1     M         1.470   1.483   1.539   1.666   1.680   1.758   1.571   1.588   1.668
2     L         0.649   0.635   0.484   0.518   0.509   0.323   0.603   0.578   0.303
3     A        -0.111  -0.076  -0.256  -0.045  -0.001  -0.293  -0.171  -0.122  -0.373
4     R        -0.954  -0.926  -0.889  -1.135  -1.105  -1.027  -0.945  -0.914  -0.837
5     S        -0.958  -0.916  -0.890  -1.107  -1.043  -0.985  -0.937  -0.886  -0.834
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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
17    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
18    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
19    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
20    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
21    L        -0.958  -0.983  -0.900  -0.783  -0.825  -0.730  -0.937  -0.961  -0.845
22    G        -0.958  -0.969  -0.905  -0.860  -0.876  -0.773  -0.937  -0.947  -0.851
23    Y        -1.375  -1.372  -1.302  -1.195  -1.192  -1.102  -1.138  -1.132  -1.025
24    R         1.470   1.483   1.539   1.459   1.470   1.558   1.571   1.588   1.668
25    L        -1.375  -1.370  -1.306  -1.411  -1.411  -1.277  -1.138  -1.130  -1.028
26    I        -0.111  -0.192  -0.286  -0.192  -0.294  -0.408  -0.171  -0.283  -0.414
27    S        -1.375  -1.370  -1.306  -1.074  -1.078  -0.947  -1.138  -1.130  -1.028
28    T        -1.375  -1.362  -1.308  -1.348  -1.345  -1.270  -1.138  -1.123  -1.030
29    S        -0.111  -0.130  -0.266  -0.039  -0.078  -0.260  -0.171  -0.202  -0.387
30    R        -0.374  -0.368  -0.358  -0.456  -0.449  -0.432  -0.558  -0.547  -0.519
31    I        -0.795  -0.680  -0.814  -0.558  -0.380  -0.610  -0.751  -0.614  -0.752
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    L        -0.374  -0.391  -0.360  -0.707  -0.733  -0.663  -0.558  -0.578  -0.522
35    Y        -0.954  -0.921  -0.889  -0.729  -0.663  -0.627  -0.945  -0.907  -0.837
36    N        -0.111  -0.130  -0.266  -0.001  -0.040  -0.222  -0.171  -0.202  -0.387
37    K        -1.375  -1.364  -1.301  -1.233  -1.212  -1.137  -1.138  -1.124  -1.024
38    P        -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    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
47    V        -0.958  -0.999  -0.911  -0.972  -1.018  -0.879  -0.937  -0.977  -0.856
48    K        -0.958  -0.968  -0.903  -1.082  -1.081  -0.985  -0.937  -0.946  -0.848
49    S        -1.375  -1.344  -1.300  -1.351  -1.307  -1.215  -1.138  -1.104  -1.023
50    V        -0.374  -0.350  -0.343  -0.325  -0.287  -0.266  -0.558  -0.516  -0.497
51    V        -0.374  -0.415  -0.361  -0.573  -0.616  -0.520  -0.558  -0.600  -0.523
52    S         1.470   1.483   1.539   1.394   1.407   1.494   1.571   1.588   1.668
53    S         1.470   1.483   1.539   1.394   1.407   1.494   1.571   1.588   1.668
54    C         0.649   0.563   0.471   0.977   0.855   0.692   0.603   0.462   0.280
55    P        -0.795  -0.793  -0.843  -0.756  -0.762  -0.912  -0.751  -0.750  -0.784
56    A         1.470   1.483   1.539   1.352   1.358   1.454   1.571   1.588   1.668
57    G         1.470   1.483   1.539   1.658   1.674   1.750   1.571   1.588   1.668
58    T         1.470   1.483   1.539   1.532   1.545   1.628   1.571   1.588   1.668
59    S        -0.374  -0.340  -0.350  -0.383  -0.333  -0.351  -0.558  -0.503  -0.508
60    L         1.470   1.483   1.539   1.217   1.239   1.323   1.571   1.588   1.668
61    N        -0.111  -0.146  -0.275  -0.102  -0.163  -0.394  -0.171  -0.223  -0.398
62    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
63    L         0.649   0.563   0.471   0.530   0.434   0.327   0.603   0.462   0.280
64    N        -0.374  -0.316  -0.350  -0.546  -0.458  -0.493  -0.558  -0.487  -0.508
65    I        -0.374  -0.322  -0.343  -0.294  -0.226  -0.228  -0.558  -0.488  -0.499
66    W        -0.954  -0.955  -0.896  -0.943  -0.919  -0.803  -0.945  -0.939  -0.843
67    K         1.470   1.483   1.539   1.251   1.272   1.356   1.571   1.588   1.668
68    S        -0.795  -0.836  -0.854  -0.790  -0.864  -0.904  -0.751  -0.798  -0.796
69    G         1.470   1.483   1.539   1.658   1.674   1.750   1.571   1.588   1.668
70    K        -0.374  -0.424  -0.373  -0.515  -0.567  -0.469  -0.558  -0.613  -0.537
71    D         0.207   0.219   0.303   0.108   0.131   0.254  -0.171  -0.152  -0.030
72    A         0.649   0.649   0.487   0.791   0.782   0.527   0.603   0.602   0.309
73    V         1.470   1.483   1.539   1.476   1.489   1.573   1.571   1.588   1.668
74    A         1.470   1.483   1.539   1.352   1.358   1.454   1.571   1.588   1.668
75    L         0.649   0.635   0.484   0.430   0.417   0.165   0.603   0.578   0.303
76    E         1.470   1.483   1.539   1.508   1.528   1.604   1.571   1.588   1.668
77    D         1.470   1.483   1.539   1.564   1.576   1.659   1.571   1.588   1.668
78    K        -0.111  -0.076  -0.256  -0.043  -0.001  -0.251  -0.171  -0.122  -0.373
79    E         1.470   1.483   1.539   1.508   1.528   1.604   1.571   1.588   1.668
80    Y         1.470   1.483   1.539   1.705   1.717   1.795   1.571   1.588   1.668
81    P         1.470   1.483   1.539   1.556   1.563   1.651   1.571   1.588   1.668
82    N        -0.111  -0.192  -0.286   0.064  -0.044  -0.205  -0.171  -0.283  -0.414
83    W         1.470   1.483   1.539   1.658   1.673   1.750   1.571   1.588   1.668
84    L         1.470   1.483   1.539   1.217   1.239   1.323   1.571   1.588   1.668
85    W         1.470   1.483   1.539   1.658   1.673   1.750   1.571   1.588   1.668
86    S        -0.374  -0.385  -0.364  -0.332  -0.355  -0.325  -0.558  -0.574  -0.528
87    V        -0.795  -0.839  -0.867  -0.482  -0.544  -0.547  -0.751  -0.801  -0.810
88    L         1.470   1.483   1.539   1.217   1.239   1.323   1.571   1.588   1.668
89    D         1.470   1.483   1.539   1.564   1.576   1.659   1.571   1.588   1.668
90    S        -1.375  -1.300  -1.290  -1.280  -1.152  -1.176  -1.138  -1.063  -1.015
91    D        -1.796  -1.777  -1.660  -1.680  -1.668  -1.479  -1.332  -1.311  -1.165
92    H        -1.796  -1.777  -1.660  -1.581  -1.550  -1.383  -1.332  -1.311  -1.165
93    V        -1.375  -1.344  -1.300  -1.233  -1.174  -1.147  -1.138  -1.104  -1.023
94    V        -1.375  -1.400  -1.312  -1.481  -1.551  -1.397  -1.138  -1.156  -1.034
95    E        -0.954  -0.936  -0.891  -1.018  -1.005  -0.925  -0.945  -0.922  -0.839
96    H        -0.374  -0.367  -0.354  -0.585  -0.569  -0.506  -0.558  -0.545  -0.514
97    A        -0.374  -0.373  -0.353  -0.669  -0.659  -0.603  -0.558  -0.551  -0.513
98    A        -0.374  -0.358  -0.354  -0.612  -0.573  -0.563  -0.558  -0.528  -0.515
99    E         0.445   0.454   0.398   0.240   0.245   0.171   0.264   0.276   0.148
100   D         0.445   0.484   0.404   0.579   0.632   0.491   0.264   0.329   0.159
101   P         0.445   0.484   0.404   0.496   0.549   0.403   0.264   0.329   0.159
102   E        -0.425  -0.415  -0.381  -0.556  -0.540  -0.516  -0.606  -0.591  -0.544
103   G        -0.425  -0.415  -0.380  -0.366  -0.349  -0.298  -0.606  -0.592  -0.542
104   Q        -0.425  -0.413  -0.388  -0.323  -0.301  -0.280  -0.606  -0.588  -0.553
105   A        -0.425  -0.413  -0.388  -0.366  -0.344  -0.352  -0.606  -0.588  -0.553
106   L        -0.795  -0.780  -0.839  -0.790  -0.775  -0.807  -0.751  -0.735  -0.780
107   L        -0.374  -0.395  -0.367  -0.684  -0.708  -0.672  -0.558  -0.589  -0.533
108   K        -0.954  -0.920  -0.891  -1.032  -0.983  -0.977  -0.945  -0.908  -0.839
109   R         0.649   0.563   0.471   0.695   0.563   0.409   0.603   0.462   0.280
110   R         0.310   0.370   0.365   0.096   0.209   0.160   0.023   0.128   0.088
111   K         0.649   0.635   0.484   0.534   0.523   0.321   0.603   0.578   0.303
112   N        -0.795  -0.871  -0.862  -0.676  -0.818  -0.851  -0.751  -0.836  -0.805
113   I        -0.374  -0.419  -0.360  -0.431  -0.481  -0.415  -0.558  -0.606  -0.521
114   R        -0.795  -0.839  -0.867  -0.737  -0.831  -0.887  -0.751  -0.801  -0.810
115   K        -0.795  -0.777  -0.841  -0.830  -0.821  -0.874  -0.751  -0.732  -0.782
116   A        -0.795  -0.836  -0.854  -0.782  -0.852  -0.873  -0.751  -0.798  -0.796
117   N         0.649   0.563   0.471   0.662   0.539   0.378   0.603   0.462   0.280
118   R        -0.795  -0.839  -0.867  -0.727  -0.817  -0.873  -0.751  -0.801  -0.810
119   Q        -0.795  -0.780  -0.837  -0.745  -0.733  -0.800  -0.751  -0.731  -0.777
120   R        -1.375  -1.390  -1.303  -1.355  -1.349  -1.221  -1.138  -1.148  -1.026
121   I         0.649   0.563   0.471   0.876   0.766   0.633   0.603   0.462   0.280
122   K        -0.111  -0.150  -0.281  -0.187  -0.231  -0.418  -0.171  -0.228  -0.407
123   Q        -0.374  -0.424  -0.373  -0.343  -0.409  -0.348  -0.558  -0.613  -0.537
124   N         0.649   0.704   0.500   0.683   0.759   0.465   0.603   0.688   0.332
125   N         1.470   1.483   1.539   1.427   1.446   1.526   1.571   1.588   1.668
126   F         1.470   1.483   1.539   1.666   1.682   1.758   1.571   1.588   1.668
127   L         0.649   0.563   0.471   0.477   0.367   0.230   0.603   0.462   0.280
128   S        -0.374  -0.301  -0.337  -0.560  -0.444  -0.496  -0.558  -0.458  -0.491
129   Q         0.310   0.335   0.346   0.054   0.095   0.115   0.023   0.064   0.052
130   L        -0.374  -0.336  -0.356  -0.480  -0.425  -0.408  -0.558  -0.519  -0.517
131   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
132   -        -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/P36532
Output conservation file - output/P36532
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
