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#! perl -slw
use strict;
...

__DATA__
AGAGGTCAGTCTGCATCGTATCGATCGTCGACGATCGATACGATGCAGACTGACGAGAG

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[13:44:54.28] C:\test>1085446
AGAGGTCAGTCTGCATCGTATCGATCGTCGACGATCGATACGATGCAGACTGACGAGAG
...
                               CGATCG at 31
                                 ATCGAT at 33
                                           TGCA at 43