1     M         1.552   1.574   1.693   1.737   1.765   1.966   1.705   1.740   1.940
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     P        -0.487  -0.507  -0.430  -0.632  -0.655  -0.534  -0.673  -0.686  -0.574
5     Q        -1.022  -1.054  -0.995  -1.019  -1.051  -0.969  -0.995  -1.011  -0.908
6     Y         1.552   1.574   1.693   1.533   1.564   1.764   1.705   1.740   1.940
7     F        -0.053  -0.182  -0.323  -0.003  -0.188  -0.444  -0.042  -0.219  -0.421
8     A        -0.375  -0.340  -0.396  -0.350  -0.304  -0.413  -0.518  -0.473  -0.532
9     I         1.552   1.574   1.693   1.491   1.521   1.723   1.705   1.740   1.940
10    I         0.725   0.687   0.523   0.749   0.701   0.464   0.752   0.692   0.386
11    G         1.552   1.574   1.693   1.680   1.718   1.909   1.705   1.740   1.940
12    K        -0.053   0.103  -0.277   0.113   0.323  -0.232  -0.042   0.173  -0.356
13    K        -1.422  -1.407  -1.413  -1.159  -1.146  -1.146  -1.154  -1.134  -1.089
14    D         1.552   1.574   1.693   1.562   1.599   1.793   1.705   1.740   1.940
15    N         0.725   0.807   0.538   0.848   0.953   0.611   0.752   0.876   0.414
16    P         1.552   1.574   1.693   1.662   1.695   1.892   1.705   1.740   1.940
17    V        -0.623  -0.632  -0.482  -1.021  -1.033  -0.794  -0.836  -0.847  -0.642
18    Y         1.552   1.574   1.693   1.533   1.564   1.764   1.705   1.740   1.940
19    E         0.725   0.687   0.523   0.853   0.805   0.561   0.752   0.692   0.386
20    I        -1.022  -0.981  -0.988  -1.175  -1.117  -1.096  -0.995  -0.947  -0.904
21    E         1.552   1.574   1.693   1.598   1.630   1.828   1.705   1.740   1.940
22    F         0.725   0.637   0.518   0.783   0.673   0.517   0.752   0.611   0.377
23    T        -0.623  -0.626  -0.477  -0.786  -0.786  -0.564  -0.836  -0.840  -0.637
24    N        -1.572  -1.536  -1.463  -1.518  -1.465  -1.333  -1.312  -1.277  -1.136
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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
38    A        -1.243  -1.224  -1.058  -1.252  -1.220  -0.979  -1.213  -1.189  -0.973
39    E        -1.243  -1.224  -1.058  -1.236  -1.220  -0.964  -1.213  -1.189  -0.973
40    N        -0.774  -0.795  -0.924  -0.508  -0.542  -0.774  -0.677  -0.704  -0.826
41    P        -1.173  -1.138  -1.026  -1.159  -1.112  -0.927  -1.154  -1.113  -0.943
42    Q        -1.022  -1.054  -0.995  -1.054  -1.094  -1.000  -0.995  -1.011  -0.908
43    G        -1.971  -2.006  -1.849  -1.644  -1.692  -1.482  -1.471  -1.491  -1.288
44    F         0.725   0.637   0.518   0.717   0.590   0.372   0.752   0.611   0.377
45    P        -1.422  -1.485  -1.433  -1.184  -1.293  -1.243  -1.154  -1.213  -1.108
46    Q        -1.022  -1.070  -0.994  -0.874  -0.940  -0.818  -0.995  -1.043  -0.911
47    D        -0.473  -0.401  -0.416  -0.656  -0.569  -0.548  -0.677  -0.601  -0.563
48    L        -1.572  -1.562  -1.459  -1.667  -1.650  -1.465  -1.312  -1.297  -1.134
49    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
50    K         0.725   0.637   0.518   0.825   0.706   0.505   0.752   0.611   0.377
51    E         0.725   0.637   0.518   0.885   0.777   0.622   0.752   0.611   0.377
52    L         0.725   0.773   0.536   0.582   0.647   0.306   0.752   0.826   0.410
53    N        -0.375  -0.382  -0.399  -0.508  -0.500  -0.552  -0.518  -0.516  -0.531
54    P         0.725   0.637   0.518   0.926   0.811   0.631   0.752   0.611   0.377
55    F         0.725   0.715   0.526   0.749   0.739   0.456   0.752   0.736   0.392
56    I         1.552   1.574   1.693   1.491   1.521   1.723   1.705   1.740   1.940
57    L        -1.022  -1.002  -0.991  -1.205  -1.177  -1.122  -0.995  -0.979  -0.908
58    H         0.346   0.393   0.399   0.448   0.526   0.488   0.117   0.195   0.155
59    A         0.175   0.208   0.332  -0.082  -0.038   0.165  -0.201  -0.147   0.027
60    S        -0.053  -0.114  -0.305   0.034  -0.053  -0.329  -0.042  -0.124  -0.395
61    L         0.725   0.687   0.523   0.582   0.531   0.283   0.752   0.692   0.386
62    D         1.552   1.574   1.693   1.562   1.599   1.793   1.705   1.740   1.940
63    I        -0.375  -0.382  -0.399  -0.563  -0.555  -0.586  -0.518  -0.516  -0.531
64    V        -0.375  -0.361  -0.385  -0.393  -0.356  -0.395  -0.518  -0.489  -0.513
65    E         0.346   0.321   0.359   0.270   0.222   0.244   0.117   0.065   0.080
66    D        -0.375  -0.437  -0.413  -0.407  -0.510  -0.476  -0.518  -0.611  -0.556
67    L        -0.774  -0.762  -0.940  -0.833  -0.818  -1.078  -0.677  -0.659  -0.845
68    Q         0.346   0.347   0.361   0.352   0.344   0.341   0.117   0.113   0.083
69    W        -0.053  -0.064  -0.298   0.360   0.344  -0.073  -0.042  -0.056  -0.385
70    Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
71    I        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
72    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
73    P        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
74    T        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
75    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
76    Q        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
77    L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
78    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
79    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
80    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
81    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
82    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
83    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
84    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
85    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
86    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
87    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
88    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
89    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
90    G        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
91    F        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
92    L        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
93    R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
94    S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
95    R        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
96    A        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
97    V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
98    N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
99    N        -1.022  -0.986  -0.966  -0.995  -0.920  -0.896  -0.995  -0.939  -0.878
100   T        -0.053  -0.158  -0.311   0.110  -0.048  -0.293  -0.042  -0.186  -0.403
101   D        -0.375  -0.318  -0.383  -0.425  -0.313  -0.437  -0.518  -0.424  -0.509
102   N        -1.022  -1.063  -1.000  -0.962  -1.017  -0.911  -0.995  -1.033  -0.916
103   C        -1.173  -1.166  -1.025  -1.287  -1.305  -1.096  -1.154  -1.138  -0.942
104   Y        -0.053   0.013  -0.298   0.036   0.132  -0.354  -0.042   0.052  -0.385
105   L         0.725   0.637   0.518   0.626   0.514   0.370   0.752   0.611   0.377
106   G        -0.053  -0.182  -0.323   0.233   0.062  -0.168  -0.042  -0.219  -0.421
107   K         0.346   0.285   0.348   0.270   0.158   0.229   0.117  -0.002   0.059
108   V         0.175   0.183   0.320  -0.095  -0.091   0.118  -0.201  -0.195   0.004
109   D         1.552   1.574   1.693   1.562   1.599   1.793   1.705   1.740   1.940
110   H        -1.173  -1.176  -1.028  -1.147  -1.163  -0.941  -1.154  -1.146  -0.945
111   F         1.552   1.574   1.693   1.503   1.535   1.734   1.705   1.740   1.940
112   Y         0.725   0.637   0.518   0.821   0.713   0.562   0.752   0.611   0.377
113   G        -0.053  -0.182  -0.323   0.188   0.007  -0.256  -0.042  -0.219  -0.421
114   L        -0.053  -0.182  -0.323  -0.055  -0.220  -0.377  -0.042  -0.219  -0.421
115   A        -1.572  -1.564  -1.461  -1.654  -1.658  -1.493  -1.312  -1.300  -1.135
116   I         0.175   0.187   0.323  -0.119  -0.102   0.112  -0.201  -0.186   0.009
117   T        -0.623  -0.551  -0.447  -0.871  -0.758  -0.603  -0.836  -0.736  -0.596
118   A         0.725   0.715   0.526   0.932   0.921   0.658   0.752   0.736   0.392
119   Y         0.175   0.183   0.320  -0.147  -0.141   0.069  -0.201  -0.195   0.002
120   I        -0.623  -0.570  -0.470  -0.951  -0.845  -0.733  -0.836  -0.762  -0.626
121   S        -0.053   0.070  -0.265   0.052   0.223  -0.321  -0.042   0.128  -0.338
122   Y        -1.022  -1.094  -1.006  -0.975  -1.064  -0.921  -0.995  -1.058  -0.921
123   S         0.175   0.191   0.322  -0.032  -0.007   0.182  -0.201  -0.179   0.007
124   G        -1.022  -0.987  -0.965  -0.959  -0.894  -0.865  -0.995  -0.940  -0.876
125   M        -1.022  -0.961  -0.975  -0.995  -0.911  -0.907  -0.995  -0.930  -0.891
126   K         0.725   0.637   0.518   0.866   0.759   0.594   0.752   0.611   0.377
127   F         0.725   0.687   0.523   0.742   0.693   0.435   0.752   0.692   0.386
128   V        -1.173  -1.138  -1.026  -1.265  -1.194  -1.059  -1.154  -1.113  -0.943
129   M         0.175   0.215   0.332  -0.152  -0.103   0.098  -0.201  -0.134   0.026
130   I        -1.022  -0.956  -0.970  -1.064  -0.978  -0.982  -0.995  -0.918  -0.881
131   H         0.346   0.393   0.399   0.435   0.513   0.472   0.117   0.195   0.155
132   G        -1.422  -1.473  -1.446  -1.147  -1.220  -1.224  -1.154  -1.201  -1.119
133   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
134   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
135   -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
136   N        -0.544  -0.564  -0.454  -0.820  -0.867  -0.711  -0.727  -0.759  -0.605
137   S        -0.544  -0.597  -0.468  -0.832  -0.944  -0.742  -0.727  -0.801  -0.623
138   A        -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   N        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
145   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
146   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
147   V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
148   V        -1.422  -1.384  -1.422  -1.263  -1.213  -1.300  -1.154  -1.114  -1.098
149   I        -1.971  -2.006  -1.849  -1.780  -1.809  -1.585  -1.471  -1.491  -1.288
150   D        -1.022  -1.094  -1.006  -1.051  -1.151  -1.036  -0.995  -1.058  -0.921
151   D        -0.375  -0.452  -0.408  -0.399  -0.503  -0.447  -0.518  -0.614  -0.550
152   N        -1.572  -1.628  -1.454  -1.577  -1.649  -1.395  -1.312  -1.349  -1.130
153   N        -1.572  -1.538  -1.455  -1.514  -1.476  -1.322  -1.312  -1.278  -1.131
154   M        -0.774  -0.662  -0.921  -0.638  -0.489  -0.844  -0.677  -0.541  -0.823
155   R         0.175   0.183   0.320   0.073   0.077   0.283  -0.201  -0.195   0.004
156   S        -0.473  -0.520  -0.426  -0.673  -0.748  -0.613  -0.677  -0.721  -0.575
157   F         1.552   1.574   1.693   1.503   1.535   1.734   1.705   1.740   1.940
158   Y         0.175   0.215   0.332  -0.153  -0.083   0.091  -0.201  -0.134   0.026
159   Q        -0.053  -0.038  -0.287   0.160   0.178  -0.210  -0.042  -0.019  -0.370
160   E         1.552   1.574   1.693   1.598   1.630   1.828   1.705   1.740   1.940
161   V         0.725   0.637   0.518   0.819   0.692   0.469   0.752   0.611   0.377
162   H        -0.375  -0.361  -0.385  -0.242  -0.209  -0.287  -0.518  -0.489  -0.513
163   E         0.725   0.687   0.523   0.848   0.802   0.550   0.752   0.692   0.386
164   L         1.552   1.574   1.693   1.344   1.374   1.578   1.705   1.740   1.940
165   Y         1.552   1.574   1.693   1.533   1.564   1.764   1.705   1.740   1.940
166   V        -1.022  -1.023  -0.974  -1.109  -1.122  -1.065  -0.995  -0.994  -0.890
167   K         1.552   1.574   1.693   1.586   1.622   1.817   1.705   1.740   1.940
168   T         0.346   0.393   0.399   0.382   0.449   0.468   0.117   0.195   0.155
169   L         0.725   0.807   0.538   0.582   0.690   0.311   0.752   0.876   0.414
170   M         0.346   0.348   0.368   0.324   0.314   0.266   0.117   0.114   0.096
171   N         0.346   0.285   0.348   0.215   0.091   0.155   0.117  -0.002   0.059
172   P         1.552   1.574   1.693   1.662   1.695   1.892   1.705   1.740   1.940
173   F         1.552   1.574   1.693   1.503   1.535   1.734   1.705   1.740   1.940
174   Y         1.552   1.574   1.693   1.533   1.564   1.764   1.705   1.740   1.940
175   K        -1.572  -1.561  -1.455  -1.524  -1.504  -1.363  -1.312  -1.295  -1.130
176   I        -0.774  -0.724  -0.919  -0.574  -0.498  -0.818  -0.677  -0.621  -0.821
177   T        -0.774  -0.616  -0.893  -0.588  -0.362  -0.775  -0.677  -0.484  -0.791
178   D         0.346   0.285   0.348   0.268   0.161   0.240   0.117  -0.002   0.059
179   P        -0.375  -0.288  -0.373  -0.295  -0.165  -0.293  -0.518  -0.402  -0.495
180   I         0.725   0.807   0.538   0.705   0.817   0.400   0.752   0.876   0.414
181   R        -1.022  -1.019  -0.995  -0.899  -0.903  -0.885  -0.995  -0.987  -0.911
182   S         0.725   0.715   0.526   0.743   0.727   0.458   0.752   0.736   0.392
183   P        -0.053  -0.158  -0.311   0.180   0.032  -0.231  -0.042  -0.186  -0.403
184   A        -1.022  -0.993  -0.984  -1.016  -0.954  -0.985  -0.995  -0.956  -0.898
185   F         1.552   1.574   1.693   1.503   1.535   1.734   1.705   1.740   1.940
186   D         1.552   1.574   1.693   1.562   1.599   1.793   1.705   1.740   1.940
187   S        -1.572  -1.545  -1.458  -1.652  -1.630  -1.448  -1.312  -1.283  -1.133
188   R         0.175   0.177   0.318   0.073   0.062   0.274  -0.201  -0.206  -0.001
189   V        -0.375  -0.350  -0.406  -0.482  -0.449  -0.595  -0.518  -0.491  -0.547
190   R         0.175   0.183   0.322   0.042   0.055   0.272  -0.201  -0.194   0.006
191   T        -1.971  -1.883  -1.827  -1.742  -1.631  -1.521  -1.471  -1.391  -1.271
192   L         0.725   0.637   0.518   0.582   0.460   0.275   0.752   0.611   0.377
193   A         0.725   0.715   0.526   0.901   0.885   0.592   0.752   0.736   0.392
194   R         0.175   0.187   0.323   0.073   0.087   0.289  -0.201  -0.186   0.009
195   K         0.346   0.297   0.352   0.326   0.245   0.319   0.117   0.020   0.065
196   H         0.643   0.720   0.507   0.742   0.843   0.567   0.624   0.744   0.357
197   L         1.552   1.574   1.693   1.344   1.374   1.578   1.705   1.740   1.940
198   S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
199   K        -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/P38334
Output conservation file - output/P38334
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
