1     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
2     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
3     -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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    -        -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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
22    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
23    -        -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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
28    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
29    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
30    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
31    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
35    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
36    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
37    M         1.165   1.244   1.303   1.343   1.466   1.541   1.265   1.373   1.465
38    S         0.508   0.280   0.287   0.349   0.044   0.047   0.498   0.110   0.080
39    V        -0.044   0.064   0.161  -0.313  -0.129   0.007  -0.488  -0.295  -0.161
40    V         0.184   0.074   0.164   0.162  -0.043   0.104  -0.050  -0.275  -0.155
41    G         1.165   1.244   1.303   1.179   1.290   1.387   1.265   1.373   1.465
42    S         1.165   1.244   1.303   0.921   1.041   1.146   1.265   1.373   1.465
43    L         1.165   1.244   1.303   1.054   1.176   1.270   1.265   1.373   1.465
44    I         1.165   1.244   1.303   1.266   1.365   1.469   1.265   1.373   1.465
45    F         1.165   1.244   1.303   1.247   1.375   1.451   1.265   1.373   1.465
46    C         1.165   1.244   1.303   1.109   1.220   1.322   1.265   1.373   1.465
47    L        -1.442  -1.238  -1.312  -1.556  -1.254  -1.372  -1.365  -1.099  -1.117
48    D        -0.406  -0.256  -0.433  -0.363  -0.187  -0.408  -0.598  -0.396  -0.611
49    C         1.165   1.244   1.303   1.109   1.220   1.322   1.265   1.373   1.465
50    G         1.165   1.244   1.303   1.179   1.290   1.387   1.265   1.373   1.465
51    D         0.184   0.331   0.229   0.117   0.341   0.157  -0.050   0.200  -0.029
52    L         1.165   1.244   1.303   1.054   1.176   1.270   1.265   1.373   1.465
53    L         0.508   0.661   0.332   0.517   0.722   0.321   0.498   0.728   0.165
54    E        -0.406  -0.557  -0.465  -0.361  -0.567  -0.455  -0.598  -0.767  -0.655
55    N        -1.556  -1.519  -1.353  -1.733  -1.655  -1.411  -1.474  -1.358  -1.153
56    P        -1.858  -1.775  -1.655  -1.598  -1.612  -1.354  -1.584  -1.438  -1.264
57    N        -1.884  -1.730  -1.659  -1.929  -1.732  -1.643  -1.597  -1.398  -1.266
58    A        -1.643  -1.492  -1.370  -1.775  -1.516  -1.380  -1.540  -1.326  -1.166
59    V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
60    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
61    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
62    L        -1.744  -1.687  -1.647  -1.830  -1.759  -1.689  -1.474  -1.368  -1.257
63    G        -1.442  -1.362  -1.327  -1.587  -1.453  -1.362  -1.365  -1.228  -1.132
64    S        -1.442  -1.377  -1.329  -1.550  -1.412  -1.329  -1.365  -1.239  -1.133
65    N        -2.463  -2.279  -2.150  -2.115  -1.794  -1.698  -1.803  -1.589  -1.413
66    V        -1.025  -0.912  -0.936  -1.051  -0.919  -0.925  -1.145  -0.962  -0.939
67    E        -1.744  -1.709  -1.646  -1.529  -1.464  -1.411  -1.474  -1.386  -1.257
68    C         1.165   1.244   1.303   1.109   1.220   1.322   1.265   1.373   1.465
69    S        -1.858  -1.743  -1.653  -1.952  -1.744  -1.647  -1.584  -1.415  -1.262
70    Q        -0.708  -0.695  -0.899  -0.441  -0.490  -0.791  -0.707  -0.700  -0.892
71    C         1.165   1.244   1.303   1.109   1.220   1.322   1.265   1.373   1.465
72    K        -2.160  -1.989  -1.912  -1.893  -1.647  -1.583  -1.693  -1.487  -1.344
73    A        -0.118  -0.034  -0.363  -0.063   0.068  -0.486  -0.159  -0.031  -0.504
74    I        -1.442  -1.307  -1.322  -1.533  -1.360  -1.303  -1.365  -1.187  -1.127
75    Y         0.449   0.537   0.272   0.647   0.780   0.378   0.406   0.541   0.054
76    P        -0.224  -0.140  -0.423   0.022   0.144  -0.337  -0.309  -0.172  -0.589
77    K        -1.025  -1.021  -0.948  -1.334  -1.299  -1.186  -1.145  -1.081  -0.950
78    S        -0.708  -0.869  -0.924  -0.739  -0.972  -1.020  -0.707  -0.890  -0.919
79    Q        -1.139  -1.134  -0.974  -1.173  -1.136  -0.938  -1.255  -1.175  -0.977
80    F        -0.118  -0.249  -0.393   0.121  -0.069  -0.308  -0.159  -0.362  -0.547
81    S        -1.442  -1.396  -1.335  -1.427  -1.299  -1.263  -1.365  -1.257  -1.137
82    N         0.508   0.280   0.287   0.536   0.185   0.162   0.498   0.110   0.080
83    L         0.508   0.280   0.287   0.501   0.203   0.214   0.498   0.110   0.080
84    K        -0.406  -0.500  -0.468  -0.557  -0.708  -0.668  -0.598  -0.717  -0.660
85    V         1.165   1.244   1.303   1.149   1.264   1.359   1.265   1.373   1.465
86    V        -0.118  -0.034  -0.363   0.041   0.144  -0.303  -0.159  -0.031  -0.504
87    T         1.165   1.244   1.303   1.049   1.179   1.266   1.265   1.373   1.465
88    T        -0.951  -0.674  -0.908  -1.118  -0.681  -1.046  -1.036  -0.662  -0.905
89    T         0.011   0.158   0.185  -0.441  -0.189  -0.165  -0.378  -0.114  -0.114
90    A        -0.951  -0.993  -0.943  -1.162  -1.223  -1.135  -1.036  -1.029  -0.943
91    D        -1.139  -1.088  -0.975  -1.121  -1.020  -0.875  -1.255  -1.133  -0.979
92    D        -0.406  -0.454  -0.471  -0.488  -0.673  -0.693  -0.598  -0.681  -0.664
93    A        -0.118  -0.300  -0.404  -0.038  -0.290  -0.507  -0.159  -0.422  -0.562
94    F         1.165   1.244   1.303   1.247   1.375   1.451   1.265   1.373   1.465
95    P         1.165   1.244   1.303   1.290   1.399   1.492   1.265   1.373   1.465
96    S         1.165   1.244   1.303   0.921   1.041   1.146   1.265   1.373   1.465
97    S        -1.139  -1.124  -0.972  -1.428  -1.357  -1.184  -1.255  -1.164  -0.975
98    L         0.508   0.601   0.322   0.505   0.642   0.278   0.498   0.640   0.146
99    R         0.011   0.123   0.176  -0.163   0.013   0.067  -0.378  -0.182  -0.131
100   A        -1.442  -1.388  -1.333  -1.521  -1.418  -1.287  -1.365  -1.260  -1.137
101   K         0.508   0.713   0.330   0.458   0.746   0.217   0.498   0.803   0.161
102   K        -0.951  -1.074  -0.957  -0.850  -1.056  -0.880  -1.036  -1.113  -0.959
103   S         0.508   0.280   0.287   0.358   0.058   0.069   0.498   0.110   0.080
104   V        -0.406  -0.454  -0.471  -0.377  -0.486  -0.492  -0.598  -0.681  -0.664
105   V         1.165   1.244   1.303   1.149   1.264   1.359   1.265   1.373   1.465
106   K         0.184   0.074   0.164   0.043  -0.122   0.009  -0.050  -0.275  -0.155
107   T         0.508   0.500   0.317   0.483   0.502   0.225   0.498   0.482   0.138
108   S        -0.708  -0.848  -0.922  -0.711  -0.941  -0.962  -0.707  -0.869  -0.918
109   L        -0.708  -0.912  -0.929  -0.636  -0.963  -0.989  -0.707  -0.934  -0.926
110   K        -0.951  -1.082  -0.957  -0.980  -1.115  -0.939  -1.036  -1.122  -0.960
111   K        -1.254  -1.184  -1.305  -1.100  -0.983  -1.146  -1.145  -1.050  -1.108
112   N        -1.063  -1.078  -0.973  -1.079  -1.127  -0.950  -1.168  -1.131  -0.975
113   E         0.449   0.205   0.250   0.494   0.096   0.155   0.406  -0.028   0.012
114   L        -0.224  -0.370  -0.439  -0.225  -0.470  -0.563  -0.309  -0.535  -0.612
115   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
116   K        -1.139  -1.166  -0.979  -1.273  -1.321  -1.054  -1.255  -1.209  -0.983
117   D         0.011   0.158   0.185  -0.187   0.042   0.073  -0.378  -0.114  -0.114
118   G        -0.118  -0.383  -0.419   0.064  -0.315  -0.380  -0.159  -0.528  -0.583
119   A         0.508   0.280   0.287   0.570   0.286   0.280   0.498   0.110   0.080
120   T        -0.406  -0.525  -0.457  -0.448  -0.605  -0.502  -0.598  -0.720  -0.642
121   I         0.508   0.280   0.287   0.669   0.298   0.281   0.498   0.110   0.080
122   K        -0.406  -0.510  -0.470  -0.528  -0.691  -0.626  -0.598  -0.733  -0.663
123   E         0.508   0.280   0.287   0.549   0.209   0.206   0.498   0.110   0.080
124   K         0.508   0.280   0.287   0.459   0.162   0.147   0.498   0.110   0.080
125   C         1.165   1.244   1.303   1.109   1.220   1.322   1.265   1.373   1.465
126   P         1.165   1.244   1.303   1.290   1.399   1.492   1.265   1.373   1.465
127   Q         0.184   0.370   0.233   0.043   0.336   0.113  -0.050   0.266  -0.021
128   C         1.165   1.244   1.303   1.109   1.220   1.322   1.265   1.373   1.465
129   G         0.508   0.601   0.322   0.608   0.739   0.338   0.498   0.640   0.146
130   N        -0.951  -0.942  -0.940  -0.877  -0.901  -0.888  -1.036  -0.980  -0.940
131   E        -0.535  -0.598  -0.463  -0.616  -0.669  -0.470  -0.817  -0.826  -0.652
132   E        -0.708  -0.912  -0.929  -0.519  -0.826  -0.845  -0.707  -0.934  -0.926
133   M         0.508   0.280   0.287   0.792   0.490   0.473   0.498   0.110   0.080
134   N        -1.442  -1.363  -1.329  -1.197  -1.124  -1.053  -1.365  -1.229  -1.133
135   Y         0.508   0.500   0.317   0.728   0.750   0.464   0.498   0.482   0.138
136   H        -0.118  -0.225  -0.395   0.198  -0.031  -0.271  -0.159  -0.333  -0.549
137   T        -0.118  -0.234  -0.399  -0.079  -0.261  -0.486  -0.159  -0.343  -0.555
138   L         0.508   0.280   0.287   0.488   0.180   0.178   0.498   0.110   0.080
139   Q         1.165   1.244   1.303   1.257   1.368   1.460   1.265   1.373   1.465
140   L         0.508   0.280   0.287   0.504   0.213   0.220   0.498   0.110   0.080
141   R         1.165   1.244   1.303   1.242   1.335   1.447   1.265   1.373   1.465
142   S         1.165   1.244   1.303   0.921   1.041   1.146   1.265   1.373   1.465
143   A         1.165   1.244   1.303   1.119   1.252   1.332   1.265   1.373   1.465
144   D         1.165   1.244   1.303   1.174   1.294   1.383   1.265   1.373   1.465
145   E         1.165   1.244   1.303   1.129   1.232   1.341   1.265   1.373   1.465
146   G         1.165   1.244   1.303   1.179   1.290   1.387   1.265   1.373   1.465
147   A         0.184   0.074   0.164   0.022  -0.234  -0.124  -0.050  -0.275  -0.155
148   T         1.165   1.244   1.303   1.049   1.179   1.266   1.265   1.373   1.465
149   V         0.508   0.280   0.287   0.600   0.297   0.306   0.498   0.110   0.080
150   F         0.508   0.280   0.287   0.667   0.347   0.312   0.498   0.110   0.080
151   Y         1.165   1.244   1.303   1.281   1.409   1.483   1.265   1.373   1.465
152   T        -0.118  -0.383  -0.419  -0.081  -0.456  -0.525  -0.159  -0.528  -0.583
153   C         1.165   1.244   1.303   1.109   1.220   1.322   1.265   1.373   1.465
154   T        -0.224  -0.277  -0.437  -0.168  -0.233  -0.428  -0.309  -0.378  -0.610
155   S        -2.160  -2.036  -1.919  -2.078  -1.848  -1.733  -1.693  -1.519  -1.349
156   C         1.165   1.244   1.303   1.109   1.220   1.322   1.265   1.373   1.465
157   G        -0.708  -0.553  -0.863  -0.462  -0.265  -0.690  -0.707  -0.485  -0.849
158   Y         0.508   0.280   0.287   0.711   0.396   0.369   0.498   0.110   0.080
159   K        -0.044   0.043   0.155  -0.310  -0.166   0.011  -0.488  -0.337  -0.172
160   F        -0.118  -0.225  -0.395   0.186   0.057  -0.165  -0.159  -0.333  -0.549
161   R         0.184   0.074   0.164   0.143  -0.160  -0.027  -0.050  -0.275  -0.155
162   T         0.508   0.280   0.287   0.483   0.183   0.173   0.498   0.110   0.080
163   N         1.165   1.244   1.303   1.134   1.251   1.345   1.265   1.373   1.465
164   N         1.165   1.244   1.303   1.134   1.251   1.345   1.265   1.373   1.465
* 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/P32529
Output conservation file - output/P32529
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
