1     M         0.835   0.897   0.921   1.099   1.167   1.187   0.878   0.952   0.990
2     S        -0.941  -0.886  -1.283  -0.700  -0.681  -1.211  -0.867  -0.782  -1.244
3     T        -3.191  -2.770  -2.750  -2.311  -1.930  -1.833  -2.477  -2.033  -1.876
4     Q        -3.767  -3.374  -3.083  -3.332  -2.761  -2.414  -2.745  -2.312  -1.967
5     L        -1.951  -1.658  -1.891  -2.151  -1.672  -2.053  -1.751  -1.380  -1.561
6     A        -1.817  -1.536  -1.328  -2.571  -2.055  -1.700  -1.985  -1.561  -1.297
7     S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
8     N        -1.472  -1.529  -1.331  -1.023  -1.186  -0.967  -1.576  -1.554  -1.300
9     I        -2.248  -1.832  -1.916  -1.992  -1.361  -1.584  -2.102  -1.573  -1.585
10    Y        -0.155  -0.492  -0.484   0.200  -0.407  -0.550  -0.174  -0.677  -0.699
11    A        -0.941  -1.035  -1.294  -0.812  -0.931  -1.169  -0.867  -0.999  -1.256
12    P         0.835   0.897   0.921   1.181   1.263   1.253   0.878   0.952   0.990
13    L        -3.191  -2.942  -2.763  -3.164  -2.799  -2.452  -2.477  -2.162  -1.884
14    Y        -0.838  -0.683  -0.505  -0.889  -0.638  -0.390  -1.269  -0.995  -0.734
15    A        -0.074  -0.395  -0.453  -0.121  -0.570  -0.667  -0.062  -0.524  -0.648
16    P        -0.074  -0.395  -0.453   0.367  -0.119  -0.327  -0.062  -0.524  -0.648
17    F         0.835   0.897   0.921   1.016   1.098   1.121   0.878   0.952   0.990
18    F        -1.338  -1.185  -1.294  -1.370  -1.076  -1.426  -1.403  -1.125  -1.257
19    G         0.835   0.897   0.921   0.400   0.526   0.632   0.878   0.952   0.990
20    F        -0.074  -0.203  -0.444   0.234   0.069  -0.330  -0.062  -0.235  -0.632
21    A         0.835   0.897   0.921   0.693   0.798   0.865   0.878   0.952   0.990
22    G         0.835   0.897   0.921   0.400   0.526   0.632   0.878   0.952   0.990
23    C        -0.941  -1.357  -1.319  -0.412  -1.129  -1.244  -0.867  -1.345  -1.287
24    A        -0.523  -0.584  -0.501  -0.653  -0.716  -0.541  -0.733  -0.828  -0.727
25    A        -0.941  -0.526  -1.264  -0.952  -0.391  -1.458  -0.867  -0.334  -1.221
26    A        -0.074  -0.395  -0.453  -0.121  -0.570  -0.667  -0.062  -0.524  -0.648
27    M         0.835   0.897   0.921   1.099   1.167   1.187   0.878   0.952   0.990
28    V        -0.762  -0.677  -0.506  -1.215  -1.083  -0.768  -1.135  -0.984  -0.735
29    L        -0.523  -0.673  -0.506  -0.839  -1.037  -0.726  -0.733  -0.978  -0.735
30    S        -0.074  -0.203  -0.444  -0.002  -0.204  -0.723  -0.062  -0.235  -0.632
31    C        -0.523  -0.467  -0.493  -0.245  -0.194  -0.380  -0.733  -0.638  -0.714
32    L        -0.838  -0.684  -0.505  -1.561  -1.261  -0.928  -1.269  -0.997  -0.733
33    G         0.835   0.897   0.921   0.400   0.526   0.632   0.878   0.952   0.990
34    A         0.835   0.897   0.921   0.693   0.798   0.865   0.878   0.952   0.990
35    A        -0.074  -0.395  -0.453  -0.189  -0.715  -0.884  -0.062  -0.524  -0.648
36    I        -0.523  -0.673  -0.506  -0.658  -0.850  -0.559  -0.733  -0.978  -0.735
37    G         0.835   0.897   0.921   0.400   0.526   0.632   0.878   0.952   0.990
38    T         0.835   0.897   0.921   1.232   1.301   1.293   0.878   0.952   0.990
39    A         0.835   0.897   0.921   0.693   0.798   0.865   0.878   0.952   0.990
40    K        -0.074  -0.395  -0.453   0.389  -0.145  -0.406  -0.062  -0.524  -0.648
41    S        -0.074  -0.395  -0.453   0.039  -0.461  -0.619  -0.062  -0.524  -0.648
42    G         0.835   0.897   0.921   0.400   0.526   0.632   0.878   0.952   0.990
43    I        -0.074  -0.395  -0.453  -0.035  -0.408  -0.459  -0.062  -0.524  -0.648
44    G         0.835   0.897   0.921   0.400   0.526   0.632   0.878   0.952   0.990
45    I         0.835   0.897   0.921   0.715   0.831   0.882   0.878   0.952   0.990
46    A        -0.523  -0.186  -0.462  -0.777  -0.248  -0.682  -0.733  -0.209  -0.662
47    G        -0.074  -0.395  -0.453  -0.445  -0.898  -0.965  -0.062  -0.524  -0.648
48    I        -0.523  -0.673  -0.506  -0.774  -1.077  -0.767  -0.733  -0.978  -0.735
49    G         0.835   0.897   0.921   0.400   0.526   0.632   0.878   0.952   0.990
50    T        -0.941  -1.055  -1.290  -0.426  -0.714  -1.184  -0.867  -1.018  -1.252
51    F         0.835   0.897   0.921   1.016   1.098   1.121   0.878   0.952   0.990
52    K        -0.523  -0.673  -0.506  -0.116  -0.406  -0.194  -0.733  -0.978  -0.735
53    P         0.835   0.897   0.921   1.181   1.263   1.253   0.878   0.952   0.990
54    E        -0.074  -0.203  -0.444   0.480   0.324  -0.102  -0.062  -0.235  -0.632
55    L        -0.074  -0.395  -0.453  -0.257  -0.697  -0.821  -0.062  -0.524  -0.648
56    I        -0.074  -0.395  -0.453  -0.106  -0.561  -0.676  -0.062  -0.524  -0.648
57    M         0.835   0.897   0.921   1.099   1.167   1.187   0.878   0.952   0.990
58    K         0.835   0.897   0.921   1.242   1.314   1.301   0.878   0.952   0.990
59    S        -0.074  -0.203  -0.444   0.118  -0.026  -0.363  -0.062  -0.235  -0.632
60    L         0.835   0.897   0.921   0.582   0.715   0.776   0.878   0.952   0.990
61    I         0.835   0.897   0.921   0.715   0.831   0.882   0.878   0.952   0.990
62    P         0.835   0.897   0.921   1.181   1.263   1.253   0.878   0.952   0.990
63    V         0.835   0.897   0.921   0.824   0.895   0.969   0.878   0.952   0.990
64    V         0.835   0.897   0.921   0.824   0.895   0.969   0.878   0.952   0.990
65    M         0.835   0.897   0.921   1.099   1.167   1.187   0.878   0.952   0.990
66    S         0.835   0.897   0.921   0.878   0.965   1.012   0.878   0.952   0.990
67    G         0.835   0.897   0.921   0.400   0.526   0.632   0.878   0.952   0.990
68    I         0.835   0.897   0.921   0.715   0.831   0.882   0.878   0.952   0.990
69    L        -0.523  -0.673  -0.506  -0.942  -1.217  -0.913  -0.733  -0.978  -0.735
70    A        -1.517  -1.523  -1.314  -1.967  -2.022  -1.677  -1.672  -1.546  -1.280
71    I        -0.523  -0.227  -0.453  -0.702  -0.243  -0.646  -0.733  -0.269  -0.647
72    Y         0.835   0.897   0.921   1.166   1.240   1.241   0.878   0.952   0.990
73    G        -0.074  -0.203  -0.444  -0.445  -0.588  -0.948  -0.062  -0.235  -0.632
74    L         0.835   0.897   0.921   0.582   0.715   0.776   0.878   0.952   0.990
75    V         0.835   0.897   0.921   0.824   0.895   0.969   0.878   0.952   0.990
76    V        -0.074  -0.395  -0.453   0.043  -0.407  -0.476  -0.062  -0.524  -0.648
77    A        -0.838  -0.688  -0.506  -1.335  -1.066  -0.748  -1.269  -1.003  -0.735
78    V         0.835   0.897   0.921   0.824   0.895   0.969   0.878   0.952   0.990
79    L         0.835   0.897   0.921   0.582   0.715   0.776   0.878   0.952   0.990
80    I         0.835   0.897   0.921   0.715   0.831   0.882   0.878   0.952   0.990
81    A         0.835   0.897   0.921   0.693   0.798   0.865   0.878   0.952   0.990
82    G        -0.074  -0.203  -0.444  -0.346  -0.443  -0.652  -0.062  -0.235  -0.632
83    N        -2.354  -1.988  -1.917  -2.448  -1.737  -1.684  -2.209  -1.744  -1.586
84    L        -0.074  -0.395  -0.453  -0.199  -0.581  -0.642  -0.062  -0.524  -0.648
85    S        -0.074  -0.203  -0.444  -0.002  -0.204  -0.723  -0.062  -0.235  -0.632
86    P         0.835   0.897   0.921   1.181   1.263   1.253   0.878   0.952   0.990
87    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
88    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
89    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
90    T        -1.757  -1.931  -1.918  -1.108  -1.490  -1.513  -1.538  -1.684  -1.585
91    E        -0.941  -1.357  -1.319  -0.251  -0.802  -0.819  -0.867  -1.345  -1.287
92    D        -2.196  -1.980  -1.907  -1.559  -1.266  -1.186  -2.074  -1.735  -1.576
93    Y         0.835   0.897   0.921   1.166   1.240   1.241   0.878   0.952   0.990
94    T        -0.762  -0.477  -0.476  -0.850  -0.415  -0.411  -1.135  -0.653  -0.685
95    L         0.835   0.897   0.921   0.582   0.715   0.776   0.878   0.952   0.990
96    F         0.835   0.897   0.921   1.016   1.098   1.121   0.878   0.952   0.990
97    N        -0.074  -0.395  -0.453   0.463  -0.039  -0.260  -0.062  -0.524  -0.648
98    G         0.835   0.897   0.921   0.400   0.526   0.632   0.878   0.952   0.990
99    F        -0.074   0.193  -0.428   0.254   0.568  -0.245  -0.062   0.296  -0.606
100   M        -0.074  -0.395  -0.453   0.263  -0.252  -0.452  -0.062  -0.524  -0.648
101   H         0.835   0.897   0.921   1.338   1.400   1.378   0.878   0.952   0.990
102   L         0.835   0.897   0.921   0.582   0.715   0.776   0.878   0.952   0.990
103   S        -0.838  -0.684  -0.505  -1.335  -1.056  -0.742  -1.269  -0.997  -0.733
104   C        -0.074  -0.395  -0.453   0.404  -0.116  -0.360  -0.062  -0.524  -0.648
105   G         0.835   0.897   0.921   0.400   0.526   0.632   0.878   0.952   0.990
106   L         0.835   0.897   0.921   0.582   0.715   0.776   0.878   0.952   0.990
107   C        -1.778  -1.608  -1.334  -1.921  -1.739  -1.326  -1.940  -1.648  -1.304
108   V         0.835   0.897   0.921   0.824   0.895   0.969   0.878   0.952   0.990
109   G         0.835   0.897   0.921   0.400   0.526   0.632   0.878   0.952   0.990
110   F        -0.523  -0.673  -0.506  -0.556  -0.966  -0.732  -0.733  -0.978  -0.735
111   A        -0.523  -0.673  -0.506  -0.657  -0.835  -0.531  -0.733  -0.978  -0.735
112   C        -1.338  -1.264  -1.321  -1.217  -1.422  -1.508  -1.403  -1.331  -1.290
113   L        -0.074  -0.395  -0.453  -0.241  -0.675  -0.770  -0.062  -0.524  -0.648
114   S        -0.762  -0.477  -0.476  -1.205  -0.707  -0.706  -1.135  -0.653  -0.685
115   S        -0.523  -0.673  -0.506  -0.657  -1.027  -0.749  -0.733  -0.978  -0.735
116   G         0.835   0.897   0.921   0.400   0.526   0.632   0.878   0.952   0.990
117   Y         0.835   0.897   0.921   1.166   1.240   1.241   0.878   0.952   0.990
118   A        -0.941  -0.835  -1.281  -0.862  -0.702  -1.272  -0.867  -0.729  -1.242
119   I         0.835   0.897   0.921   0.715   0.831   0.882   0.878   0.952   0.990
120   G         0.835   0.897   0.921   0.400   0.526   0.632   0.878   0.952   0.990
121   M        -0.941  -1.051  -1.292  -0.875  -1.090  -1.354  -0.867  -1.014  -1.254
122   V         0.835   0.897   0.921   0.824   0.895   0.969   0.878   0.952   0.990
123   G         0.835   0.897   0.921   0.400   0.526   0.632   0.878   0.952   0.990
124   D         0.835   0.897   0.921   1.288   1.335   1.338   0.878   0.952   0.990
125   V        -2.196  -2.250  -1.927  -1.894  -1.854  -1.428  -2.074  -1.964  -1.594
126   G         0.835   0.897   0.921   0.400   0.526   0.632   0.878   0.952   0.990
127   V         0.835   0.897   0.921   0.824   0.895   0.969   0.878   0.952   0.990
128   R        -0.074  -0.395  -0.453   0.543   0.085  -0.065  -0.062  -0.524  -0.648
129   K        -2.354  -1.975  -1.917  -1.933  -1.563  -1.387  -2.209  -1.733  -1.585
130   Y        -0.762  -0.477  -0.476  -0.768  -0.316  -0.353  -1.135  -0.653  -0.685
131   M         0.835   0.897   0.921   1.099   1.167   1.187   0.878   0.952   0.990
132   H        -1.338  -1.532  -1.325  -0.953  -1.282  -1.111  -1.403  -1.557  -1.294
133   Q         0.835   0.897   0.921   1.318   1.371   1.362   0.878   0.952   0.990
134   P        -0.941  -1.357  -1.319  -0.373  -0.970  -1.019  -0.867  -1.345  -1.287
135   R         0.835   0.897   0.921   1.298   1.345   1.346   0.878   0.952   0.990
136   L        -0.523  -0.673  -0.506  -0.942  -1.217  -0.913  -0.733  -0.978  -0.735
137   F         0.835   0.897   0.921   1.016   1.098   1.121   0.878   0.952   0.990
138   V         0.835   0.897   0.921   0.824   0.895   0.969   0.878   0.952   0.990
139   G        -0.074  -0.395  -0.453  -0.417  -0.838  -0.875  -0.062  -0.524  -0.648
140   I        -0.523  -0.673  -0.506  -0.681  -0.897  -0.600  -0.733  -0.978  -0.735
141   V         0.835   0.897   0.921   0.824   0.895   0.969   0.878   0.952   0.990
142   L         0.835   0.897   0.921   0.582   0.715   0.776   0.878   0.952   0.990
143   I         0.835   0.897   0.921   0.715   0.831   0.882   0.878   0.952   0.990
144   L         0.835   0.897   0.921   0.582   0.715   0.776   0.878   0.952   0.990
145   I         0.835   0.897   0.921   0.715   0.831   0.882   0.878   0.952   0.990
146   F         0.835   0.897   0.921   1.016   1.098   1.121   0.878   0.952   0.990
147   S        -1.517  -1.414  -1.313  -1.967  -1.788  -1.673  -1.672  -1.421  -1.279
148   E         0.835   0.897   0.921   1.237   1.321   1.297   0.878   0.952   0.990
149   V         0.835   0.897   0.921   0.824   0.895   0.969   0.878   0.952   0.990
150   L         0.835   0.897   0.921   0.582   0.715   0.776   0.878   0.952   0.990
151   G         0.835   0.897   0.921   0.400   0.526   0.632   0.878   0.952   0.990
152   L         0.835   0.897   0.921   0.582   0.715   0.776   0.878   0.952   0.990
153   Y         0.835   0.897   0.921   1.166   1.240   1.241   0.878   0.952   0.990
154   G         0.835   0.897   0.921   0.400   0.526   0.632   0.878   0.952   0.990
155   M        -0.523  -0.673  -0.506  -0.474  -0.907  -0.681  -0.733  -0.978  -0.735
156   I         0.835   0.897   0.921   0.715   0.831   0.882   0.878   0.952   0.990
157   V        -0.838  -0.616  -0.490  -1.359  -0.940  -0.727  -1.269  -0.881  -0.709
158   A        -0.074  -0.395  -0.453  -0.189  -0.715  -0.884  -0.062  -0.524  -0.648
159   L         0.835   0.897   0.921   0.582   0.715   0.776   0.878   0.952   0.990
160   I         0.835   0.897   0.921   0.715   0.831   0.882   0.878   0.952   0.990
161   L         0.835   0.897   0.921   0.582   0.715   0.776   0.878   0.952   0.990
162   N        -0.074  -0.395  -0.453   0.524   0.086  -0.078  -0.062  -0.524  -0.648
163   T         0.835   0.897   0.921   1.232   1.301   1.293   0.878   0.952   0.990
164   R        -0.523  -0.217  -0.452  -0.116   0.301  -0.108  -0.733  -0.254  -0.645
165   G        -0.941  -1.357  -1.319  -1.159  -1.646  -1.484  -0.867  -1.345  -1.287
166   S        -0.074  -0.203  -0.444   0.118  -0.027  -0.363  -0.062  -0.235  -0.632
167   E        -1.338  -1.374  -1.307  -1.589  -1.526  -1.298  -1.403  -1.365  -1.272
168   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
169   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
170   -        -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/P32842
Output conservation file - output/P32842
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
