1     M         1.619   1.621   1.642   2.002   2.003   2.034   1.723   1.725   1.750
2     S         1.619   1.621   1.642   1.547   1.552   1.582   1.723   1.725   1.750
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    A        -0.163  -0.162  -0.139  -0.586  -0.585  -0.541  -0.357  -0.354  -0.316
37    T        -0.163  -0.162  -0.139  -0.095  -0.079  -0.053  -0.357  -0.354  -0.316
38    A         1.619   1.621   1.642   1.218   1.217   1.254   1.723   1.725   1.750
39    K        -0.163  -0.162  -0.139  -0.736  -0.736  -0.691  -0.357  -0.354  -0.316
40    H         1.619   1.621   1.642   1.741   1.761   1.774   1.723   1.725   1.750
41    D         1.619   1.621   1.642   1.701   1.701   1.734   1.723   1.725   1.750
42    S        -0.163  -0.162  -0.139  -0.586  -0.585  -0.541  -0.357  -0.354  -0.316
43    N        -0.163  -0.162  -0.139  -0.139  -0.122  -0.096  -0.357  -0.354  -0.316
44    A        -0.163  -0.162  -0.139  -0.489  -0.488  -0.445  -0.357  -0.354  -0.316
45    S        -0.163  -0.162  -0.139  -0.586  -0.585  -0.541  -0.357  -0.354  -0.316
46    P        -0.163  -0.162  -0.139  -0.038  -0.036   0.004  -0.357  -0.354  -0.316
47    N        -0.163  -0.162  -0.139  -0.168  -0.166  -0.125  -0.357  -0.354  -0.316
48    S        -0.163  -0.162  -0.139  -0.457  -0.456  -0.413  -0.357  -0.354  -0.316
49    D        -0.163  -0.162  -0.139  -0.489  -0.488  -0.445  -0.357  -0.354  -0.316
50    S        -0.163  -0.162  -0.139  -0.197  -0.181  -0.155  -0.357  -0.354  -0.316
51    E        -0.163  -0.162  -0.139  -0.066  -0.065  -0.024  -0.357  -0.354  -0.316
52    D        -0.163  -0.162  -0.139  -0.066  -0.065  -0.024  -0.357  -0.354  -0.316
53    G        -0.163  -0.162  -0.139  -0.153  -0.152  -0.111  -0.357  -0.354  -0.316
54    H        -0.163  -0.162  -0.139  -0.333  -0.316  -0.290  -0.357  -0.354  -0.316
55    H        -1.206  -1.203  -1.180  -0.970  -0.974  -0.924  -1.050  -1.046  -1.005
56    H         1.619   1.621   1.642   1.828   1.829   1.861   1.723   1.725   1.750
57    N        -0.018  -0.041  -0.073  -0.053  -0.094  -0.172  -0.126  -0.162  -0.211
58    N        -1.206  -1.203  -1.180  -0.892  -0.886  -0.846  -1.050  -1.046  -1.005
59    K        -0.018   0.008  -0.053   0.092   0.138   0.021  -0.126  -0.086  -0.179
60    K        -0.018  -0.041  -0.073  -0.076  -0.109  -0.149  -0.126  -0.162  -0.211
61    E        -0.018  -0.013  -0.048   0.092   0.100   0.029  -0.126  -0.119  -0.173
62    C        -0.018  -0.041  -0.073   0.334   0.299   0.239  -0.126  -0.162  -0.211
63    A        -1.206  -1.203  -1.180  -1.241  -1.223  -1.193  -1.050  -1.046  -1.005
64    I        -1.206  -1.203  -1.180  -0.960  -0.965  -0.914  -1.050  -1.046  -1.005
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    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
68    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
69    E        -1.206  -1.203  -1.180  -1.092  -1.087  -1.046  -1.050  -1.046  -1.005
70    Y        -1.206  -1.203  -1.180  -1.176  -1.175  -1.129  -1.050  -1.046  -1.005
71    L        -0.018  -0.013  -0.048  -0.132  -0.122  -0.159  -0.126  -0.119  -0.173
72    K        -1.206  -1.203  -1.180  -1.144  -1.139  -1.097  -1.050  -1.046  -1.005
73    A        -1.206  -1.203  -1.180  -1.072  -1.056  -1.025  -1.050  -1.046  -1.005
74    R        -0.163  -0.162  -0.139   0.116   0.118   0.157  -0.357  -0.354  -0.316
75    L        -0.018  -0.041  -0.073  -0.285  -0.320  -0.370  -0.126  -0.162  -0.211
76    N        -0.018  -0.013  -0.048   0.001   0.011  -0.060  -0.126  -0.119  -0.173
77    S        -0.018  -0.041  -0.073  -0.228  -0.272  -0.346  -0.126  -0.162  -0.211
78    A        -1.206  -1.203  -1.180  -1.176  -1.166  -1.129  -1.050  -1.046  -1.005
79    S        -0.018   0.008  -0.053  -0.352  -0.313  -0.401  -0.126  -0.086  -0.179
80    A        -1.206  -1.203  -1.180  -1.431  -1.420  -1.383  -1.050  -1.046  -1.005
81    V        -1.206  -1.203  -1.180  -1.144  -1.142  -1.097  -1.050  -1.046  -1.005
82    A        -1.206  -1.203  -1.180  -1.351  -1.337  -1.303  -1.050  -1.046  -1.005
83    C        -1.206  -1.203  -1.180  -0.911  -0.915  -0.865  -1.050  -1.046  -1.005
84    G        -0.018  -0.013  -0.048   0.159   0.168   0.109  -0.126  -0.119  -0.173
85    Y        -0.018  -0.041  -0.073   0.077   0.036  -0.027  -0.126  -0.162  -0.211
86    L        -1.206  -1.203  -1.180  -1.262  -1.247  -1.215  -1.050  -1.046  -1.005
87    Q         1.619   1.621   1.642   1.879   1.880   1.912   1.723   1.725   1.750
88    A         1.619   1.621   1.642   1.218   1.217   1.254   1.723   1.725   1.750
89    F        -0.163  -0.162  -0.139   0.019   0.021   0.060  -0.357  -0.354  -0.316
90    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
91    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
92    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
93    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
94    V        -1.206  -1.203  -1.180  -1.241  -1.248  -1.193  -1.050  -1.046  -1.005
95    S        -0.018   0.008  -0.053  -0.352  -0.313  -0.401  -0.126  -0.086  -0.179
96    K        -1.206  -1.203  -1.180  -0.990  -0.979  -0.944  -1.050  -1.046  -1.005
97    T        -0.018  -0.013  -0.048  -0.053  -0.049  -0.126  -0.126  -0.119  -0.173
98    Q        -0.018  -0.041  -0.073   0.167   0.127   0.058  -0.126  -0.162  -0.211
99    D        -1.206  -1.203  -1.180  -1.061  -1.066  -1.015  -1.050  -1.046  -1.005
100   F        -1.206  -1.203  -1.180  -1.340  -1.350  -1.292  -1.050  -1.046  -1.005
101   A        -0.018  -0.041  -0.073  -0.260  -0.296  -0.324  -0.126  -0.162  -0.211
102   K        -1.206  -1.203  -1.180  -1.187  -1.177  -1.140  -1.050  -1.046  -1.005
103   V        -1.206  -1.203  -1.180  -1.123  -1.113  -1.077  -1.050  -1.046  -1.005
104   C        -1.206  -1.203  -1.180  -1.134  -1.134  -1.087  -1.050  -1.046  -1.005
105   F        -1.206  -1.203  -1.180  -1.051  -1.056  -1.005  -1.050  -1.046  -1.005
106   L        -1.206  -1.203  -1.180  -0.980  -0.963  -0.934  -1.050  -1.046  -1.005
107   E         1.619   1.621   1.642   1.795   1.796   1.828   1.723   1.725   1.750
108   L         1.619   1.621   1.642   1.358   1.363   1.394   1.723   1.725   1.750
109   Q         1.619   1.621   1.642   1.844   1.846   1.877   1.723   1.725   1.750
110   N         1.619   1.621   1.642   1.697   1.701   1.731   1.723   1.725   1.750
111   P         1.619   1.621   1.642   1.971   1.973   2.003   1.723   1.725   1.750
112   V         1.619   1.621   1.642   1.547   1.547   1.582   1.723   1.725   1.750
113   V         1.619   1.621   1.642   1.547   1.547   1.582   1.723   1.725   1.750
114   L        -0.018  -0.041  -0.073  -0.411  -0.453  -0.521  -0.126  -0.162  -0.211
115   V        -0.018  -0.041  -0.073   0.039   0.006  -0.027  -0.126  -0.162  -0.211
116   N         1.619   1.621   1.642   1.697   1.701   1.731   1.723   1.725   1.750
117   L        -1.206  -1.203  -1.180  -1.262  -1.247  -1.215  -1.050  -1.046  -1.005
118   L        -0.018  -0.013  -0.048  -0.147  -0.140  -0.176  -0.126  -0.119  -0.173
119   L         1.619   1.621   1.642   1.358   1.363   1.394   1.723   1.725   1.750
120   H        -0.018   0.008  -0.053   0.218   0.257   0.169  -0.126  -0.086  -0.179
121   S        -0.018  -0.041  -0.073  -0.228  -0.272  -0.346  -0.126  -0.162  -0.211
122   S        -0.018  -0.041  -0.073  -0.228  -0.272  -0.346  -0.126  -0.162  -0.211
123   V        -0.018  -0.041  -0.073  -0.108  -0.147  -0.202  -0.126  -0.162  -0.211
124   V        -0.018  -0.041  -0.073   0.024  -0.011  -0.045  -0.126  -0.162  -0.211
125   C        -1.206  -1.203  -1.180  -0.911  -0.910  -0.865  -1.050  -1.046  -1.005
126   Y        -0.018   0.008  -0.053   0.152   0.190   0.099  -0.126  -0.086  -0.179
127   L         1.619   1.621   1.642   1.358   1.363   1.394   1.723   1.725   1.750
128   C        -0.018   0.008  -0.053  -0.100  -0.063  -0.128  -0.126  -0.086  -0.179
129   N        -0.018  -0.013  -0.048   0.167   0.176   0.127  -0.126  -0.119  -0.173
130   G        -0.018  -0.013  -0.048   0.092   0.102   0.033  -0.126  -0.119  -0.173
131   Y         1.619   1.621   1.642   1.746   1.749   1.780   1.723   1.725   1.750
132   A         1.619   1.621   1.642   1.288   1.286   1.324   1.723   1.725   1.750
133   N        -0.018  -0.013  -0.048   0.001   0.011  -0.060  -0.126  -0.119  -0.173
134   H        -0.163  -0.162  -0.139  -0.009  -0.006   0.033  -0.357  -0.354  -0.316
135   N        -1.206  -1.203  -1.180  -1.051  -1.050  -1.005  -1.050  -1.046  -1.005
136   A        -1.206  -1.203  -1.180  -1.021  -1.003  -0.974  -1.050  -1.046  -1.005
137   R         1.619   1.621   1.642   1.892   1.892   1.924   1.723   1.725   1.750
138   F         1.619   1.621   1.642   1.860   1.861   1.893   1.723   1.725   1.750
139   L         1.619   1.621   1.642   1.358   1.363   1.394   1.723   1.725   1.750
140   K        -0.018  -0.013  -0.048  -0.030  -0.023  -0.062  -0.126  -0.119  -0.173
141   G         1.619   1.621   1.642   1.763   1.765   1.796   1.723   1.725   1.750
142   K         1.619   1.621   1.642   1.479   1.481   1.514   1.723   1.725   1.750
143   P        -0.018   0.008  -0.053   0.092   0.129   0.060  -0.126  -0.086  -0.179
144   N        -0.018   0.008  -0.053   0.145   0.184   0.088  -0.126  -0.086  -0.179
145   S        -1.206  -1.203  -1.180  -1.165  -1.160  -1.118  -1.050  -1.046  -1.005
146   T        -1.206  -1.203  -1.180  -0.843  -0.840  -0.798  -1.050  -1.046  -1.005
147   V        -0.018   0.008  -0.053   0.152   0.194   0.083  -0.126  -0.086  -0.179
148   L        -0.018  -0.041  -0.073  -0.411  -0.453  -0.521  -0.126  -0.162  -0.211
149   A        -0.018  -0.041  -0.073  -0.445  -0.488  -0.544  -0.126  -0.162  -0.211
150   T        -0.018  -0.041  -0.073   0.189   0.152   0.110  -0.126  -0.162  -0.211
151   T        -1.206  -1.203  -1.180  -1.306  -1.310  -1.259  -1.050  -1.046  -1.005
152   A        -1.206  -1.203  -1.180  -1.284  -1.273  -1.237  -1.050  -1.046  -1.005
153   G        -0.018  -0.013  -0.048  -0.022  -0.015  -0.096  -0.126  -0.119  -0.173
154   A        -0.018  -0.041  -0.073  -0.445  -0.488  -0.544  -0.126  -0.162  -0.211
155   L        -1.206  -1.203  -1.180  -1.562  -1.548  -1.513  -1.050  -1.046  -1.005
156   G        -0.018   0.008  -0.053  -0.244  -0.212  -0.279  -0.126  -0.086  -0.179
157   L        -1.206  -1.203  -1.180  -1.000  -0.983  -0.954  -1.050  -1.046  -1.005
158   L        -0.018  -0.041  -0.073  -0.147  -0.175  -0.206  -0.126  -0.162  -0.211
159   T        -0.018  -0.041  -0.073  -0.053  -0.104  -0.180  -0.126  -0.162  -0.211
160   L        -0.018  -0.041  -0.073  -0.411  -0.453  -0.521  -0.126  -0.162  -0.211
161   D         1.619   1.621   1.642   1.746   1.745   1.780   1.723   1.725   1.750
162   G        -0.018  -0.041  -0.073  -0.022  -0.071  -0.150  -0.126  -0.162  -0.211
163   I        -1.206  -1.203  -1.180  -0.777  -0.775  -0.732  -1.050  -1.046  -1.005
164   I        -1.206  -1.203  -1.180  -1.197  -1.199  -1.150  -1.050  -1.046  -1.005
165   S         1.619   1.621   1.642   1.547   1.552   1.582   1.723   1.725   1.750
166   K        -1.206  -1.203  -1.180  -0.990  -0.978  -0.944  -1.050  -1.046  -1.005
167   K        -0.018  -0.041  -0.073  -0.076  -0.109  -0.149  -0.126  -0.162  -0.211
168   Y        -0.018  -0.041  -0.073   0.145   0.109   0.053  -0.126  -0.162  -0.211
169   Y         1.619   1.621   1.642   1.746   1.749   1.780   1.723   1.725   1.750
170   S        -0.018   0.008  -0.053  -0.171  -0.128  -0.228  -0.126  -0.086  -0.179
171   R        -0.018  -0.013  -0.048   0.182   0.189   0.115  -0.126  -0.119  -0.173
172   Y        -0.018   0.008  -0.053   0.269   0.311   0.211  -0.126  -0.086  -0.179
173   D         1.619   1.621   1.642   1.746   1.745   1.780   1.723   1.725   1.750
174   K         1.619   1.621   1.642   1.479   1.481   1.514   1.723   1.725   1.750
175   K        -1.206  -1.203  -1.180  -0.901  -0.886  -0.856  -1.050  -1.046  -1.005
176   -        -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/P38325
Output conservation file - output/P38325
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
