1     M         1.760   1.780   1.834   2.098   2.137   2.216   1.921   1.946   2.027
2     C        -1.445  -1.424  -1.390  -1.067  -1.063  -0.968  -1.186  -1.153  -1.091
3     S        -0.644  -0.693  -0.670  -0.589  -0.647  -0.595  -0.668  -0.725  -0.680
4     A        -0.644  -0.693  -0.670  -0.769  -0.876  -0.850  -0.668  -0.725  -0.680
5     G        -0.644  -0.653  -0.652  -0.561  -0.557  -0.543  -0.668  -0.677  -0.659
6     G         1.760   1.780   1.834   1.903   1.937   2.019   1.921   1.946   2.027
7     I         0.289   0.309   0.286   0.365   0.403   0.374   0.080   0.113   0.062
8     R         0.289   0.309   0.286   0.267   0.304   0.257   0.080   0.113   0.062
9     R         0.460   0.366   0.365   0.595   0.461   0.442   0.368   0.210   0.198
10    P         1.760   1.780   1.834   2.119   2.156   2.236   1.921   1.946   2.027
11    I         0.460   0.525   0.385   0.502   0.595   0.394   0.368   0.472   0.232
12    Q        -0.644  -0.667  -0.658  -0.552  -0.597  -0.597  -0.668  -0.693  -0.666
13    I         0.460   0.525   0.385   0.502   0.595   0.394   0.368   0.472   0.232
14    E        -1.445  -1.424  -1.390  -1.451  -1.399  -1.353  -1.186  -1.153  -1.091
15    E         0.460   0.525   0.385   0.193   0.285   0.072   0.368   0.472   0.232
16    F         1.760   1.780   1.834   2.129   2.164   2.246   1.921   1.946   2.027
17    K        -0.644  -0.693  -0.670  -0.453  -0.512  -0.475  -0.668  -0.725  -0.680
18    T         0.460   0.548   0.390   0.540   0.658   0.452   0.368   0.508   0.241
19    A         1.760   1.780   1.834   1.838   1.883   1.954   1.921   1.946   2.027
20    I         1.760   1.780   1.834   1.752   1.773   1.867   1.921   1.946   2.027
21    S        -0.644  -0.653  -0.652  -0.589  -0.587  -0.609  -0.668  -0.677  -0.659
22    G        -0.644  -0.582  -0.641  -0.804  -0.696  -0.799  -0.668  -0.581  -0.644
23    M        -0.644  -0.693  -0.670  -0.475  -0.585  -0.560  -0.668  -0.725  -0.680
24    S         0.460   0.525   0.385   0.439   0.537   0.337   0.368   0.472   0.232
25    D         0.460   0.479   0.375   0.281   0.323   0.110   0.368   0.398   0.215
26    M        -1.445  -1.424  -1.390  -1.281  -1.276  -1.183  -1.186  -1.153  -1.091
27    E         0.460   0.366   0.365   0.193   0.034   0.038   0.368   0.210   0.198
28    L         1.760   1.780   1.834   1.643   1.663   1.758   1.921   1.946   2.027
29    A        -1.445  -1.424  -1.390  -1.030  -0.956  -0.930  -1.186  -1.153  -1.091
30    Q        -1.445  -1.424  -1.390  -1.463  -1.447  -1.366  -1.186  -1.153  -1.091
31    I         0.460   0.525   0.385   0.502   0.595   0.394   0.368   0.472   0.232
32    K         0.460   0.479   0.375   0.582   0.619   0.449   0.368   0.398   0.215
33    T        -1.445  -1.424  -1.390  -1.155  -1.144  -1.056  -1.186  -1.153  -1.091
34    E         0.460   0.366   0.365   0.278   0.142   0.157   0.368   0.210   0.198
35    I        -0.644  -0.667  -0.658  -0.678  -0.739  -0.699  -0.668  -0.693  -0.666
36    E        -0.644  -0.693  -0.670  -0.940  -1.023  -0.968  -0.668  -0.725  -0.680
37    N         1.760   1.780   1.834   1.730   1.755   1.846   1.921   1.946   2.027
38    S         0.460   0.479   0.375   0.404   0.438   0.274   0.368   0.398   0.215
39    I         0.460   0.479   0.375   0.502   0.530   0.378   0.368   0.398   0.215
40    N        -1.445  -1.424  -1.390  -1.407  -1.375  -1.310  -1.186  -1.153  -1.091
41    H         0.460   0.366   0.365   0.785   0.639   0.624   0.368   0.210   0.198
42    L         1.760   1.780   1.834   1.643   1.663   1.758   1.921   1.946   2.027
43    Q        -0.644  -0.667  -0.658  -0.493  -0.572  -0.529  -0.668  -0.693  -0.666
44    R         0.460   0.366   0.365   0.537   0.393   0.361   0.368   0.210   0.198
45    S         0.460   0.366   0.365   0.468   0.336   0.346   0.368   0.210   0.198
46    N         0.460   0.366   0.365   0.400   0.242   0.229   0.368   0.210   0.198
47    A        -1.445  -1.424  -1.390  -1.553  -1.495  -1.456  -1.186  -1.153  -1.091
48    R         0.460   0.366   0.365   0.565   0.419   0.399   0.368   0.210   0.198
49    L         1.760   1.780   1.834   1.643   1.663   1.758   1.921   1.946   2.027
50    G        -0.644  -0.550  -0.638  -0.692  -0.571  -0.648  -0.668  -0.539  -0.641
51    K        -1.445  -1.424  -1.390  -1.317  -1.276  -1.218  -1.186  -1.153  -1.091
52    Y         0.460   0.366   0.365   0.709   0.533   0.505   0.368   0.210   0.198
53    I         0.460   0.479   0.375   0.502   0.530   0.378   0.368   0.398   0.215
54    A        -0.644  -0.667  -0.658  -0.584  -0.620  -0.607  -0.668  -0.693  -0.666
55    K         0.460   0.366   0.365   0.520   0.358   0.346   0.368   0.210   0.198
56    L         0.460   0.366   0.365   0.436   0.301   0.315   0.368   0.210   0.198
57    E        -0.644  -0.550  -0.638  -0.626  -0.460  -0.622  -0.668  -0.539  -0.641
58    G         0.460   0.366   0.365   0.558   0.391   0.358   0.368   0.210   0.198
59    A        -0.644  -0.550  -0.638  -0.740  -0.611  -0.701  -0.668  -0.539  -0.641
60    D        -1.445  -1.424  -1.390  -1.626  -1.577  -1.530  -1.186  -1.153  -1.091
61    D        -0.644  -0.653  -0.652  -0.631  -0.645  -0.665  -0.668  -0.677  -0.659
62    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
63    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
64    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
65    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
66    R        -0.644  -0.653  -0.652  -0.884  -0.906  -0.879  -0.668  -0.677  -0.659
67    L         1.760   1.780   1.834   1.643   1.663   1.758   1.921   1.946   2.027
68    E        -0.644  -0.693  -0.670  -0.925  -0.985  -0.950  -0.668  -0.725  -0.680
69    A        -0.644  -0.667  -0.658  -0.774  -0.825  -0.829  -0.668  -0.693  -0.666
70    D        -1.445  -1.424  -1.390  -1.606  -1.568  -1.509  -1.186  -1.153  -1.091
71    D        -0.644  -0.582  -0.641  -0.879  -0.774  -0.858  -0.668  -0.581  -0.644
72    S        -0.644  -0.598  -0.644  -0.894  -0.812  -0.908  -0.668  -0.601  -0.648
73    D        -1.445  -1.424  -1.390  -0.956  -0.882  -0.856  -1.186  -1.153  -1.091
74    D         0.460   0.479   0.375   0.340   0.382   0.190   0.368   0.398   0.215
75    L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
76    E         0.289   0.273   0.275  -0.090  -0.117  -0.132   0.080   0.051   0.042
77    N         0.289   0.273   0.275   0.122   0.093   0.069   0.080   0.051   0.042
78    I        -0.644  -0.667  -0.658  -0.649  -0.676  -0.666  -0.668  -0.693  -0.666
79    D        -0.644  -0.667  -0.658  -0.740  -0.782  -0.754  -0.668  -0.693  -0.666
80    S        -0.644  -0.693  -0.670  -0.839  -0.916  -0.892  -0.668  -0.725  -0.680
81    G        -1.445  -1.424  -1.390  -1.371  -1.331  -1.273  -1.186  -1.153  -1.091
82    D         1.760   1.780   1.834   1.665   1.705   1.780   1.921   1.946   2.027
83    L         0.460   0.525   0.385   0.343   0.434   0.220   0.368   0.472   0.232
84    A        -1.445  -1.424  -1.390  -1.489  -1.440  -1.391  -1.186  -1.153  -1.091
85    L         0.460   0.479   0.375   0.397   0.424   0.277   0.368   0.398   0.215
86    Y         0.158   0.173   0.222   0.436   0.470   0.544  -0.150  -0.125  -0.051
87    K        -0.644  -0.653  -0.652  -0.497  -0.533  -0.523  -0.668  -0.677  -0.659
88    D         0.158   0.175   0.223  -0.339  -0.314  -0.237  -0.150  -0.122  -0.050
89    S         1.760   1.780   1.834   1.676   1.701   1.791   1.921   1.946   2.027
90    V        -0.644  -0.582  -0.641  -0.678  -0.586  -0.671  -0.668  -0.581  -0.644
91    R        -0.644  -0.693  -0.670  -0.668  -0.767  -0.736  -0.668  -0.725  -0.680
92    E         1.760   1.780   1.834   1.498   1.518   1.612   1.921   1.946   2.027
93    N         1.760   1.780   1.834   1.730   1.755   1.846   1.921   1.946   2.027
94    E        -0.644  -0.693  -0.670  -0.711  -0.749  -0.698  -0.668  -0.725  -0.680
95    I        -0.644  -0.598  -0.644  -0.706  -0.632  -0.708  -0.668  -0.601  -0.648
96    V         1.760   1.780   1.834   1.912   1.952   2.028   1.921   1.946   2.027
97    L         0.460   0.366   0.365   0.343   0.181   0.186   0.368   0.210   0.198
98    N        -0.644  -0.653  -0.652  -0.904  -0.940  -0.934  -0.668  -0.677  -0.659
99    N         1.760   1.780   1.834   1.730   1.755   1.846   1.921   1.946   2.027
100   Y        -0.644  -0.667  -0.658  -0.339  -0.365  -0.374  -0.668  -0.693  -0.666
101   N         0.460   0.525   0.385   0.468   0.567   0.355   0.368   0.472   0.232
102   E         0.460   0.366   0.365   0.278   0.142   0.157   0.368   0.210   0.198
103   R         1.760   1.780   1.834   1.870   1.913   1.986   1.921   1.946   2.027
104   V         0.460   0.548   0.390   0.397   0.520   0.300   0.368   0.508   0.241
105   D        -1.445  -1.424  -1.390  -1.444  -1.362  -1.347  -1.186  -1.153  -1.091
106   A         1.760   1.780   1.834   1.838   1.883   1.954   1.921   1.946   2.027
107   L         1.760   1.780   1.834   1.643   1.663   1.758   1.921   1.946   2.027
108   E        -1.445  -1.424  -1.390  -1.495  -1.451  -1.398  -1.186  -1.153  -1.091
109   Q        -1.445  -1.424  -1.390  -1.606  -1.608  -1.509  -1.186  -1.153  -1.091
110   E         1.760   1.780   1.834   1.498   1.518   1.612   1.921   1.946   2.027
111   T        -0.644  -0.582  -0.641  -0.784  -0.704  -0.774  -0.668  -0.581  -0.644
112   V        -1.445  -1.424  -1.390  -1.161  -1.112  -1.062  -1.186  -1.153  -1.091
113   Y        -0.644  -0.693  -0.670  -0.225  -0.297  -0.262  -0.668  -0.725  -0.680
114   R         1.760   1.780   1.834   1.870   1.913   1.986   1.921   1.946   2.027
115   K        -0.644  -0.693  -0.670  -0.497  -0.552  -0.528  -0.668  -0.725  -0.680
116   T        -1.445  -1.424  -1.390  -1.371  -1.360  -1.273  -1.186  -1.153  -1.091
117   G        -0.780  -0.769  -0.721  -0.540  -0.509  -0.437  -0.841  -0.818  -0.744
118   H         0.289   0.273   0.275   0.490   0.464   0.450   0.080   0.051   0.042
119   G        -0.780  -0.769  -0.721  -0.665  -0.648  -0.563  -0.841  -0.818  -0.744
120   K        -0.780  -0.769  -0.721  -0.985  -0.965  -0.885  -0.841  -0.818  -0.744
121   S         0.289   0.329   0.291   0.273   0.349   0.256   0.080   0.147   0.071
122   K         0.289   0.273   0.275   0.211   0.181   0.154   0.080   0.051   0.042
123   H        -0.780  -0.769  -0.721  -0.755  -0.736  -0.653  -0.841  -0.818  -0.744
124   E        -0.780  -0.769  -0.721  -0.915  -0.876  -0.815  -0.841  -0.818  -0.744
125   V        -0.780  -0.769  -0.721  -0.681  -0.664  -0.580  -0.841  -0.818  -0.744
126   E         0.289   0.273   0.275  -0.022  -0.047  -0.049   0.080   0.051   0.042
127   A        -0.780  -0.769  -0.721  -0.872  -0.852  -0.771  -0.841  -0.818  -0.744
128   K        -0.780  -0.769  -0.721  -0.730  -0.697  -0.629  -0.841  -0.818  -0.744
129   D        -0.780  -0.769  -0.721  -0.985  -0.950  -0.885  -0.841  -0.818  -0.744
130   N        -0.780  -0.769  -0.721  -0.959  -0.936  -0.859  -0.841  -0.818  -0.744
131   T        -0.780  -0.769  -0.721  -0.813  -0.787  -0.712  -0.841  -0.818  -0.744
132   N         0.289   0.329   0.291   0.223   0.296   0.215   0.080   0.147   0.071
133   K         0.289   0.273   0.275   0.236   0.204   0.185   0.080   0.051   0.042
134   G         0.289   0.329   0.291   0.173   0.239   0.180   0.080   0.147   0.071
135   P        -0.780  -0.769  -0.721  -0.626  -0.605  -0.523  -0.841  -0.818  -0.744
136   D        -0.780  -0.769  -0.721  -1.048  -1.024  -0.949  -0.841  -0.818  -0.744
137   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
138   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
139   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
140   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
141   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
142   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
143   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
144   V         0.460   0.525   0.385   0.605   0.717   0.475   0.368   0.472   0.232
145   D         0.460   0.366   0.365   0.457   0.339   0.336   0.368   0.210   0.198
146   M        -0.644  -0.693  -0.670  -0.475  -0.585  -0.560  -0.668  -0.725  -0.680
147   D         0.460   0.366   0.365   0.281   0.118   0.090   0.368   0.210   0.198
148   N         0.460   0.366   0.365   0.404   0.241   0.234   0.368   0.210   0.198
149   S        -0.644  -0.653  -0.652  -0.413  -0.412  -0.435  -0.668  -0.677  -0.659
150   N         0.289   0.240   0.275   0.151   0.067   0.124   0.080  -0.006   0.042
151   V        -0.644  -0.693  -0.670  -0.631  -0.734  -0.701  -0.668  -0.725  -0.680
152   D         1.760   1.780   1.834   1.665   1.705   1.780   1.921   1.946   2.027
153   V         0.289   0.273   0.275   0.285   0.258   0.243   0.080   0.051   0.042
154   V        -0.780  -0.769  -0.721  -0.673  -0.639  -0.572  -0.841  -0.818  -0.744
155   T        -0.780  -0.769  -0.721  -0.657  -0.632  -0.555  -0.841  -0.818  -0.744
156   P         0.289   0.273   0.275   0.455   0.421   0.393   0.080   0.051   0.042
157   N         1.760   1.780   1.834   1.730   1.755   1.846   1.921   1.946   2.027
158   S         0.460   0.366   0.365   0.439   0.306   0.307   0.368   0.210   0.198
159   I         0.460   0.366   0.365   0.502   0.359   0.362   0.368   0.210   0.198
160   F        -0.644  -0.582  -0.641  -0.254  -0.151  -0.246  -0.668  -0.581  -0.644
161   I         0.460   0.548   0.390   0.343   0.468   0.229   0.368   0.508   0.241
* 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/Q12513
Output conservation file - output/Q12513
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
