.997   1.070   0.800   0.815   0.950   1.042   1.056   1.164
144   A        -0.413  -0.406  -0.215  -0.673  -0.659  -0.364  -0.779  -0.778  -0.491
145   G         0.989   0.997   1.070   0.941   0.954   1.074   1.042   1.056   1.164
146   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
147   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
148   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
149   A        -1.686  -1.708  -1.493  -1.656  -1.666  -1.387  -1.599  -1.607  -1.313
150   T        -1.686  -1.708  -1.493  -1.555  -1.562  -1.304  -1.599  -1.607  -1.313
151   T        -0.923  -0.936  -0.921  -0.866  -0.846  -0.830  -1.052  -1.038  -0.988
152   S         0.277   0.327  -0.094   0.471   0.527  -0.063   0.314   0.380  -0.279
153   R        -0.092  -0.163  -0.183  -0.335  -0.462  -0.535  -0.233  -0.355  -0.434
154   F         0.989   0.997   1.070   1.082   1.094   1.199   1.042   1.056   1.164
155   I         0.277   0.263  -0.097   0.483   0.462  -0.039   0.314   0.293  -0.285
156   P         0.989   0.997   1.070   1.020   1.034   1.144   1.042   1.056   1.164
157   L         0.989   0.997   1.070   0.887   0.897   1.026   1.042   1.056   1.164
158   K        -0.413  -0.395  -0.215  -0.926  -0.911  -0.596  -0.779  -0.759  -0.490
* 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/Q01855
Output conservation file - output/Q01855
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
