1     M         1.602   1.611   1.667   1.935   1.952   2.023   1.747   1.756   1.846
2     I         0.091   0.074   0.161  -0.018  -0.057   0.068  -0.195  -0.226  -0.100
3     K         0.479   0.506   0.321   0.320   0.351   0.118   0.452   0.493   0.179
4     Y         1.602   1.611   1.667   1.942   1.958   2.030   1.747   1.756   1.846
5     T         0.479   0.540   0.332   0.624   0.718   0.393   0.452   0.545   0.199
6     I         0.091   0.128   0.189  -0.272  -0.215  -0.108  -0.195  -0.131  -0.049
7     D         0.091   0.128   0.189  -0.358  -0.301  -0.193  -0.195  -0.131  -0.049
8     E         0.091   0.074   0.161  -0.192  -0.198  -0.050  -0.195  -0.226  -0.100
9     L         1.602   1.611   1.667   1.702   1.720   1.799   1.747   1.756   1.846
10    F        -1.389  -1.369  -1.311  -0.948  -0.913  -0.831  -1.166  -1.138  -1.048
11    Q         0.091   0.074   0.161  -0.034  -0.091   0.028  -0.195  -0.226  -0.100
12    L         0.479   0.421   0.311   0.684   0.608   0.434   0.452   0.360   0.163
13    K         0.479   0.506   0.321   0.320   0.351   0.118   0.452   0.493   0.179
14    P        -0.531  -0.599  -0.666  -0.420  -0.539  -0.714  -0.518  -0.604  -0.685
15    S        -0.766  -0.744  -0.716  -1.029  -1.006  -0.916  -0.842  -0.810  -0.750
16    L        -0.766  -0.737  -0.712  -1.065  -1.012  -0.943  -0.842  -0.802  -0.746
17    T        -1.389  -1.418  -1.346  -0.983  -1.008  -0.903  -1.166  -1.188  -1.083
18    L        -0.766  -0.744  -0.716  -0.650  -0.617  -0.561  -0.842  -0.810  -0.750
19    E        -0.766  -0.737  -0.712  -1.047  -0.981  -0.990  -0.842  -0.802  -0.746
20    V        -1.389  -1.418  -1.346  -1.124  -1.177  -1.089  -1.166  -1.188  -1.083
21    N        -0.766  -0.728  -0.713  -0.693  -0.638  -0.617  -0.842  -0.794  -0.746
22    F        -0.531  -0.599  -0.666  -0.373  -0.493  -0.677  -0.518  -0.604  -0.685
23    D        -0.531  -0.599  -0.666  -0.373  -0.474  -0.558  -0.518  -0.604  -0.685
24    A        -1.389  -1.325  -1.345  -1.112  -1.014  -1.060  -1.166  -1.090  -1.081
25    V         0.091   0.128   0.189  -0.014   0.038   0.139  -0.195  -0.131  -0.049
26    E         0.091   0.074   0.161  -0.387  -0.411  -0.264  -0.195  -0.226  -0.100
27    F         1.602   1.611   1.667   1.763   1.782   1.858   1.747   1.756   1.846
28    R         0.091   0.128   0.189   0.065   0.122   0.214  -0.195  -0.131  -0.049
29    A        -0.766  -0.728  -0.713  -1.044  -1.012  -0.922  -0.842  -0.794  -0.746
30    I        -0.531  -0.599  -0.666  -0.186  -0.272  -0.367  -0.518  -0.604  -0.685
31    I         0.479   0.421   0.311   0.699   0.628   0.453   0.452   0.360   0.163
32    E         0.479   0.421   0.311   0.240   0.162   0.002   0.452   0.360   0.163
33    K        -0.531  -0.599  -0.666  -0.743  -0.851  -0.955  -0.518  -0.604  -0.685
34    V         1.602   1.611   1.667   1.740   1.758   1.836   1.747   1.756   1.846
35    K         0.479   0.540   0.332   0.326   0.401   0.144   0.452   0.545   0.199
36    Q         0.479   0.522   0.326   0.312   0.374   0.139   0.452   0.518   0.188
37    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
38    -        -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    L        -1.389  -1.418  -1.346  -0.989  -1.025  -0.919  -1.166  -1.188  -1.083
43    Q        -0.531  -0.599  -0.666  -0.251  -0.369  -0.541  -0.518  -0.604  -0.685
44    H        -1.389  -1.370  -1.304  -1.474  -1.447  -1.329  -1.166  -1.139  -1.041
45    L        -1.389  -1.418  -1.346  -1.072  -1.110  -1.016  -1.166  -1.188  -1.083
46    K         0.091   0.095   0.160  -0.222  -0.220  -0.091  -0.195  -0.189  -0.102
47    E        -0.531  -0.599  -0.666  -0.615  -0.702  -0.741  -0.518  -0.604  -0.685
48    E        -0.531  -0.599  -0.666  -0.649  -0.737  -0.790  -0.518  -0.604  -0.685
49    E         0.091   0.074   0.161  -0.506  -0.547  -0.395  -0.195  -0.226  -0.100
50    F         0.091   0.074   0.161   0.261   0.239   0.366  -0.195  -0.226  -0.100
51    N        -0.766  -0.740  -0.681  -0.709  -0.674  -0.576  -0.842  -0.808  -0.711
52    S         0.046   0.055   0.150  -0.138  -0.124   0.026  -0.276  -0.261  -0.120
53    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
54    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
55    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
56    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
57    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
58    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
59    -        -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    -        -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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
67    H         1.602   1.611   1.667   1.728   1.748   1.824   1.747   1.756   1.846
68    H        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
69    V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
70    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
71    H         1.602   1.611   1.667   1.733   1.754   1.829   1.747   1.756   1.846
72    F        -1.389  -1.402  -1.340  -0.893  -0.908  -0.818  -1.166  -1.172  -1.076
73    G         0.340   0.349   0.269   0.429   0.442   0.314   0.230   0.245   0.091
74    R         0.479   0.421   0.311   0.609   0.516   0.299   0.452   0.360   0.163
75    R         1.602   1.611   1.667   1.717   1.735   1.814   1.747   1.756   1.846
76    R         1.602   1.611   1.667   1.717   1.735   1.814   1.747   1.756   1.846
77    S        -0.531  -0.599  -0.666  -0.301  -0.390  -0.462  -0.518  -0.604  -0.685
78    S         1.602   1.611   1.667   1.586   1.607   1.687   1.747   1.756   1.846
79    H        -0.531  -0.599  -0.666  -0.344  -0.454  -0.614  -0.518  -0.604  -0.685
80    H        -0.531  -0.599  -0.666  -0.244  -0.346  -0.466  -0.518  -0.604  -0.685
81    H        -0.531  -0.599  -0.666  -0.263  -0.364  -0.493  -0.518  -0.604  -0.685
82    G        -2.012  -1.999  -1.856  -1.566  -1.568  -1.350  -1.489  -1.468  -1.299
83    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
84    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
85    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
86    R         0.091   0.100   0.159  -0.232  -0.226  -0.102  -0.195  -0.181  -0.103
87    P         1.602   1.611   1.667   1.710   1.729   1.806   1.747   1.756   1.846
88    K         0.091   0.074   0.161  -0.255  -0.285  -0.126  -0.195  -0.226  -0.100
89    I        -0.766  -0.744  -0.716  -0.616  -0.582  -0.526  -0.842  -0.810  -0.750
90    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
91    K         1.602   1.611   1.667   1.330   1.340   1.441   1.747   1.756   1.846
92    H         0.091   0.074   0.161  -0.105  -0.161  -0.032  -0.195  -0.226  -0.100
93    N        -0.766  -0.744  -0.716  -0.739  -0.713  -0.647  -0.842  -0.810  -0.750
94    K        -0.531  -0.599  -0.666  -0.765  -0.876  -0.988  -0.518  -0.604  -0.685
95    P         0.479   0.421   0.311   0.658   0.575   0.386   0.452   0.360   0.163
96    K         0.340   0.187   0.221   0.173  -0.067   0.033   0.230  -0.029   0.007
97    V         0.046   0.072   0.163  -0.002   0.052   0.181  -0.276  -0.231  -0.095
98    T        -0.766  -0.774  -0.691  -0.909  -0.924  -0.785  -0.842  -0.842  -0.721
99    T         0.091   0.074   0.161   0.071   0.046   0.173  -0.195  -0.226  -0.100
100   D         1.602   1.611   1.667   1.571   1.581   1.672   1.747   1.756   1.846
101   S        -1.389  -1.369  -1.311  -1.601  -1.573  -1.466  -1.166  -1.138  -1.048
102   D         0.479   0.506   0.321   0.452   0.489   0.164   0.452   0.493   0.179
103   G         1.602   1.611   1.667   1.793   1.805   1.887   1.747   1.756   1.846
104   W         1.602   1.611   1.667   1.942   1.959   2.030   1.747   1.756   1.846
105   C        -0.766  -0.737  -0.712  -0.744  -0.711  -0.606  -0.842  -0.802  -0.746
106   T         1.602   1.611   1.667   1.672   1.694   1.770   1.747   1.756   1.846
107   F         0.479   0.522   0.326   0.698   0.758   0.478   0.452   0.518   0.188
108   E        -0.531  -0.599  -0.666  -0.705  -0.795  -0.872  -0.518  -0.604  -0.685
109   A        -1.389  -1.325  -1.345  -1.460  -1.381  -1.352  -1.166  -1.090  -1.081
110   K        -0.766  -0.737  -0.712  -0.892  -0.835  -0.837  -0.842  -0.802  -0.746
111   K        -0.531  -0.466  -0.601  -0.623  -0.539  -0.695  -0.518  -0.429  -0.601
112   K         1.602   1.611   1.667   1.329   1.350   1.439   1.747   1.756   1.846
113   G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
114   S        -0.732  -0.768  -0.705  -0.755  -0.795  -0.698  -0.781  -0.828  -0.735
115   G        -0.766  -0.744  -0.716  -0.645  -0.626  -0.556  -0.842  -0.810  -0.750
116   E        -1.389  -1.325  -1.345  -1.162  -1.052  -1.137  -1.166  -1.090  -1.081
117   D        -2.012  -1.999  -1.856  -1.882  -1.849  -1.654  -1.489  -1.468  -1.299
118   D        -1.389  -1.387  -1.307  -1.724  -1.726  -1.593  -1.166  -1.156  -1.044
119   E        -0.531  -0.534  -0.613  -0.663  -0.661  -0.745  -0.518  -0.519  -0.616
120   E        -1.389  -1.325  -1.345  -1.377  -1.275  -1.331  -1.166  -1.090  -1.081
121   E        -1.389  -1.369  -1.311  -1.394  -1.350  -1.283  -1.166  -1.138  -1.048
122   T        -2.012  -1.999  -1.856  -1.827  -1.787  -1.601  -1.489  -1.468  -1.299
123   E         0.479   0.540   0.332   0.244   0.335   0.042   0.452   0.545   0.199
124   T        -0.531  -0.453  -0.610  -0.727  -0.608  -0.826  -0.518  -0.412  -0.613
125   T        -0.766  -0.744  -0.716  -0.793  -0.750  -0.758  -0.842  -0.810  -0.750
126   P        -0.531  -0.599  -0.666  -0.263  -0.363  -0.480  -0.518  -0.604  -0.685
127   T        -0.766  -0.728  -0.713  -0.990  -0.953  -0.895  -0.842  -0.794  -0.746
128   S        -1.389  -1.325  -1.345  -1.134  -1.023  -1.104  -1.166  -1.090  -1.081
129   T        -1.389  -1.325  -1.345  -1.124  -1.022  -1.079  -1.166  -1.090  -1.081
130   V        -1.389  -1.325  -1.345  -1.464  -1.376  -1.343  -1.166  -1.090  -1.081
131   P        -1.389  -1.387  -1.307  -1.209  -1.206  -1.101  -1.166  -1.156  -1.044
132   V        -0.865  -0.834  -0.738  -0.787  -0.736  -0.599  -0.950  -0.907  -0.775
133   A        -0.865  -0.834  -0.738  -1.137  -1.066  -0.936  -0.950  -0.907  -0.775
134   T         0.173   0.099   0.175   0.102  -0.024   0.071  -0.051  -0.183  -0.074
135   I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
136   A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
137   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
138   Q        -0.531  -0.599  -0.666  -0.102  -0.203  -0.319  -0.518  -0.604  -0.685
139   E        -0.531  -0.599  -0.666  -0.845  -0.961  -1.083  -0.518  -0.604  -0.685
140   T        -0.531  -0.599  -0.666  -0.306  -0.409  -0.519  -0.518  -0.604  -0.685
141   L         0.091   0.116   0.179   0.082   0.129   0.212  -0.195  -0.152  -0.067
142   K         0.479   0.540   0.332   0.320   0.395   0.135   0.452   0.545   0.199
143   V         0.479   0.455   0.321   0.677   0.644   0.413   0.452   0.414   0.180
144   K         0.479   0.455   0.321   0.320   0.283   0.119   0.452   0.414   0.180
145   P         1.602   1.611   1.667   1.710   1.729   1.806   1.747   1.756   1.846
146   N         1.602   1.611   1.667   1.639   1.655   1.738   1.747   1.756   1.846
147   N         1.602   1.611   1.667   1.679   1.691   1.777   1.747   1.756   1.846
148   K         1.602   1.611   1.667   1.330   1.340   1.441   1.747   1.756   1.846
149   N         0.479   0.506   0.321   0.668   0.703   0.438   0.452   0.493   0.179
150   I         0.091   0.074   0.161   0.082   0.053   0.179  -0.195  -0.226  -0.100
151   S         0.091   0.074   0.161   0.030   0.006   0.143  -0.195  -0.226  -0.100
152   S         1.602   1.611   1.667   1.586   1.607   1.687   1.747   1.756   1.846
153   N         0.479   0.522   0.326   0.563   0.627   0.341   0.452   0.518   0.188
154   R         0.091   0.074   0.161  -0.119  -0.178  -0.045  -0.195  -0.226  -0.100
155   P         0.091   0.074   0.161  -0.018  -0.059   0.068  -0.195  -0.226  -0.100
156   A         0.091   0.074   0.161  -0.054  -0.077   0.061  -0.195  -0.226  -0.100
157   D         1.602   1.611   1.667   1.571   1.581   1.672   1.747   1.756   1.846
158   T        -1.389  -1.325  -1.345  -1.155  -1.055  -1.113  -1.166  -1.090  -1.081
159   R         0.479   0.540   0.332   0.669   0.758   0.435   0.452   0.545   0.199
160   D         0.479   0.455   0.321   0.452   0.410   0.166   0.452   0.414   0.180
161   I         0.479   0.421   0.311   0.647   0.568   0.367   0.452   0.360   0.163
162   V        -0.766  -0.774  -0.691  -0.672  -0.681  -0.568  -0.842  -0.842  -0.721
163   A         0.479   0.455   0.321   0.478   0.447   0.240   0.452   0.414   0.180
164   D         0.479   0.421   0.311   0.452   0.355   0.146   0.452   0.360   0.163
165   K         1.602   1.611   1.667   1.330   1.340   1.441   1.747   1.756   1.846
166   P        -0.766  -0.790  -0.693  -0.534  -0.560  -0.414  -0.842  -0.860  -0.722
167   I        -0.531  -0.481  -0.614  -0.327  -0.246  -0.466  -0.518  -0.448  -0.618
168   L        -1.389  -1.369  -1.311  -1.367  -1.354  -1.221  -1.166  -1.138  -1.048
169   G        -0.766  -0.789  -0.695  -0.712  -0.750  -0.611  -0.842  -0.858  -0.725
170   F         1.602   1.611   1.667   1.763   1.782   1.858   1.747   1.756   1.846
171   N         1.602   1.611   1.667   1.679   1.691   1.777   1.747   1.756   1.846
172   A         1.602   1.611   1.667   1.523   1.541   1.627   1.747   1.756   1.846
173   F         1.602   1.611   1.667   1.763   1.782   1.858   1.747   1.756   1.846
174   A         0.479   0.421   0.311   0.405   0.315   0.102   0.452   0.360   0.163
175   A         1.602   1.611   1.667   1.523   1.541   1.627   1.747   1.756   1.846
176   L         1.602   1.611   1.667   1.702   1.720   1.799   1.747   1.756   1.846
177   E         0.091   0.074   0.161  -0.220  -0.233  -0.081  -0.195  -0.226  -0.100
178   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
179   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
180   S         0.046   0.054   0.150  -0.180  -0.169  -0.013  -0.276  -0.262  -0.119
181   E        -0.732  -0.740  -0.674  -0.876  -0.896  -0.800  -0.781  -0.787  -0.695
182   D         0.340   0.360   0.280   0.181   0.213   0.040   0.230   0.262   0.110
183   E         0.091   0.116   0.179  -0.274  -0.227  -0.141  -0.195  -0.152  -0.067
184   D        -0.531  -0.548  -0.613  -0.740  -0.764  -0.849  -0.518  -0.538  -0.617
185   D         0.091   0.122   0.184  -0.274  -0.213  -0.128  -0.195  -0.141  -0.058
186   E        -0.531  -0.481  -0.614  -0.472  -0.399  -0.616  -0.518  -0.448  -0.618
187   A         0.479   0.522   0.326   0.228   0.295   0.005   0.452   0.518   0.188
* 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/P12962
Output conservation file - output/P12962
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
