I don't see any need to create a hash table.
Why do you think a hash table is necessary?
Yes, I think your regex is flawed because of this substr "window". What's up with that?

I downloaded your data file and I present one way to parse it into records.
The first record is so long that I omitted it.

Please take one of these records and show us the desired output. 

#!usr/bin/perl
use strict;
use warnings;

get_record(); # skips the first ">" line

my $record;

while ( defined ( $record = get_record() ) )
{
   process_record ($record);
}

###########

sub process_record
{
   my $record = shift;
   print "$record\n";
   
   # please explain more about to process the record
   # the spec from the prof would be appropriate
}

sub get_record  #works with Perl DATA segment
{
   my $line;
   my $record = undef;
   
   while ( defined ($line = <DATA>) and $line !~ /^>/)
   {
      chomp $line;
      next if $line =~ /^\s*$/; # skip blank lines
      $record .= $line;
   }
   
   return $record; #could return a reference, but let's get
                   #the process_record() logic right first
}

__DATA__
>211000022278617 type=golden_path_region; loc=211000022278617:1..1037;
+ ID=211000022278617; dbxref=GB:DS485855,GB:DS485855,REFSEQ:NW_0018471
+44; MD5=8fd22b4969d1f92433b80ee3837e69bc; length=1037; release=r6.18;
+ species=Dmel;
ATGACGAAAATTTCGTTTGTAAATATCAACATTTTTGCAGAGTCTGTTTTTCCAAATTTCGGGTCATCAA
+ATAATCATTT
ATTTTGCCACAACATAAAAAATAATTGTCTGAATATGGAATGTCATACCTCACTGAGCTCGTAATAAAAT
+TTCCAATCAA
ACTGTGTTCAAAAATGGAAATTAAATTTTTTGGCCATATTTTGCAAATTTTGATGACCACCCCTCCTTAC
+AAAAAATTCG
AAAATTGATCCAAAAATTAATTTCCTAAATCCTTCAAAAAGTAATAGGGATCGTTAGCACTGGTAATTAG
+CTGCTCAAAA
CAGTTATTCTTACATCTATGTGACTATTTTTAGCCAAGTTATGACGAAAATTTCGTTTGTAAATATCAAC
+ATTTTTGCAG
AGTCTGTTTTACCAAATTTCGGTCATCAAATAATCATTTATTTTGCCACAACATAAAAAATAAGTGTCTG
+AATATGGAAT
GTCATACCTCACCGATCTCGTAATAAAATTTCCAATAAAACTGTGTTCAAAAGAGGAAATTAAATTTGTT
+GGCCATATTT
TGCAAATTTTGATGACCCCCCTCCTTACAAAAAATGCGAAAATTGATCCAAAAATTAATTTCCCTAAATC
+CTTCAAAAAG
TAATAGGGATCGTTTGCACTGGTAATTAGCTGCTCAAAACAGTTATTCTTACATCTATGTGACCATTTTT
+AGCCAAGTTA
TAACGAAAATTTCGTTTGTAAATATCAACATTTTTGCAGAGTCTGTTTTTCCAAAATTTGGTCATCAAAT
+AATCATTTAT
TTTGCCACAACATTAAAAATAATTGTCAGAATATGGAATGTTATATTTCACTGAGCTCGTAATAAAATTT
+CCAATCAAAC
TGTGATCAAAAATGGAAATTAAATTTTTTGGCCATATTTTGCAAATTTTGATGACCCTCCTCCTTACAGA
+AAATGCGAAA
ATTGATCCAAAAATAAGTTTTCTAAATCCTTCAAAAAGTAATAGGGATCGTTAGCACTGGTAATTAGCTG
+CTCAAAA
>211000022278618 type=golden_path_region; loc=211000022278618:1..1452;
+ ID=211000022278618; dbxref=GB:DS484811,GB:DS484811,REFSEQ:NW_0018461
+00; MD5=28b88781b6ffbac76cf0ccd6f47258a1; length=1452; release=r6.18;
+ species=Dmel;
ATTTTGAGCAGCTAATTATCAGTGCTAACGATCCCTATTACTTTTTGAAGGATTTAGGGAAATTATTTTT
+TGGATCAATT
TTCGCATTTTTTGTAAGGAAGGGGGTCATCAAAATTTGCCAAATATGGCCAAAAAATTCAATTTCTATTT
+TTGAACACAG
TTTGATTGGATATTTTATTACGAGCTCAGTGAGGTATGACATTCCATGTTCAGACAATTATTTTTTATGT
+TGTGGCAAAA
TAAATGATTATTTGATGACCAAAATTTGGAAAAACAGATTCTGCAAAATGTAATATTTACAAACGAAATT
+TTCGTCATAA
CTTGGTTAAAAATGGTCACATAGATGTAAGAATAACTGTTTTGAGCAGCTAATAACCAGTGCTAACGATC
+CCTATTACTT
TTTGAAGGATTTAGGGAAATTAATTTTTGGATCAATTTTCGCATTTTATGTAAGGAGGGGGGTCATCAAA
+ATTTGCAAAA
TTATGCCAAAAAATTTAATTTCCATTTTTGAACACAGTTTGATTGGAAATTTTATTACGAGCTCAGTGAG
+GTATGACCTT
CCATATTCAGACAATTATTTTTTATGTTGTGGCAAAATAAATGATTATTTGATGACCGAAATTTGGAAAA
+ACAGATTCTG
CCAAAGAAGTAGATATTTACAAACGAAATTTTCGTCATAACTTGGTTAAAAATGGTCACATAGATGTAAG
+AATAACTGTT
TTGAGCAGCTAATTATCAGTGCAAACGATCCCTATTACTTTTTGAAGGATTTAGGGAAATTAATTTTTGG
+ATCAATTTTC
GCATTTTATGTAAGGAGGGGGGTCATCAAAATTTGCAAAATATGGCCAAAAAATTTAATTTCCATTTTTG
+AACACAGTTT
GATTGGAAATTTTATTACGAGCTCAGTGAGGTATGACATTCCATATTCAGACAATTATTTTTTATGTTGT
+GGCAAAATAA
ATGATTATTTGATGACCAAAATTTGGAAAAACAGACTCTGCAAAAATGTAGATATTTACAAACGAAATTT
+TCGTTATAAC
TTGGCTAAAAATGGTCACATAGATGTAAGAATAACTGTTTTGAGCAGCTAATAACCAGTGCTAACGATCC
+CTATTACTTT
TTGAAGGATTTAGGGAAATTAATTTTTGGATCAATTTTCGCATTTTATGTAAGGAGGGGGGTCATCAAAA
+TTTGCAAAAT
ATGGCCAAAAAATTTAATTTCCATTTTTGAACACAGTTTGATTGGAAATTTTATTACGAGCTCAGTGAGG
+TATGACATTC
CATATTCAGACAATTATTTTTTATGTTGTGGCAAAATAAATGATTATTTGATGACCAAAATTTGGAAAAA
+CAGACTCTGC
AAAAATGTAGATATTTACAAACGAAATTTTCGTTATAACTTGGCTAAAAATGGTCACATAGATGTAAGAA
+TAACTGTTTG
AGCAGCTAAAAC
>211000022278619 type=golden_path_region; loc=211000022278619:1..1986;
+ ID=211000022278619; dbxref=GB:DS484504,GB:DS484504,REFSEQ:NW_0018457
+93; MD5=35ebd37874cb5c55b4804e9786d17bfe; length=1986; release=r6.18;
+ species=Dmel;
ACAGTTATTCTTACATCTATGTGACAATTTTTAGCCAAGTTATAACGAAAATTTCGTTTGTAAATATCAT
+TACTTTGGCA
GAATCTGTTTTTCCACATTTCGGTCTTCAAATATCATTTATTTTGCCACAACATTAAAAATAATTGTCTG
+AATATGGAAT
GTCATACCTCACTGAGCTTGTAGTAAAATTTCCAATCAAACTGTGTTCAAAAATGGAATTAAATTTTTTG
+GCCATATTTT
GCAAATTTTGATGACCTTCTTCCAAAAATTGCAAAAATTGATCTAAAAATTAGTTTCCCTAAATCCTTCA
+AAAAGTAATA
GGGATCGTTAGCACTGGTAATTAGCTGCTCAAAACAGTTATTCTTAGATCTATGTGACCATTTTTAGCCA
+AGTTATAACG
AAAATTTCGTTTGTAAATATCAATATTTTGGCAGAATCTGTTTTTCCAAATTTCGGTCAAAAAATAATGA
+TTTATTTTGC
CACAACATAAAAAATAATTGTCTGAATATGGAATGTCATACCTCACTGAGCTTGTAATAAAATTTCCAAT
+CAAACTGTGT
TCAAAAATGGAAATTAAATTTTTTGGCCATATTTTGCAAATTTTGATGACCCCCGTCGTTACAAAAAATG
+TGAAAATTGA
TCGAAAAATTAATTTCCCTAAGTCCTTCAAAAAGTAATAGCGATCGTTAGCACTGGTAATTAGCTGCTCA
+AAACAGTTAT
TCTTACATCCACGTGACAGTTTTTAGCCAAGTTATAACGAAAATTTCGTTTGTAAATATCAACATTTTTG
+CAGAGTCTGT
TTTTCCAAAATTCGGTCATCAAATAATCATTTATTTTGCCACATTAAAAATAATTGTCAGAATATAGAAT
+GTCATACTTC
ACTGACTCGGAATAAAATTTCCAATCAAACTGGGTTCAAAAAATGGAAATTAAACTTTTTGGCCCTATAT
+TACAAATTTT
GATGACCTCCCTCCTTCCCAAAAATGTGAAAATTGATCTAAAAATTAATTTTCCTAAATCCTTCAAAAAG
+AAATAGCGAT
CATTAGCACTGGTAATTAGCTGCTCAAAACAGTTATTCTTACATCTATGTGACAATTTTTAGCCAAGTTA
+TAATGAAAAT
TTCGTTTGTAAATATCATTACTTTGGAAGAATCTGTTTTTCCACATTTCGGTCTTCAAATAATCATTTAT
+TTTGCCGCAA
CATTAAAAATTATTGTCAGAATATAGAATGTCATACTTCACTGAGCTCATTATAAAATTTCCAATCAAAC
+TGTATTCAAA
AATGGAAATTAAATTTTTTGGCCATATTTTGCAAATTTTGATGACCCCCAACTTCCAAAAATTGTGAAAA
+TTGATCCGAA
AATTAATTTCCCTAAATCCTTCAAAAAGAAATAGCGATCGTTAGCACTGGTAATTAGCTGCTCAAAACAG
+TTATTCTTAC
ATCTATGTGACAATTTTTAGCCAAGTTATAACGAAAATTTCGTTTGTAAATATCATTACTTTGGCAGAAT
+CTGTTTTTCC
ACATTTCGGTCTTCAAATATCATTTATTTTGCCACAACATTAAAAATAATTGTCTGAATATGGAATGTCA
+TACCTCACTG
AGCTTGTAGTAACATTTCCAATCAAACTGTGTTCAAAAAATGGAAATTACATTTTTTGGTCATATTTTGC
+AAATTTTGAT
GACCCCCGTCCTTATAAAAAATGTGAAAATTGTTCGAAAAATTAATTTCCCTAAATCCTTCAAAAAGTAA
+AAGCGATCGT
TAGCACTGGTAATTAGCTGCTCAAAACAGTTATTCTTACATCTATGTGACAATTTTTAGCCAAGTTATAA
+CGAAAATTTC
GTTTGTAAATATCATTACTTTGGCAGAATCTGTTTTTCCACATTTCGGTCTTCAAATATCATTTATTTTG
+CCACAACATT
AAAAATAATTGTCTGAATATGGAATGTCATACCTCACTGAGCTTGTAGTAAAATTTCCAATCAAAC

[download]

In reply to Re: unique sequences by Marshall
in thread unique sequences by Anonymous Monk

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