1     M         0.884   0.917   0.958   1.235   1.270   1.284   0.905   0.951   1.014
2     V        -1.223  -1.359  -1.330  -1.348  -1.487  -1.471  -1.165  -1.302  -1.254
3     A        -1.223  -1.359  -1.330  -1.252  -1.464  -1.441  -1.165  -1.302  -1.254
4     Q        -1.223  -1.064  -1.310  -0.907  -0.665  -1.164  -1.165  -0.948  -1.231
5     V         0.018  -0.349  -0.454  -0.061  -0.501  -0.657   0.077  -0.434  -0.628
6     Q         0.018  -0.349  -0.454   0.407  -0.091  -0.350   0.077  -0.434  -0.628
7     K        -1.223  -1.064  -1.310  -0.993  -0.784  -1.057  -1.165  -0.948  -1.231
8     Q         0.018   0.180  -0.427   0.239   0.414  -0.337   0.077   0.278  -0.585
9     A         0.884   0.917   0.958   0.691   0.750   0.841   0.905   0.951   1.014
10    P         0.884   0.917   0.958   0.900   0.948   1.011   0.905   0.951   1.014
11    T        -2.371  -2.184  -1.978  -2.249  -2.056  -1.761  -2.096  -1.912  -1.590
12    F         0.884   0.917   0.958   0.885   0.922   0.999   0.905   0.951   1.014
13    K         0.884   0.917   0.958   0.806   0.859   0.934   0.905   0.951   1.014
14    K         0.018  -0.349  -0.454   0.111  -0.371  -0.562   0.077  -0.434  -0.628
15    T         0.884   0.917   0.958   0.900   0.956   1.011   0.905   0.951   1.014
16    A         0.884   0.917   0.958   0.691   0.750   0.841   0.905   0.951   1.014
17    V         0.884   0.917   0.958   0.625   0.702   0.787   0.905   0.951   1.014
18    V        -1.442  -1.288  -1.329  -1.613  -1.363  -1.375  -1.475  -1.247  -1.254
19    D        -0.814  -1.182  -1.335  -0.466  -0.959  -1.206  -0.647  -1.103  -1.261
20    G         0.884   0.917   0.958   0.833   0.869   0.956   0.905   0.951   1.014
21    V        -0.814  -1.016  -1.319  -0.721  -1.038  -1.328  -0.647  -0.931  -1.242
22    F         0.884   0.917   0.958   0.885   0.922   0.999   0.905   0.951   1.014
23    D        -0.697  -0.481  -0.475  -0.908  -0.577  -0.594  -0.958  -0.634  -0.662
24    E         0.018   0.073  -0.432   0.087   0.165  -0.524   0.077   0.146  -0.594
25    V         0.018  -0.349  -0.454  -0.061  -0.501  -0.657   0.077  -0.434  -0.628
26    S        -1.223  -1.359  -1.330  -0.989  -1.205  -1.234  -1.165  -1.302  -1.254
27    L         0.884   0.917   0.958   0.707   0.760   0.853   0.905   0.951   1.014
28    D        -1.512  -1.644  -1.356  -1.652  -1.838  -1.426  -1.579  -1.655  -1.286
29    K        -1.512  -1.639  -1.361  -1.436  -1.577  -1.213  -1.579  -1.648  -1.291
30    Y         0.018   0.002  -0.434   0.413   0.387  -0.291   0.077   0.055  -0.596
31    K         0.884   0.917   0.958   0.806   0.859   0.934   0.905   0.951   1.014
32    G         0.884   0.917   0.958   0.833   0.869   0.956   0.905   0.951   1.014
33    K         0.884   0.917   0.958   0.806   0.859   0.934   0.905   0.951   1.014
34    Y        -0.822  -0.649  -0.497  -0.677  -0.420  -0.264  -1.165  -0.902  -0.697
35    V         0.884   0.917   0.958   0.625   0.702   0.787   0.905   0.951   1.014
36    V        -1.442  -1.586  -1.353  -1.739  -1.886  -1.530  -1.475  -1.580  -1.282
37    L         0.884   0.917   0.958   0.707   0.760   0.853   0.905   0.951   1.014
38    A         0.018  -0.349  -0.454  -0.005  -0.478  -0.645   0.077  -0.434  -0.628
39    F         0.884   0.917   0.958   0.885   0.922   0.999   0.905   0.951   1.014
40    I        -1.969  -2.056  -1.955  -1.704  -1.799  -1.726  -1.682  -1.746  -1.570
41    P         0.884   0.917   0.958   0.900   0.948   1.011   0.905   0.951   1.014
42    L         0.884   0.917   0.958   0.707   0.760   0.853   0.905   0.951   1.014
43    A         0.018  -0.349  -0.454   0.003  -0.461  -0.620   0.077  -0.434  -0.628
44    F         0.884   0.917   0.958   0.885   0.922   0.999   0.905   0.951   1.014
45    T         0.884   0.917   0.958   0.900   0.956   1.011   0.905   0.951   1.014
46    F         0.884   0.917   0.958   0.885   0.922   0.999   0.905   0.951   1.014
47    V         0.884   0.917   0.958   0.625   0.702   0.787   0.905   0.951   1.014
48    C         0.884   0.917   0.958   1.206   1.241   1.261   0.905   0.951   1.014
49    P         0.884   0.917   0.958   0.900   0.948   1.011   0.905   0.951   1.014
50    T        -0.431  -0.213  -0.436  -0.351  -0.057  -0.416  -0.544  -0.237  -0.599
51    E         0.884   0.917   0.958   0.776   0.836   0.909   0.905   0.951   1.014
52    I         0.884   0.917   0.958   0.911   0.954   1.020   0.905   0.951   1.014
53    I        -0.697  -0.699  -0.514  -0.903  -0.972  -0.721  -0.958  -0.984  -0.725
54    A         0.884   0.917   0.958   0.691   0.750   0.841   0.905   0.951   1.014
55    F        -0.822  -0.715  -0.511  -0.899  -0.771  -0.464  -1.165  -1.010  -0.720
56    S         0.884   0.917   0.958   0.945   0.983   1.047   0.905   0.951   1.014
57    E         0.018   0.002  -0.434   0.087   0.083  -0.527   0.077   0.055  -0.596
58    A         0.884   0.917   0.958   0.691   0.750   0.841   0.905   0.951   1.014
59    A        -0.822  -0.715  -0.511  -1.369  -1.186  -0.856  -1.165  -1.010  -0.720
60    K        -0.431  -0.633  -0.512  -0.443  -0.782  -0.602  -0.544  -0.876  -0.722
61    K        -1.223  -1.067  -1.313  -1.019  -0.812  -1.111  -1.165  -0.952  -1.236
62    F         0.884   0.917   0.958   0.885   0.922   0.999   0.905   0.951   1.014
63    E        -1.512  -1.416  -1.350  -1.779  -1.624  -1.484  -1.579  -1.429  -1.278
64    E        -0.697  -0.475  -0.473  -1.001  -0.631  -0.686  -0.958  -0.625  -0.659
65    Q        -2.898  -2.602  -2.449  -2.619  -2.234  -1.991  -2.303  -2.046  -1.764
66    G        -1.442  -1.601  -1.353  -1.403  -1.596  -1.248  -1.475  -1.599  -1.283
67    A         0.018   0.073  -0.432   0.004   0.081  -0.581   0.077   0.146  -0.594
68    Q        -0.431  -0.405  -0.489  -0.200  -0.189  -0.451  -0.544  -0.518  -0.685
69    V         0.884   0.917   0.958   0.625   0.702   0.787   0.905   0.951   1.014
70    L         0.018  -0.349  -0.454   0.021  -0.444  -0.598   0.077  -0.434  -0.628
71    F         0.018  -0.349  -0.454   0.174  -0.339  -0.560   0.077  -0.434  -0.628
72    A         0.018  -0.349  -0.454   0.004  -0.453  -0.615   0.077  -0.434  -0.628
73    S         0.884   0.917   0.958   0.945   0.983   1.047   0.905   0.951   1.014
74    T         0.884   0.917   0.958   0.900   0.956   1.011   0.905   0.951   1.014
75    D         0.884   0.917   0.958   0.889   0.930   1.002   0.905   0.951   1.014
76    S         0.884   0.917   0.958   0.945   0.983   1.047   0.905   0.951   1.014
77    E         0.884   0.917   0.958   0.776   0.836   0.909   0.905   0.951   1.014
78    Y         0.884   0.917   0.958   1.102   1.143   1.176   0.905   0.951   1.014
79    S        -0.431  -0.213  -0.436  -0.320  -0.036  -0.402  -0.544  -0.237  -0.599
80    L        -1.223  -1.359  -1.330  -1.064  -1.211  -1.109  -1.165  -1.302  -1.254
81    L         0.884   0.917   0.958   0.707   0.760   0.853   0.905   0.951   1.014
82    A         0.884   0.917   0.958   0.691   0.750   0.841   0.905   0.951   1.014
83    W         0.018  -0.349  -0.454   0.481  -0.012  -0.280   0.077  -0.434  -0.628
84    T         0.018  -0.349  -0.454   0.215  -0.252  -0.460   0.077  -0.434  -0.628
85    N         0.884   0.917   0.958   1.048   1.088   1.131   0.905   0.951   1.014
86    I        -0.814  -1.028  -1.322  -0.741  -1.028  -1.385  -0.647  -0.943  -1.245
87    P        -0.697  -0.701  -0.514  -0.981  -1.010  -0.701  -0.958  -0.988  -0.726
88    R         0.884   0.917   0.958   1.070   1.107   1.149   0.905   0.951   1.014
89    K         0.018   0.184  -0.425   0.145   0.329  -0.401   0.077   0.282  -0.581
90    E        -0.431  -0.573  -0.509  -0.409  -0.679  -0.638  -0.544  -0.779  -0.717
91    G         0.884   0.917   0.958   0.833   0.869   0.956   0.905   0.951   1.014
92    G         0.884   0.917   0.958   0.833   0.869   0.956   0.905   0.951   1.014
93    L        -0.431  -0.213  -0.436  -0.550  -0.257  -0.570  -0.544  -0.237  -0.599
94    G         0.884   0.917   0.958   0.833   0.869   0.956   0.905   0.951   1.014
95    P        -1.223  -1.359  -1.330  -1.058  -1.262  -1.291  -1.165  -1.302  -1.254
96    I        -0.697  -0.719  -0.515  -1.036  -1.074  -0.731  -0.958  -1.017  -0.728
97    N        -0.822  -0.732  -0.508  -0.931  -0.799  -0.472  -1.165  -1.039  -0.715
98    I        -1.223  -1.000  -1.312  -1.042  -0.751  -1.270  -1.165  -0.879  -1.233
99    P         0.884   0.917   0.958   0.900   0.948   1.011   0.905   0.951   1.014
100   L        -0.431  -0.213  -0.436  -0.632  -0.312  -0.693  -0.544  -0.237  -0.599
101   L        -0.431  -0.279  -0.486  -0.550  -0.345  -0.649  -0.544  -0.331  -0.680
102   A         0.884   0.917   0.958   0.691   0.750   0.841   0.905   0.951   1.014
103   D         0.884   0.917   0.958   0.889   0.930   1.002   0.905   0.951   1.014
104   T         0.018  -0.349  -0.454   0.213  -0.254  -0.465   0.077  -0.434  -0.628
105   N         0.018  -0.349  -0.454   0.366  -0.115  -0.341   0.077  -0.434  -0.628
106   H         0.884   0.917   0.958   1.196   1.220   1.252   0.905   0.951   1.014
107   S        -1.587  -1.602  -1.375  -1.508  -1.613  -1.320  -1.579  -1.602  -1.306
108   L         0.018  -0.349  -0.454  -0.015  -0.515  -0.728   0.077  -0.434  -0.628
109   S         0.018   0.073  -0.432   0.232   0.289  -0.481   0.077   0.146  -0.594
110   R        -0.431  -0.405  -0.489  -0.224  -0.218  -0.459  -0.544  -0.518  -0.685
111   D         0.884   0.917   0.958   0.889   0.930   1.002   0.905   0.951   1.014
112   Y         0.884   0.917   0.958   1.102   1.143   1.176   0.905   0.951   1.014
113   G         0.884   0.917   0.958   0.833   0.869   0.956   0.905   0.951   1.014
114   V         0.884   0.917   0.958   0.625   0.702   0.787   0.905   0.951   1.014
115   L         0.884   0.917   0.958   0.707   0.760   0.853   0.905   0.951   1.014
116   I         0.018   0.073  -0.432   0.201   0.261  -0.499   0.077   0.146  -0.594
117   E         0.018   0.002  -0.434   0.089   0.086  -0.522   0.077   0.055  -0.596
118   E        -0.697  -0.717  -0.515  -0.908  -0.975  -0.656  -0.958  -1.014  -0.728
119   E        -1.223  -1.353  -1.354  -1.208  -1.500  -1.452  -1.165  -1.365  -1.284
120   G         0.884   0.917   0.958   0.833   0.869   0.956   0.905   0.951   1.014
121   V        -0.431  -0.217  -0.448  -0.630  -0.319  -0.648  -0.544  -0.242  -0.618
122   A         0.884   0.917   0.958   0.691   0.750   0.841   0.905   0.951   1.014
123   L         0.018  -0.349  -0.454   0.018  -0.453  -0.610   0.077  -0.434  -0.628
124   R         0.884   0.917   0.958   1.070   1.107   1.149   0.905   0.951   1.014
125   G         0.884   0.917   0.958   0.833   0.869   0.956   0.905   0.951   1.014
126   L        -0.822  -0.715  -0.511  -1.165  -1.020  -0.683  -1.165  -1.010  -0.720
127   F         0.884   0.917   0.958   0.885   0.922   0.999   0.905   0.951   1.014
128   I        -0.822  -0.698  -0.508  -1.165  -0.993  -0.680  -1.165  -0.982  -0.716
129   I         0.884   0.917   0.958   0.911   0.954   1.020   0.905   0.951   1.014
130   D         0.884   0.917   0.958   0.889   0.930   1.002   0.905   0.951   1.014
131   P         0.884   0.917   0.958   0.900   0.948   1.011   0.905   0.951   1.014
132   K         0.884   0.917   0.958   0.806   0.859   0.934   0.905   0.951   1.014
133   G         0.884   0.917   0.958   0.833   0.869   0.956   0.905   0.951   1.014
134   V        -0.431  -0.217  -0.448  -0.630  -0.319  -0.648  -0.544  -0.242  -0.618
135   I        -1.512  -1.311  -1.348  -1.861  -1.586  -1.513  -1.579  -1.353  -1.277
136   R         0.884   0.917   0.958   1.070   1.107   1.149   0.905   0.951   1.014
137   H        -0.822  -0.649  -0.497  -0.672  -0.440  -0.262  -1.165  -0.902  -0.697
138   I         0.884   0.917   0.958   0.911   0.954   1.020   0.905   0.951   1.014
139   T         0.884   0.917   0.958   0.900   0.956   1.011   0.905   0.951   1.014
140   I         0.018   0.073  -0.432   0.191   0.254  -0.532   0.077   0.146  -0.594
141   N         0.884   0.917   0.958   1.048   1.088   1.131   0.905   0.951   1.014
142   D         0.884   0.917   0.958   0.889   0.930   1.002   0.905   0.951   1.014
143   L         0.884   0.917   0.958   0.707   0.760   0.853   0.905   0.951   1.014
144   P         0.884   0.917   0.958   0.900   0.948   1.011   0.905   0.951   1.014
145   V         0.884   0.917   0.958   0.625   0.702   0.787   0.905   0.951   1.014
146   G         0.884   0.917   0.958   0.833   0.869   0.956   0.905   0.951   1.014
147   R         0.884   0.917   0.958   1.070   1.107   1.149   0.905   0.951   1.014
148   N        -0.822  -0.649  -0.497  -0.887  -0.646  -0.437  -1.165  -0.902  -0.697
149   V         0.884   0.917   0.958   0.625   0.702   0.787   0.905   0.951   1.014
150   D        -0.431  -0.573  -0.509  -0.489  -0.727  -0.649  -0.544  -0.779  -0.717
151   E         0.884   0.917   0.958   0.776   0.836   0.909   0.905   0.951   1.014
152   A        -1.512  -1.433  -1.346  -1.633  -1.536  -1.349  -1.579  -1.453  -1.275
153   L         0.884   0.917   0.958   0.707   0.760   0.853   0.905   0.951   1.014
154   R         0.884   0.917   0.958   1.070   1.107   1.149   0.905   0.951   1.014
155   L         0.884   0.917   0.958   0.707   0.760   0.853   0.905   0.951   1.014
156   V        -1.442  -1.442  -1.354  -1.734  -1.740  -1.522  -1.475  -1.467  -1.284
157   E        -0.431  -0.633  -0.512  -0.489  -0.829  -0.653  -0.544  -0.876  -0.722
158   A        -0.697  -0.475  -0.473  -1.013  -0.672  -0.678  -0.958  -0.625  -0.659
159   F         0.884   0.917   0.958   0.885   0.922   0.999   0.905   0.951   1.014
160   Q         0.884   0.917   0.958   1.102   1.144   1.176   0.905   0.951   1.014
161   W        -0.822  -0.649  -0.497  -0.855  -0.637  -0.413  -1.165  -0.902  -0.697
162   T         0.018  -0.349  -0.454   0.180  -0.321  -0.585   0.077  -0.434  -0.628
163   D        -0.822  -0.649  -0.497  -1.125  -0.856  -0.630  -1.165  -0.902  -0.697
164   K         0.018  -0.349  -0.454   0.104  -0.380  -0.588   0.077  -0.434  -0.628
165   N        -1.750  -1.709  -1.374  -1.450  -1.408  -0.981  -1.786  -1.722  -1.305
166   G         0.884   0.917   0.958   0.833   0.869   0.956   0.905   0.951   1.014
167   T        -0.822  -0.649  -0.497  -1.117  -0.843  -0.624  -1.165  -0.902  -0.697
168   V         0.884   0.917   0.958   0.625   0.702   0.787   0.905   0.951   1.014
169   L        -0.822  -0.649  -0.497  -0.890  -0.574  -0.431  -1.165  -0.902  -0.697
170   P         0.884   0.917   0.958   0.900   0.948   1.011   0.905   0.951   1.014
171   C        -0.822  -0.649  -0.497  -0.981  -0.770  -0.518  -1.165  -0.902  -0.697
172   N         0.884   0.917   0.958   1.048   1.088   1.131   0.905   0.951   1.014
173   W         0.884   0.917   0.958   1.171   1.212   1.231   0.905   0.951   1.014
174   T        -1.750  -1.666  -1.374  -1.540  -1.421  -1.046  -1.786  -1.677  -1.305
175   P        -0.431  -0.633  -0.512  -0.390  -0.762  -0.621  -0.544  -0.876  -0.722
176   G         0.884   0.917   0.958   0.833   0.869   0.956   0.905   0.951   1.014
177   A        -1.750  -1.459  -1.328  -1.880  -1.432  -1.290  -1.786  -1.432  -1.253
178   A        -1.750  -1.709  -1.374  -2.035  -1.970  -1.464  -1.786  -1.722  -1.305
179   T         0.884   0.917   0.958   0.900   0.956   1.011   0.905   0.951   1.014
180   I         0.884   0.917   0.958   0.911   0.954   1.020   0.905   0.951   1.014
181   K         0.884   0.917   0.958   0.804   0.854   0.932   0.905   0.951   1.014
182   P        -0.052  -0.218  -0.473   0.105  -0.121  -0.596  -0.012  -0.244  -0.658
183   T        -2.515  -2.325  -1.977  -2.458  -2.227  -1.775  -2.200  -1.997  -1.589
184   V        -1.442  -1.603  -1.357  -1.628  -1.796  -1.426  -1.475  -1.602  -1.287
185   E        -2.352  -2.470  -2.443  -1.979  -2.242  -2.228  -1.786  -1.906  -1.759
186   D        -2.371  -2.249  -1.977  -2.316  -2.117  -1.737  -2.096  -1.950  -1.589
187   S        -0.814  -1.182  -1.335  -0.451  -0.976  -1.291  -0.647  -1.103  -1.261
188   K         0.018  -0.349  -0.454   0.104  -0.380  -0.588   0.077  -0.434  -0.628
189   E         0.018  -0.349  -0.454   0.077  -0.396  -0.596   0.077  -0.434  -0.628
190   Y         0.884   0.917   0.958   1.102   1.143   1.176   0.905   0.951   1.014
191   F         0.884   0.917   0.958   0.885   0.922   0.999   0.905   0.951   1.014
192   E        -3.042  -2.824  -2.443  -2.815  -2.550  -2.071  -2.406  -2.188  -1.759
193   A        -2.352  -1.843  -2.419  -1.909  -1.305  -2.100  -1.786  -1.291  -1.741
194   A        -0.759  -0.710  -0.515  -1.280  -1.227  -0.884  -1.060  -1.002  -0.727
195   N         0.884   0.917   0.958   1.051   1.091   1.134   0.905   0.951   1.014
196   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
197   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
198   K        -1.606  -1.639  -1.941  -1.156  -1.238  -1.567  -1.268  -1.349  -1.557
* 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/P34760
Output conservation file - output/P34760
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
