1     M         1.499   1.501   1.520   1.755   1.759   1.783   1.578   1.580   1.603
2     M         0.000   0.024  -0.034  -0.510  -0.491  -0.522  -0.131  -0.094  -0.184
3     S        -1.088  -1.086  -1.066  -1.245  -1.220  -1.211  -0.985  -0.983  -0.947
4     Q         0.000   0.024  -0.034  -0.555  -0.535  -0.573  -0.131  -0.094  -0.184
5     V        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
6     S        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
7     H        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
8     S         1.499   1.501   1.520   0.869   0.871   0.898   1.578   1.580   1.603
9     Q        -0.133  -0.132  -0.112   0.058   0.060   0.089  -0.344  -0.343  -0.309
10    E        -1.088  -1.086  -1.066  -0.637  -0.633  -0.605  -0.985  -0.983  -0.947
11    G         1.499   1.501   1.520   1.586   1.589   1.614   1.578   1.580   1.603
12    S         1.499   1.501   1.520   0.753   0.750   0.783   1.578   1.580   1.603
13    G         0.000  -0.001  -0.042   0.127   0.128   0.052  -0.131  -0.132  -0.197
14    R         0.000  -0.018  -0.045   0.152   0.127   0.080  -0.131  -0.159  -0.203
15    F        -1.088  -1.086  -1.066  -0.611  -0.608  -0.579  -0.985  -0.983  -0.947
16    W         1.499   1.501   1.520   1.842   1.845   1.870   1.578   1.580   1.603
17    N        -1.088  -1.086  -1.066  -1.213  -1.229  -1.179  -0.985  -0.983  -0.947
18    K         1.499   1.501   1.520   1.513   1.518   1.542   1.578   1.580   1.603
19    F         0.000  -0.018  -0.045   0.333   0.309   0.264  -0.131  -0.159  -0.203
20    K         1.499   1.501   1.520   1.513   1.518   1.542   1.578   1.580   1.603
21    S         0.000  -0.001  -0.042  -0.658  -0.662  -0.698  -0.131  -0.132  -0.197
22    S         0.000  -0.018  -0.045  -0.606  -0.630  -0.641  -0.131  -0.159  -0.203
23    T         1.499   1.501   1.520   1.495   1.499   1.523   1.578   1.580   1.603
24    K         1.499   1.501   1.520   1.513   1.518   1.542   1.578   1.580   1.603
25    S         1.499   1.501   1.520   0.753   0.750   0.783   1.578   1.580   1.603
26    L         1.499   1.501   1.520   1.595   1.597   1.623   1.578   1.580   1.603
27    S         1.499   1.501   1.520   0.753   0.750   0.783   1.578   1.580   1.603
28    T         0.000   0.024  -0.034  -0.658  -0.632  -0.690  -0.131  -0.094  -0.184
29    S         1.499   1.501   1.520   0.753   0.750   0.783   1.578   1.580   1.603
30    L         0.000  -0.018  -0.045   0.266   0.242   0.206  -0.131  -0.159  -0.203
31    A        -1.088  -1.086  -1.066  -1.194  -1.193  -1.160  -0.985  -0.983  -0.947
32    H         0.000  -0.001  -0.042   0.353   0.353   0.284  -0.131  -0.132  -0.197
33    L         1.499   1.501   1.520   1.595   1.597   1.623   1.578   1.580   1.603
34    S         0.000  -0.018  -0.045  -0.581  -0.603  -0.611  -0.131  -0.159  -0.203
35    I         0.000  -0.018  -0.045   0.404   0.376   0.331  -0.131  -0.159  -0.203
36    K         1.499   1.501   1.520   1.513   1.518   1.542   1.578   1.580   1.603
37    A        -1.088  -1.086  -1.066  -0.818  -0.815  -0.785  -0.985  -0.983  -0.947
38    E         1.499   1.501   1.520   1.658   1.661   1.686   1.578   1.580   1.603
39    K        -1.088  -1.086  -1.066  -0.785  -0.774  -0.753  -0.985  -0.983  -0.947
40    D         1.499   1.501   1.520   1.676   1.680   1.704   1.578   1.580   1.603
41    G         1.499   1.501   1.520   1.586   1.589   1.614   1.578   1.580   1.603
42    D         0.000  -0.001  -0.042  -0.108  -0.110  -0.243  -0.131  -0.132  -0.197
43    T         1.499   1.501   1.520   1.495   1.499   1.523   1.578   1.580   1.603
44    V         0.000   0.024  -0.034   0.221   0.256   0.174  -0.131  -0.094  -0.184
45    N         0.000  -0.001  -0.042   0.144   0.145   0.068  -0.131  -0.132  -0.197
46    T         0.000   0.024  -0.034  -0.658  -0.632  -0.690  -0.131  -0.094  -0.184
47    T         1.499   1.501   1.520   1.495   1.499   1.523   1.578   1.580   1.603
48    L         0.000  -0.001  -0.042   0.238   0.236   0.178  -0.131  -0.132  -0.197
49    V         1.499   1.501   1.520   1.720   1.721   1.748   1.578   1.580   1.603
50    H         1.499   1.501   1.520   1.746   1.749   1.774   1.578   1.580   1.603
51    K         1.499   1.501   1.520   1.513   1.518   1.542   1.578   1.580   1.603
52    G         0.000   0.024  -0.034   0.209   0.247   0.152  -0.131  -0.094  -0.184
53    L         1.499   1.501   1.520   1.595   1.597   1.623   1.578   1.580   1.603
54    V         1.499   1.501   1.520   1.720   1.721   1.748   1.578   1.580   1.603
55    K         1.499   1.501   1.520   1.513   1.518   1.542   1.578   1.580   1.603
56    F         0.000  -0.018  -0.045   0.380   0.359   0.319  -0.131  -0.159  -0.203
57    Y         1.499   1.501   1.520   1.825   1.828   1.852   1.578   1.580   1.603
58    E        -1.088  -1.086  -1.066  -1.290  -1.310  -1.256  -0.985  -0.983  -0.947
59    N        -1.088  -1.086  -1.066  -1.162  -1.180  -1.129  -0.985  -0.983  -0.947
60    Q         1.499   1.501   1.520   1.676   1.678   1.704   1.578   1.580   1.603
61    H         0.000   0.024  -0.034   0.306   0.340   0.257  -0.131  -0.094  -0.184
62    P         1.499   1.501   1.520   1.577   1.581   1.605   1.578   1.580   1.603
63    F         1.499   1.501   1.520   1.702   1.707   1.730   1.578   1.580   1.603
64    Q         1.499   1.501   1.520   1.676   1.678   1.704   1.578   1.580   1.603
65    G         1.499   1.501   1.520   1.586   1.589   1.614   1.578   1.580   1.603
66    F         1.499   1.501   1.520   1.702   1.707   1.730   1.578   1.580   1.603
67    P         1.499   1.501   1.520   1.577   1.581   1.605   1.578   1.580   1.603
68    G         0.000  -0.018  -0.045   0.189   0.164   0.118  -0.131  -0.159  -0.203
69    W         1.499   1.501   1.520   1.842   1.845   1.870   1.578   1.580   1.603
70    L         1.499   1.501   1.520   1.595   1.597   1.623   1.578   1.580   1.603
71    G         1.499   1.501   1.520   1.586   1.589   1.614   1.578   1.580   1.603
72    E         0.000   0.024  -0.034   0.345   0.382   0.288  -0.131  -0.094  -0.184
73    K         0.000  -0.018  -0.045   0.060   0.035  -0.019  -0.131  -0.159  -0.203
74    E         0.000  -0.018  -0.045   0.234   0.206   0.156  -0.131  -0.159  -0.203
75    D         1.499   1.501   1.520   1.676   1.680   1.704   1.578   1.580   1.603
76    L         0.000  -0.018  -0.045   0.164   0.137   0.087  -0.131  -0.159  -0.203
77    P         1.499   1.501   1.520   1.577   1.581   1.605   1.578   1.580   1.603
78    N        -1.088  -1.086  -1.066  -0.679  -0.671  -0.646  -0.985  -0.983  -0.947
79    E         1.499   1.501   1.520   1.658   1.661   1.686   1.578   1.580   1.603
80    R        -1.088  -1.086  -1.066  -0.791  -0.785  -0.758  -0.985  -0.983  -0.947
81    K         1.499   1.501   1.520   1.459   1.461   1.488   1.578   1.580   1.603
82    I         1.499   1.501   1.520   1.776   1.778   1.803   1.578   1.580   1.603
83    L         1.499   1.501   1.520   1.595   1.597   1.623   1.578   1.580   1.603
84    D        -1.088  -1.086  -1.066  -1.277  -1.296  -1.243  -0.985  -0.983  -0.947
85    T        -1.088  -1.086  -1.066  -0.885  -0.876  -0.852  -0.985  -0.983  -0.947
86    Q         0.000  -0.018  -0.045  -0.108  -0.155  -0.254  -0.131  -0.159  -0.203
87    V         0.000  -0.001  -0.042   0.329   0.328   0.262  -0.131  -0.132  -0.197
88    K         0.000  -0.001  -0.042   0.110   0.113   0.046  -0.131  -0.132  -0.197
89    H         0.000  -0.018  -0.045   0.353   0.326   0.278  -0.131  -0.159  -0.203
90    D        -1.088  -1.086  -1.066  -0.721  -0.718  -0.688  -0.985  -0.983  -0.947
91    M        -1.088  -1.086  -1.066  -1.035  -1.034  -1.001  -0.985  -0.983  -0.947
92    K         0.000  -0.018  -0.045   0.060   0.035  -0.019  -0.131  -0.159  -0.203
93    K        -1.088  -1.086  -1.066  -1.343  -1.340  -1.309  -0.985  -0.983  -0.947
94    Q        -1.088  -1.086  -1.066  -1.232  -1.234  -1.198  -0.985  -0.983  -0.947
95    N        -1.088  -1.086  -1.066  -0.721  -0.712  -0.688  -0.985  -0.983  -0.947
96    S         0.000  -0.001  -0.042  -0.658  -0.662  -0.698  -0.131  -0.132  -0.197
97    -        -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000  -1.000     *
98    R        -1.088  -1.086  -1.066  -1.245  -1.260  -1.211  -0.985  -0.983  -0.947
99    H         0.000   0.024  -0.034  -0.515  -0.497  -0.528  -0.131  -0.094  -0.184
100   F        -1.088  -1.086  -1.066  -0.591  -0.587  -0.558  -0.985  -0.983  -0.947
101   S        -1.088  -1.086  -1.066  -1.377  -1.352  -1.343  -0.985  -0.983  -0.947
102   P        -1.088  -1.086  -1.066  -1.181  -1.176  -1.147  -0.985  -0.983  -0.947
103   S         0.000  -0.001  -0.042  -0.647  -0.651  -0.686  -0.131  -0.132  -0.197
104   F         0.000  -0.018  -0.045  -0.082  -0.127  -0.228  -0.131  -0.159  -0.203
105   S        -1.088  -1.086  -1.066  -1.225  -1.201  -1.192  -0.985  -0.983  -0.947
106   N        -1.088  -1.086  -1.066  -1.245  -1.243  -1.211  -0.985  -0.983  -0.947
107   R        -1.088  -1.086  -1.066  -0.753  -0.746  -0.720  -0.985  -0.983  -0.947
108   R         0.000  -0.018  -0.045   0.110   0.085   0.031  -0.131  -0.159  -0.203
109   K        -1.088  -1.086  -1.066  -0.748  -0.738  -0.715  -0.985  -0.983  -0.947
110   A        -1.088  -1.086  -1.066  -1.257  -1.277  -1.224  -0.985  -0.983  -0.947
111   S        -1.088  -1.086  -1.066  -1.144  -1.118  -1.110  -0.985  -0.983  -0.947
112   S         1.499   1.501   1.520   0.753   0.750   0.783   1.578   1.580   1.603
113   E         1.499   1.501   1.520   1.658   1.661   1.686   1.578   1.580   1.603
114   D        -1.088  -1.086  -1.066  -0.658  -0.650  -0.625  -0.985  -0.983  -0.947
115   P         0.000  -0.001  -0.042   0.148   0.150   0.078  -0.131  -0.132  -0.197
116   M        -1.088  -1.086  -1.066  -0.566  -0.563  -0.533  -0.985  -0.983  -0.947
117   G        -1.088  -1.086  -1.066  -1.238  -1.256  -1.204  -0.985  -0.983  -0.947
118   T        -1.088  -1.086  -1.066  -0.737  -0.725  -0.704  -0.985  -0.983  -0.947
119   P         0.000  -0.018  -0.045   0.193   0.169   0.124  -0.131  -0.159  -0.203
120   S        -1.088  -1.086  -1.066  -1.175  -1.149  -1.141  -0.985  -0.983  -0.947
121   S         0.000  -0.001  -0.042  -0.581  -0.585  -0.608  -0.131  -0.132  -0.197
122   N        -0.133  -0.132  -0.112  -0.069  -0.066  -0.037  -0.344  -0.343  -0.309
123   G        -0.133  -0.132  -0.112  -0.690  -0.688  -0.657  -0.344  -0.343  -0.309
124   N        -0.133  -0.132  -0.112  -0.001   0.002   0.031  -0.344  -0.343  -0.309
125   T        -1.088  -1.086  -1.066  -0.818  -0.809  -0.785  -0.985  -0.983  -0.947
126   P        -1.088  -1.086  -1.066  -1.232  -1.229  -1.198  -0.985  -0.983  -0.947
127   E        -1.088  -1.086  -1.066  -0.705  -0.702  -0.672  -0.985  -0.983  -0.947
128   Y         0.000   0.024  -0.034   0.254   0.286   0.214  -0.131  -0.094  -0.184
129   T         1.499   1.501   1.520   1.495   1.499   1.523   1.578   1.580   1.603
130   P         0.000  -0.001  -0.042   0.119   0.121   0.044  -0.131  -0.132  -0.197
131   A         0.000  -0.018  -0.045   0.209   0.183   0.133  -0.131  -0.159  -0.203
132   S         0.000  -0.001  -0.042  -0.606  -0.611  -0.638  -0.131  -0.132  -0.197
133   K        -1.088  -1.086  -1.066  -1.219  -1.233  -1.185  -0.985  -0.983  -0.947
134   S         0.000  -0.018  -0.045  -0.581  -0.603  -0.611  -0.131  -0.159  -0.203
135   F         1.499   1.501   1.520   1.702   1.707   1.730   1.578   1.580   1.603
136   Q        -1.088  -1.086  -1.066  -0.653  -0.650  -0.620  -0.985  -0.983  -0.947
137   D        -1.088  -1.086  -1.066  -1.225  -1.227  -1.192  -0.985  -0.983  -0.947
138   I         0.000  -0.018  -0.045   0.349   0.320   0.266  -0.131  -0.159  -0.203
139   Y         0.000  -0.018  -0.045   0.442   0.415   0.367  -0.131  -0.159  -0.203
140   N        -0.133  -0.132  -0.112  -0.008  -0.006   0.023  -0.344  -0.343  -0.309
141   N        -0.133  -0.132  -0.112  -0.123  -0.121  -0.092  -0.344  -0.343  -0.309
142   H        -0.133  -0.132  -0.112   0.030   0.032   0.061  -0.344  -0.343  -0.309
143   T         0.000  -0.018  -0.045  -0.289  -0.335  -0.431  -0.131  -0.159  -0.203
144   S         1.499   1.501   1.520   0.753   0.750   0.783   1.578   1.580   1.603
145   S         1.499   1.501   1.520   0.753   0.750   0.783   1.578   1.580   1.603
146   S        -1.088  -1.086  -1.066  -1.343  -1.317  -1.309  -0.985  -0.983  -0.947
147   S         0.000  -0.001  -0.042  -0.555  -0.559  -0.579  -0.131  -0.132  -0.197
148   A        -1.088  -1.086  -1.066  -0.742  -0.738  -0.709  -0.985  -0.983  -0.947
149   T        -1.088  -1.086  -1.066  -1.257  -1.253  -1.224  -0.985  -0.983  -0.947
150   P        -1.088  -1.086  -1.066  -1.363  -1.364  -1.329  -0.985  -0.983  -0.947
151   R        -1.088  -1.086  -1.066  -1.187  -1.203  -1.154  -0.985  -0.983  -0.947
152   R        -1.088  -1.086  -1.066  -0.721  -0.713  -0.688  -0.985  -0.983  -0.947
153   A         0.000  -0.001  -0.042  -0.153  -0.156  -0.287  -0.131  -0.132  -0.197
154   S         0.000  -0.001  -0.042  -0.611  -0.615  -0.644  -0.131  -0.132  -0.197
155   S         1.499   1.501   1.520   0.753   0.750   0.783   1.578   1.580   1.603
156   R        -0.133  -0.132  -0.112   0.039   0.041   0.070  -0.344  -0.343  -0.309
157   P        -0.133  -0.132  -0.112  -0.114  -0.111  -0.082  -0.344  -0.343  -0.309
158   T         0.000  -0.001  -0.042  -0.289  -0.292  -0.420  -0.131  -0.132  -0.197
159   R        -1.088  -1.086  -1.066  -0.802  -0.795  -0.769  -0.985  -0.983  -0.947
160   P        -1.088  -1.086  -1.066  -1.290  -1.308  -1.256  -0.985  -0.983  -0.947
161   S        -1.088  -1.086  -1.066  -1.297  -1.271  -1.263  -0.985  -0.983  -0.947
162   A         0.000  -0.018  -0.045   0.168   0.141   0.085  -0.131  -0.159  -0.203
163   G        -1.088  -1.086  -1.066  -1.310  -1.328  -1.276  -0.985  -0.983  -0.947
164   Q        -1.088  -1.086  -1.066  -1.113  -1.112  -1.080  -0.985  -0.983  -0.947
165   E        -1.088  -1.086  -1.066  -0.785  -0.781  -0.753  -0.985  -0.983  -0.947
166   F         0.000  -0.001  -0.042   0.388   0.390   0.333  -0.131  -0.132  -0.197
167   R        -0.133  -0.132  -0.112  -0.616  -0.614  -0.583  -0.344  -0.343  -0.309
168   A        -1.088  -1.086  -1.066  -1.138  -1.134  -1.104  -0.985  -0.983  -0.947
169   S         0.000  -0.001  -0.042  -0.566  -0.570  -0.591  -0.131  -0.132  -0.197
170   L        -1.088  -1.086  -1.066  -0.710  -0.704  -0.678  -0.985  -0.983  -0.947
171   G        -1.088  -1.086  -1.066  -0.737  -0.730  -0.704  -0.985  -0.983  -0.947
172   R         0.000   0.024  -0.034  -0.622  -0.597  -0.648  -0.131  -0.094  -0.184
173   S         0.000  -0.001  -0.042  -0.581  -0.585  -0.608  -0.131  -0.132  -0.197
174   K         0.000  -0.018  -0.045   0.102   0.078   0.031  -0.131  -0.159  -0.203
175   T         0.000  -0.001  -0.042   0.177   0.178   0.126  -0.131  -0.132  -0.197
176   S         0.000  -0.018  -0.045  -0.581  -0.603  -0.611  -0.131  -0.159  -0.203
177   N        -1.088  -1.086  -1.066  -1.283  -1.283  -1.250  -0.985  -0.983  -0.947
178   S        -1.088  -1.086  -1.066  -1.277  -1.253  -1.243  -0.985  -0.983  -0.947
179   F        -1.088  -1.086  -1.066  -0.721  -0.717  -0.688  -0.985  -0.983  -0.947
180   N         0.000   0.024  -0.034   0.094   0.131   0.042  -0.131  -0.094  -0.184
181   T        -1.088  -1.086  -1.066  -0.748  -0.738  -0.715  -0.985  -0.983  -0.947
182   S         1.499   1.501   1.520   0.753   0.750   0.783   1.578   1.580   1.603
183   S         0.000   0.024  -0.034  -0.289  -0.236  -0.398  -0.131  -0.094  -0.184
184   T        -1.088  -1.086  -1.066  -0.758  -0.749  -0.726  -0.985  -0.983  -0.947
185   P        -1.088  -1.086  -1.066  -1.245  -1.262  -1.211  -0.985  -0.983  -0.947
186   T         0.000   0.024  -0.034  -0.658  -0.632  -0.690  -0.131  -0.094  -0.184
187   P        -1.088  -1.086  -1.066  -0.824  -0.818  -0.791  -0.985  -0.983  -0.947
188   P        -1.088  -1.086  -1.066  -0.637  -0.626  -0.605  -0.985  -0.983  -0.947
189   P        -1.088  -1.086  -1.066  -0.737  -0.728  -0.704  -0.985  -0.983  -0.947
190   D         0.000   0.024  -0.034  -0.555  -0.534  -0.573  -0.131  -0.094  -0.184
191   A         0.000  -0.018  -0.045   0.270   0.245   0.204  -0.131  -0.159  -0.203
192   S         0.000  -0.001  -0.042  -0.510  -0.514  -0.527  -0.131  -0.132  -0.197
193   S         0.000  -0.001  -0.042  -0.555  -0.559  -0.579  -0.131  -0.132  -0.197
194   G        -1.088  -1.086  -1.066  -0.807  -0.801  -0.774  -0.985  -0.983  -0.947
195   V        -1.088  -1.086  -1.066  -0.647  -0.647  -0.615  -0.985  -0.983  -0.947
196   M         0.000  -0.001  -0.042   0.329   0.330   0.255  -0.131  -0.132  -0.197
197   A        -1.088  -1.086  -1.066  -0.606  -0.600  -0.574  -0.985  -0.983  -0.947
198   M         0.000  -0.018  -0.045  -0.030  -0.076  -0.178  -0.131  -0.159  -0.203
199   K         0.000   0.024  -0.034   0.110   0.151   0.051  -0.131  -0.094  -0.184
200   D        -1.088  -1.086  -1.066  -0.700  -0.696  -0.667  -0.985  -0.983  -0.947
201   R         1.499   1.501   1.520   1.559   1.563   1.587   1.578   1.580   1.603
202   L         0.000  -0.018  -0.045   0.254   0.230   0.192  -0.131  -0.159  -0.203
203   K        -1.088  -1.086  -1.066  -0.813  -0.804  -0.780  -0.985  -0.983  -0.947
204   R         1.499   1.501   1.520   1.559   1.563   1.587   1.578   1.580   1.603
205   R         0.000  -0.018  -0.045   0.234   0.212   0.176  -0.131  -0.159  -0.203
206   N         1.499   1.501   1.520   1.604   1.608   1.632   1.578   1.580   1.603
207   N        -1.088  -1.086  -1.066  -1.343  -1.362  -1.309  -0.985  -0.983  -0.947
208   D        -1.088  -1.086  -1.066  -1.245  -1.264  -1.211  -0.985  -0.983  -0.947
209   -        -0.133  -0.132  -0.112  -0.684  -0.682  -0.651  -0.344  -0.343  -0.309
210   -        -0.133  -0.132  -0.112  -0.001   0.002   0.031  -0.344  -0.343  -0.309
211   Y        -1.088  -1.086  -1.066  -0.627  -0.627  -0.594  -0.985  -0.983  -0.947
212   G        -1.088  -1.086  -1.066  -0.721  -0.713  -0.688  -0.985  -0.983  -0.947
213   F        -1.088  -1.086  -1.066  -0.576  -0.571  -0.543  -0.985  -0.983  -0.947
* 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/P53604
Output conservation file - output/P53604
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
