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use strict;
use warnings;
...
A 163    ARG       B  83    ARG^?     
A 222    ARG       B  5     ARG^?

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A  83    GLU       A  90    GLU^?     
A 163    ARG       A  83    ARG^?     
...
A 257    ALA       A 118    ALA~?     
A 328    ASP       A  95    ASP~?