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#!/usr/bin/perl 
use strict;
...
}
close (B);

Data File 1 (match_super.dat):

...
2-Match:    GGAAAGTCAAGCCCATCTA    9    3254
3-Match:    GTTCTTATTTGCACCTACT    6    180
4-Match:    GATGAGGAACAGCAACCTT    5    844

Data file 2 (M23263_rna_300-1.dat_1.ct)

...
298    U    297    299    0    298
299    G    298    300    0    299
300    A    299    0    0    300