1     M         1.821   1.851   2.000   2.026   2.066   2.274   1.990   2.044   2.302
2     F         1.081   0.998   0.904   1.298   1.199   1.046   1.124   0.986   0.785
3     P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
4     I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
5     A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
6     S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
7     R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
8     R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
9     I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
10    L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
11    L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
12    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
13    A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
14    S         0.256   0.144   0.022   0.453   0.275   0.027   0.212   0.037  -0.157
15    V        -1.225  -1.154  -1.092  -1.201  -1.039  -0.933  -1.080  -0.997  -0.901
16    L        -0.621  -0.710  -0.662  -0.678  -0.880  -0.860  -0.649  -0.766  -0.693
17    P        -0.621  -0.704  -0.678  -0.564  -0.722  -0.716  -0.649  -0.758  -0.711
18    L         0.838   0.756   0.768   0.679   0.594   0.579   0.723   0.560   0.521
19    R        -0.689  -0.567  -0.564  -0.589  -0.423  -0.457  -0.757  -0.593  -0.576
20    L         0.256   0.113   0.025   0.249   0.061  -0.132   0.212  -0.005  -0.152
21    -        -0.793  -0.787  -0.683  -0.910  -0.976  -0.843  -0.869  -0.853  -0.717
22    C        -0.647  -0.637  -0.598  -0.778  -0.688  -0.587  -0.732  -0.700  -0.627
23    N        -1.116  -1.035  -1.048  -0.794  -0.615  -0.637  -0.979  -0.877  -0.857
24    R         1.821   1.851   2.000   1.859   1.904   2.108   1.990   2.044   2.302
25    N        -1.585  -1.565  -1.481  -1.211  -1.230  -1.097  -1.227  -1.191  -1.070
26    F         1.821   1.851   2.000   1.917   1.960   2.165   1.990   2.044   2.302
27    T         0.375   0.287   0.097   0.496   0.405   0.174   0.382   0.246  -0.043
28    T        -0.904  -0.962  -1.045  -0.551  -0.675  -0.825  -0.732  -0.799  -0.854
29    T        -0.563  -0.623  -0.609  -0.422  -0.493  -0.427  -0.608  -0.680  -0.641
30    R        -1.245  -1.207  -1.108  -0.884  -0.844  -0.681  -1.103  -1.052  -0.918
31    I        -1.116  -1.129  -1.093  -0.789  -0.873  -0.813  -0.979  -0.988  -0.905
32    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
33    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
34    S         0.716   0.728   0.733   0.730   0.737   0.684   0.505   0.507   0.450
35    Y        -0.563  -0.614  -0.619  -0.401  -0.508  -0.520  -0.608  -0.667  -0.648
36    N         1.081   0.998   0.904   1.356   1.265   1.139   1.124   0.986   0.785
37    V        -0.647  -0.643  -0.621  -0.595  -0.549  -0.486  -0.732  -0.709  -0.652
38    I         0.716   0.694   0.716   0.842   0.794   0.771   0.505   0.443   0.415
39    Q        -0.094  -0.077  -0.052  -0.077  -0.067  -0.002  -0.361  -0.344  -0.287
40    D         0.716   0.644   0.694   0.665   0.502   0.495   0.505   0.348   0.371
41    L         1.081   1.018   0.915   0.991   0.934   0.731   1.124   1.018   0.805
42    Y         1.821   1.851   2.000   1.986   2.028   2.234   1.990   2.044   2.302
43    L         0.052   0.007  -0.014   0.083   0.058   0.025  -0.113  -0.179  -0.218
44    R        -0.223  -0.217  -0.125  -0.160  -0.165  -0.033  -0.484  -0.492  -0.376
45    E         0.375   0.394   0.117   0.319   0.349   0.054   0.382   0.401  -0.012
46    L         0.052   0.007  -0.014   0.061   0.029  -0.014  -0.113  -0.179  -0.218
47    K         1.081   1.018   0.915   1.207   1.139   1.012   1.124   1.018   0.805
48    D         0.375   0.370   0.113   0.243   0.240  -0.096   0.382   0.368  -0.019
49    T        -0.647  -0.643  -0.620  -0.405  -0.353  -0.296  -0.732  -0.709  -0.652
50    K         0.716   0.998   0.936   0.764   1.131   1.069   0.505   0.985   0.845
51    L        -0.647  -0.632  -0.616  -0.775  -0.741  -0.734  -0.732  -0.697  -0.646
52    A        -0.647  -0.634  -0.605  -0.568  -0.540  -0.526  -0.732  -0.699  -0.636
53    P         0.375   0.297   0.115   0.482   0.369   0.089   0.382   0.262  -0.015
54    S        -0.647  -0.604  -0.618  -0.514  -0.459  -0.470  -0.732  -0.675  -0.651
55    T        -0.094  -0.130  -0.054  -0.136  -0.189  -0.086  -0.361  -0.401  -0.290
56    L        -1.457  -1.490  -1.464  -1.336  -1.399  -1.276  -1.103  -1.128  -1.056
57    Q        -0.647  -0.645  -0.608  -0.777  -0.719  -0.649  -0.732  -0.711  -0.639
58    D         1.821   1.851   2.000   1.853   1.898   2.102   1.990   2.044   2.302
59    A         1.081   1.083   0.924   0.870   0.883   0.717   1.124   1.124   0.822
60    E        -0.563  -0.453  -0.509  -0.658  -0.517  -0.576  -0.608  -0.451  -0.509
61    G         0.716   0.742   0.752   0.831   0.863   0.816   0.505   0.533   0.488
62    N        -0.775  -0.737  -0.675  -0.843  -0.736  -0.639  -0.855  -0.819  -0.713
63    V         1.081   1.124   0.935   1.160   1.219   1.010   1.124   1.189   0.842
64    K         1.081   0.998   0.904   1.149   1.038   0.867   1.124   0.986   0.785
65    P        -0.289  -0.356  -0.538  -0.119  -0.227  -0.532  -0.237  -0.330  -0.544
66    W         0.521   0.533   0.650   0.646   0.644   0.794   0.134   0.128   0.280
67    N        -0.904  -0.789  -0.673  -0.755  -0.614  -0.448  -0.979  -0.862  -0.711
68    P        -0.775  -0.666  -0.616  -0.884  -0.752  -0.707  -0.855  -0.725  -0.646
69    P         1.821   1.851   2.000   1.722   1.759   1.972   1.990   2.044   2.302
70    Q        -0.904  -1.003  -1.036  -0.826  -0.966  -0.949  -0.732  -0.843  -0.845
71    K        -0.094  -0.079  -0.032  -0.318  -0.244  -0.190  -0.361  -0.315  -0.250
72    P         1.821   1.851   2.000   1.722   1.759   1.972   1.990   2.044   2.302
73    N        -0.563  -0.554  -0.606  -0.375  -0.369  -0.408  -0.608  -0.600  -0.633
74    L        -1.116  -1.173  -1.111  -1.161  -1.254  -1.205  -0.979  -1.023  -0.920
75    P         1.821   1.851   2.000   1.722   1.759   1.972   1.990   2.044   2.302
76    E         0.052  -0.007  -0.017  -0.145  -0.219  -0.209  -0.113  -0.201  -0.229
77    L        -0.689  -0.737  -0.664  -0.895  -0.972  -0.907  -0.757  -0.808  -0.699
78    E         1.081   1.083   0.924   0.862   0.874   0.692   1.124   1.124   0.822
79    L        -0.904  -1.007  -1.062  -0.676  -0.822  -0.890  -0.732  -0.848  -0.871
80    Q        -1.457  -1.521  -1.477  -1.002  -1.143  -1.090  -1.103  -1.155  -1.067
81    G        -1.116  -1.173  -1.106  -1.132  -1.212  -1.083  -0.979  -1.023  -0.916
82    P         0.116   0.117  -0.007  -0.040  -0.046  -0.192   0.010   0.000  -0.201
83    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
84    E        -0.563  -0.668  -0.616  -0.573  -0.800  -0.790  -0.608  -0.727  -0.648
85    A        -0.289  -0.432  -0.548  -0.453  -0.681  -0.906  -0.237  -0.425  -0.556
86    L         1.081   1.083   0.924   1.032   1.067   0.836   1.124   1.124   0.822
87    K         0.375   0.334   0.130   0.600   0.551   0.269   0.382   0.314   0.007
88    A        -0.563  -0.560  -0.598  -0.871  -0.909  -0.934  -0.608  -0.619  -0.629
89    Y         1.821   1.851   2.000   1.986   2.028   2.234   1.990   2.044   2.302
90    T        -0.647  -0.601  -0.614  -1.021  -0.941  -0.898  -0.732  -0.670  -0.646
91    E        -0.647  -0.642  -0.607  -0.925  -0.906  -0.858  -0.732  -0.704  -0.637
92    Q        -0.904  -1.024  -1.060  -0.741  -0.929  -1.002  -0.732  -0.864  -0.869
93    N        -1.245  -1.180  -1.099  -0.971  -0.957  -0.815  -1.103  -1.030  -0.910
94    V         1.821   1.851   2.000   1.734   1.781   1.984   1.990   2.044   2.302
95    E         1.081   1.018   0.915   0.862   0.797   0.679   1.124   1.018   0.805
96    T         0.716   0.644   0.694   0.747   0.620   0.641   0.505   0.348   0.371
97    A        -0.775  -0.655  -0.613  -1.216  -1.092  -1.023  -0.855  -0.726  -0.646
98    H        -0.775  -0.737  -0.675  -0.667  -0.574  -0.507  -0.855  -0.819  -0.713
99    V        -1.245  -1.145  -1.087  -1.169  -0.950  -0.874  -1.103  -0.999  -0.900
100   A        -1.116  -1.143  -1.096  -1.344  -1.380  -1.260  -0.979  -0.999  -0.908
101   K        -1.116  -1.145  -1.091  -0.688  -0.738  -0.654  -0.979  -0.999  -0.903
102   E        -0.775  -0.758  -0.674  -1.242  -1.229  -1.081  -0.855  -0.837  -0.712
103   S        -1.585  -1.567  -1.459  -1.464  -1.493  -1.369  -1.227  -1.193  -1.052
104   E        -0.647  -0.601  -0.614  -0.957  -0.906  -0.914  -0.732  -0.670  -0.646
105   E         0.521   0.545   0.652  -0.114  -0.098   0.030   0.134   0.154   0.285
106   G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
107   E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
108   S        -1.247  -1.122  -1.097  -1.404  -1.200  -1.229  -1.089  -0.965  -0.905
109   E        -1.116  -1.160  -1.094  -1.186  -1.235  -1.098  -0.979  -1.014  -0.906
110   P        -1.116  -0.984  -1.028  -1.156  -0.983  -0.998  -0.979  -0.822  -0.837
111   I        -1.585  -1.555  -1.474  -1.437  -1.310  -1.224  -1.227  -1.184  -1.064
112   E         0.052  -0.050  -0.037  -0.155  -0.288  -0.246  -0.113  -0.268  -0.260
113   E         0.716   0.998   0.936   0.440   0.797   0.744   0.505   0.985   0.845
114   D         1.081   1.091   0.923   1.286   1.307   1.123   1.124   1.136   0.819
115   W         1.821   1.851   2.000   2.014   2.060   2.262   1.990   2.044   2.302
116   L         0.716   0.742   0.752   0.604   0.662   0.646   0.505   0.533   0.488
117   V         1.081   1.018   0.915   1.089   1.008   0.827   1.124   1.018   0.805
118   L        -0.094  -0.130  -0.065  -0.208  -0.233  -0.165  -0.361  -0.402  -0.303
119   D         0.375   0.370   0.113   0.250   0.247  -0.090   0.382   0.368  -0.019
120   D         1.081   1.091   0.919   0.862   0.883   0.685   1.124   1.137   0.814
121   A        -0.689  -0.552  -0.578  -1.080  -0.839  -0.935  -0.757  -0.575  -0.593
122   E         1.821   1.851   2.000   1.450   1.496   1.701   1.990   2.044   2.302
123   E        -0.563  -0.433  -0.501  -0.621  -0.442  -0.501  -0.608  -0.426  -0.499
124   T        -0.689  -0.735  -0.654  -0.837  -0.837  -0.686  -0.757  -0.806  -0.690
125   K        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
126   E        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
127   S        -0.094  -0.074  -0.044  -0.152  -0.180  -0.147  -0.361  -0.341  -0.278
128   H         1.081   1.018   0.915   1.397   1.326   1.174   1.124   1.018   0.805
* 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/Q12349
Output conservation file - output/Q12349
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
