my $blastSeq = "";      # holds the sequence

my $blast_filehandle = "";    # file handlers
my $ref_filehandle = "";

my $oldRefFile = "";     # old reference file path and name

my $species_filter = "";
my $chromo_filter = "";       # filters
my @species_filter;
my @chromo_filter;
my @advanced_filter;
my $state;    # determines the state of input

my $email;    ## has email variables been activated


my $show_all;           # show summary info check box
my $show_filter;        # show only filtered hits check box
           
# time stamp parameters
my $date;

my @OrigRef;              # arrays of the files
my @blastLine;

my @refsubjects;  # reference to empty array
my $refalignment = {};       # builds alignments from reference file


my @refelements;        # stores the split GI line from reference line
my @blast_elements;     # stores the split GI line from new blast line

my %refList;# holds the accessions from the GI line in ref file
my %blastList; # holds the accessions from the GI line in blast file

my $boolean;   # determines the array to use for the output
my @subjects;  # stores the whole GI line from blast file

my $alignment = {};    # holds alignments from blast file