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#!/usr/bin/perl
use strict;
...
    print "\n";
}

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C:\Old_Data\perlp>perl test3.pl fasta_dat.txt
...
For id: >NR_037806 1
QUERY: TTTTT    appears 6 times  position 693 837 838 839 840 1114
REVCOMP: AAAAA  appears 3 times position 1292 1293 1322