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C:\test>dir randDNA.txt
10/06/2012  01:13     1,036,000,000 randDNA.txt
...
GTCATGAGTCCAATTTGGGGTTAGCTGAAATAACCTGCTGTCCCCTAAAATTGTCGCATTCAAGCAGGGT
+GG
CGGGTACACATGCTAGCATCCGGACGCTATAAGGGCTCCCTTAGTAACATTTCCACTTTCTTGATATTTG
+TG
GGTGCGTTTAACGACGTCATTACTATGAGAGTCGGTATAGCCATCACATAATGACTCGAGCTTACGTCCT
+AC

#! perl -slw
use strict;
...
C:\test>DNAsearch1 randDNA.txt | wc -l
Took 11.281 seconds
  15313

#! perl -slw
use strict;
...
1441865

[ 4:12:28.90] C:\test>