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file1:
ATCGATGTGT
...

file2:
CCGATGCTGAggatgtcgcgcagatttaggCCGATGCTGAgagcatgaa...

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  my $matched='';
        foreach (@probes){
                                chomp $_;
...
                                $matched.= "$_\t$position\n";
                                }
         }