viral_seq 0.3.0

data/lib/viral_seq/misc.rb

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+# viral_seq/misc.rb
+
+# miscellaneous methods
+# including
+#   Hash#copyhash
+#   Hash#difference
+#   Hash#uniq_hash
+#   ViralSeq::tail
+
+class Hash
+
+  # Hash#copyhash
+  # copy a hash
+  # different from "="
+  #   # example
+  #   h1 = {1=>'a'}
+  #   h2 = h1
+  #   h3 = h1.copyhash
+  #   h1.object_id == h2.object_id
+  #   => true
+  #   h1.object_id == h3.object_id
+  #   => false
+
+  def copyhash
+    h = Hash.new
+    self.each do |pair|
+      h.store(pair[0], pair[1])
+    end
+    return h
+  end
+
+  # subtract one hash (h2) from the other (h1) if the keys are identical
+  # example:
+  # h1 = {"Cat" => 100, "Dog" => 5, "Bird" => 2, "Snake" => 10}
+  # h2 = {"Cat" => 100, "Dog" => 5, "Bison" => 30}
+  # h1.difference(h2) = {"Bird" => 2, "Snake" => 10}
+
+  def difference(other)
+    reject do |k,_v|
+      other.has_key? k
+    end
+  end
+
+  # input hash A, return hash B with the unique values of hash A as keys,
+  # and the keys of the unique values of hash A as values of hash B
+  #   # example
+  #   hash = {1=>"A", 2=>"A", 3=>"C", 4=>"C", 5=>"T"}
+  #   p hash.uniq_hash
+  #   => {"A"=>[1, 2], "C"=>[3, 4], "T"=>[5]}
+
+  def uniq_hash
+    uniq_values = self.values.uniq
+    out_hash = {}
+    uniq_values.each do |uniq_va|
+      self.each do |k,v|
+        if v == uniq_va
+          if out_hash[uniq_va]
+            out_hash[uniq_va] << k
+          else
+            out_hash[uniq_va] = []
+            out_hash[uniq_va] << k
+          end
+        end
+      end
+    end
+    return out_hash
+  end
+end
+
+# Tail function for file as 'tail' in bash.
+def ViralSeq.tail(path, n)
+  file = File.open(path, "r")
+  buffer_s = 512
+  line_count = 0
+  file.seek(0, IO::SEEK_END)
+
+  offset = file.pos # we start at the end
+
+  while line_count <= n && offset > 0
+    to_read = if (offset - buffer_s) < 0
+                offset
+              else
+                buffer_s
+              end
+
+    file.seek(offset-to_read)
+    data = file.read(to_read)
+
+    data.reverse.each_char do |c|
+      if line_count > n
+        offset += 1
+        break
+      end
+      offset -= 1
+      if c == "\n"
+        line_count += 1
+      end
+    end
+  end
+
+  file.seek(offset)
+  file.read
+end

data/lib/viral_seq/muscle.rb

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+# viral_seq/muscle.rb
+# wrapper for MUSCLE (http://www.drive5.com/muscle)
+# Including Methods as:
+#   ViralSeq::check_muscle
+#   ViralSeq::muscle_align
+#   ViralSeq::muscle_align_multi
+
+# ViralSeq.check_muscle?(path_to_muscle)
+#   # check if the path_to_muscle provided is valid,
+#   # prompt error messages if MUSCLE is not found.
+
+# ViralSeq.muscle_align(reference_seq, test_sequence, path_to_muscle)
+#   # takes a reference sequence and a test sequence as String object
+#   # without specification on path_to_muscle, MuscleBio will be called to run Muscle
+#   # specify path_to_muscle if other source of muscle needed
+#   # returns aligned reference sequence and test sequences
+
+# ViralSeq.muscle_align_multi(sequence_hash, path_to_muscle)
+#   # input a sequence_hash object {:name=>:sequence,...}
+#   # without specification on path_to_muscle, MuscleBio will be called to run Muscle
+#   # specify path_to_muscle if other source of muscle needed
+#   # return aligned sequences an hash
+
+module ViralSeq
+
+  # check if path_to_muscle is correct
+  def self.check_muscle?(path_to_muscle)
+    begin
+      `#{path_to_muscle} -version`
+      return true
+    rescue Errno::ENOENT
+      puts "
+            Error: MUSCLE is not found for at the provided {path_to_muscle}!!
+            MUSLCE can be download at http://www.drive5.com/muscle
+            Add MUSCLE excutable path to $PATH using
+            $  export PATH=$PATH:/path/to/muscle
+            or
+            provide path_to_MUSCLE in the function arguments\n
+            "
+      return false
+    end
+  end
+
+  def self.muscle_align(ref_seq = "", test_seq = "", path_to_muscle = false)
+    temp_dir=File.dirname($0)
+    temp_file = temp_dir + "/_temp_muscle_in"
+    temp_aln = temp_dir + "/_temp_muscle_aln"
+    name = ">test"
+    temp_in = File.open(temp_file,"w")
+    temp_in.puts ">ref"
+    temp_in.puts ref_seq
+    temp_in.puts name
+    temp_in.puts test_seq
+    temp_in.close
+    if path_to_muscle
+      unless ViralSeq.check_muscle?(path_to_muscle)
+        File.unlink(temp_file)
+        return nil;
+      end
+      print `#{path_to_muscle} -in #{temp_file} -out #{temp_aln} -quiet`
+    else
+      MuscleBio.run("muscle -in #{temp_file} -out #{temp_aln} -quiet")
+    end
+    aln_seq_hash = ViralSeq.fasta_to_hash(temp_aln)
+    File.unlink(temp_file)
+    File.unlink(temp_aln)
+    return [aln_seq_hash[">ref"], aln_seq_hash[">test"]]
+  end
+
+  def self.muscle_align_multi(seq_hash = {}, path_to_muscle = false)
+    temp_dir=File.dirname($0)
+    temp_file = temp_dir + "/_temp_muscle_in"
+    temp_aln = temp_dir + "/_temp_muscle_aln"
+    File.open(temp_file, 'w'){|f| seq_hash.each {|k,v| f.puts k; f.puts v}}
+    if path_to_muscle
+      unless ViralSeq.check_muscle?(path_to_muscle)
+        File.unlink(temp_file)
+        return nil
+      end
+      print `#{path_to_muscle} -in #{temp_file} -out #{temp_aln} -quiet`
+    else
+      MuscleBio.run("muscle -in #{temp_file} -out #{temp_aln} -quiet")
+    end
+    out_seq_hash = ViralSeq.fasta_to_hash(temp_aln)
+    File.unlink(temp_file)
+    File.unlink(temp_aln)
+    return out_seq_hash
+  end
+end

data/lib/viral_seq/nt_variation.rb

@@ -0,0 +1,148 @@
+# viral_seq/nt_variation
+
+# contain functions to cacluate shannon's entropy, pairwise diversity, and TN93 distance
+#   ViralSeq::shannons_entropy
+#   ViralSeq::nucleotide_pi
+#   ViralSeq::TN93
+
+# ViralSeq.shannons_entropy(sequences)
+#   # calculate Shannon's entropy, Euler's number as the base of logarithm
+#   # https://en.wikipedia.org/wiki/Entropy_(information_theory)
+#   # input sequences alignment in Array [:seq1, :seq2, ...] or Hash [:name => :sequence] object
+#   # it works on both nt and aa sequences
+#   # return a Hash object for entropy score at each position in the alignment {:position => :entropy, ...}
+#   # position starts at 1.
+# =Usage
+#   # example
+#   sequence_file = 'spec/sample_files/sample_sequence_alignment_for_entropy.fasta'
+#   sequence_hash = ViralSeq.fasta_to_hash(sequence_file)
+#   entropy_hash = ViralSeq.shannons_entropy(sequence_hash)
+#   entropy_hash[3]
+#   => 0.0
+#   entropy_hash[14].round(3)
+#   => 0.639
+#   # This example is the sample input of LANL Entropy-One
+#   # https://www.hiv.lanl.gov/content/sequence/ENTROPY/entropy_one.html?sample_input=1
+
+# ViralSeq.nucleotide_pi(sequences)
+#   # Function to calculate nucleotide diversity π.
+#   # Refer to https://en.wikipedia.org/wiki/Nucleotide_diversity
+#   # input sequences alignment in Array [:seq1, :seq2, ...] or Hash [:name => :sequence] object
+#   # nt sequence only
+#   # return π as a Float object
+# =Usage
+#   # example
+#   sequences = %w{ AAGGCCTT ATGGCCTT AAGGCGTT AAGGCCTT AACGCCTT AAGGCCAT }
+#   ViralSeq.nucleotide_pi(sequences)
+#   => 0.16667
+
+# ViralSeq.tn93(sequences)
+#   # TN93 distance function
+#   # tabulate pairwise comparison of sequence pairs in a sequence alignment
+#   # input sequences alignment in Array [:seq1, :seq2, ...] or Hash [:name => :sequence] object
+#   # nt sequence only
+#   # return pairwise distance table in Hash object {:diff => :freq, ... }
+#   # Note: :diff in different positions (Integer), not percentage.
+# =Usage
+#   sequences = %w{ AAGGCCTT ATGGCCTT AAGGCGTT AAGGCCTT AACGCCTT AAGGCCAT }
+#   ViralSeq.tn93(sequences)
+#   => {0=>1, 1=>8, 2=>6}
+
+module ViralSeq
+  # calculate Shannon's entropy, Euler's number as the base of logarithm
+
+  def self.shannons_entropy(sequences)
+    sequences = if sequences.is_a?(Hash)
+                  sequences.values
+                elsif sequences.is_a?(Array)
+                  sequences
+                else
+                  raise ArgumentError.new("Wrong type of input sequences. it has to be Hash or Array object")
+                end
+    entropy_hash = {}
+    seq_l = sequences[0].size
+    (0..(seq_l - 1)).each do |position|
+      element = []
+      sequences.each do |seq|
+        element << seq[position]
+      end
+      entropy = 0
+      element.delete('*')
+      element_size = element.size
+      ViralSeq.count(element).each do |_k,v|
+        p = v/element_size.to_f
+        entropy += (-p * Math.log(p))
+      end
+      entropy_hash[(position + 1)] = entropy
+    end
+    return entropy_hash
+  end
+
+  # nucleotide pairwise diversity
+  def self.nucleotide_pi(sequences)
+    sequences = if sequences.is_a?(Hash)
+                  sequences.values
+                elsif sequences.is_a?(Array)
+                  sequences
+                else
+                  raise ArgumentError.new("Wrong type of input sequences. it has to be Hash or Array object")
+                end
+    seq_length = sequences[0].size - 1
+    nt_position_hash = {}
+    (0..seq_length).each do |n|
+      nt_position_hash[n] = []
+      sequences.each do |s|
+        nt_position_hash[n] << s[n]
+      end
+    end
+    diver = 0
+    com = 0
+    nt_position_hash.each do |_p,nt|
+      nt.delete_if {|n| n =~ /[^A|^C|^G|^T]/}
+      next if nt.size == 1
+      nt_count = ViralSeq.count(nt)
+      combination = (nt.size)*(nt.size - 1)/2
+      com += combination
+      a = nt_count["A"]
+      c = nt_count["C"]
+      t = nt_count["T"]
+      g = nt_count["G"]
+      div = a*c + a*t + a*g + c*t + c*g + t*g
+      diver += div
+    end
+    pi = (diver/com.to_f).round(5)
+    return pi
+  end
+
+  # TN93 distance function. Input: sequence Array/Hash, output hash: {diff => counts, ...}
+  def self.tn93(sequences)
+    sequences = if sequences.is_a?(Hash)
+                  sequences.values
+                elsif sequences.is_a?(Array)
+                  sequences
+                else
+                  raise ArgumentError.new("Wrong type of input sequences. it has to be Hash or Array object")
+                end
+    diff = []
+    seq_hash = ViralSeq.count(sequences)
+    seq_hash.values.each do |v|
+      comb = v * (v - 1) / 2
+      comb.times {diff << 0}
+    end
+
+    seq_hash.keys.combination(2).to_a.each do |pair|
+      s1 = pair[0]
+      s2 = pair[1]
+      diff_temp = ViralSeq.compare_two_seq(s1,s2)
+      comb = seq_hash[s1] * seq_hash[s2]
+      comb.times {diff << diff_temp}
+    end
+
+    count_diff = ViralSeq.count(diff)
+    out_hash = Hash.new(0)
+    Hash[count_diff.sort_by{|k,_v|k}].each do |k,v|
+      out_hash[k] = v
+    end
+    return out_hash
+  end
+end

data/lib/viral_seq/poisson_cutoff.rb

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+# viral_seq/poisson_cutoff.rb
+# define Poission cut-off for minority variants.
+# (Ref: Zhou, et al. J Virol 2015)
+#   ViralSeq::poisson_minority_cutoff
+
+# ViralSeq.poisson_minority_cutoff(sequences, error_rate, fold_cutoff)
+#   # sequences: input sequences alignment in Array [:seq1, :seq2, ...] or Hash [:name => :sequence] object
+#   # error_rate: the redisual sequencing error rate (default = 0.0001),
+#   # fold_cutoff: a fold cut-off to determine poisson minority cut-off. default = 20. i.e. <5% mutations from randome method error.
+#   # example: cut-off = 2 means that mutations appear at least 2 times are very likely to be a true mutation instead of residual methods errors.
+# =Usage
+#   sequence_file = 'spec/sample_files/sample_sequence_for_poisson.fasta'
+#   sequences = ViralSeq.fasta_to_hash(sequence_file)
+#   ViralSeq.poisson_minority_cutoff(sequences)
+#   => 2
+
+
+module ViralSeq
+
+  def self.poisson_minority_cutoff(sequences, error_rate = 0.0001, fold_cutoff = 20)
+    sequences = if sequences.is_a?(Hash)
+                  sequences.values
+                elsif sequences.is_a?(Array)
+                  sequences
+                else
+                  raise ArgumentError.new("Wrong type of input sequences. it has to be Hash or Array object")
+                end
+    if sequences.size == 0
+      return 0
+    else
+      cut_off = 1
+      l = sequences[0].size
+      rate = sequences.size * error_rate
+      count_mut = ViralSeq.variant_for_poisson(sequences)
+      max_count = count_mut.keys.max
+      poisson_hash = ViralSeq.poisson_distribution(rate, max_count)
+
+      poisson_hash.each do |k,v|
+        cal = l * v
+        obs = count_mut[k] ? count_mut[k] : 0
+        if obs >= fold_cutoff * cal
+          cut_off = k
+          break
+        end
+      end
+      return cut_off
+    end
+  end
+
+  # Input sequence array. output Variant distribution for Poisson cut-off
+  def self.variant_for_poisson(seq)
+    seq_size = seq.size
+    l = seq[0].size - 1
+    var = []
+    (0..l).to_a.each do |pos|
+      nt = []
+      seq.each do |s|
+        nt << s[pos]
+      end
+      count_nt = ViralSeq.count(nt)
+      v = seq_size - count_nt.values.max
+      var << v
+    end
+    var_count = count(var)
+    var_count.sort_by{|key,_value|key}.to_h
+  end
+
+end

data/lib/viral_seq/refseq.rb

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+# viral_seq/refseq.rb
+# store constants of reference sequences
+
+# sequence of HIV-1 HXB2 (Genbank accession number K03455)
+# https://www.ncbi.nlm.nih.gov/nuccore/K03455
+
+# sequence of for HIV-1 NL43 (Genbank accession number AF324493)
+# https://www.ncbi.nlm.nih.gov/nuccore/AF324493
+
+# sequence of SIV MAC239 (Genbank accession number M33262)
+# https://www.ncbi.nlm.nih.gov/nucleotide/M33262
+
+# ViralSeq::HXB2
+# ViralSeq::NL43
+# ViralSeq::MAC239
+# ViralSeq::check_ref
+
+module ViralSeq
+  HXB2 = "TGGAAGGGCTAATTCACTCCCAACGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTAGCAGAACTACACACCAGGGCCAGGGATCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGAGAAGTTAGAAGAAGCCAACAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGAATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACATGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCAGTGGCGCCCGAACAGGGACCTGAAAGCGAAAGGGAAACCAGAGGAGCTCTCTCGACGCAGGACTCGGCTTGCTGAAGCGCGCACGGCAAGAGGCGAGGGGCGGCGACTGGTGAGTACGCCAAAAATTTTGACTAGCGGAGGCTAGAAGGAGAGAGATGGGTGCGAGAGCGTCAGTATTAAGCGGGGGAGAATTAGATCGATGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAATTAAAACATATAGTATGGGCAAGCAGGGAGCTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATACTGGGACAGCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAGATCATTATATAATACAGTAGCAACCCTCTATTGTGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGACAAGATAGAGGAAGAGCAAAACAAAAGTAAGAAAAAAGCACAGCAAGCAGCAGCTGACACAGGACACAGCAATCAGGTCAGCCAAAATTACCCTATAGTGCAGAACATCCAGGGGCAAATGGTACATCAGGCCATATCACCTAGAACTTTAAATGCATGGGTAAAAGTAGTAGAAGAGAAGGCTTTCAGCCCAGAAGTGATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAACACCATGCTAAACACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGAGACCATCAATGAGGAAGCTGCAGAATGGGATAGAGTGCATCCAGTGCATGCAGGGCCTATTGCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTACTAGTACCCTTCAGGAACAAATAGGATGGATGACAAATAATCCACCTATCCCAGTAGGAGAAATTTATAAAAGATGGATAATCCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTACCAGCATTCTGGACATAAGACAAGGACCAAAGGAACCCTTTAGAGACTATGTAGACCGGTTCTATAAAACTCTAAGAGCCGAGCAAGCTTCACAGGAGGTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAGACTATTTTAAAAGCATTGGGACCAGCGGCTACACTAGAAGAAATGATGACAGCATGTCAGGGAGTAGGAGGACCCGGCCATAAGGCAAGAGTTTTGGCTGAAGCAATGAGCCAAGTAACAAATTCAGCTACCATAATGATGCAGAGAGGCAATTTTAGGAACCAAAGAAAGATTGTTAAGTGTTTCAATTGTGGCAAAGAAGGGCACACAGCCAGAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGAAAGGAAGGACACCAAATGAAAGATTGTACTGAGAGACAGGCTAATTTTTTAGGGAAGATCTGGCCTTCCTACAAGGGAAGGCCAGGGAATTTTCTTCAGAGCAGACCAGAGCCAACAGCCCCACCAGAAGAGAGCTTCAGGTCTGGGGTAGAGACAACAACTCCCCCTCAGAAGCAGGAGCCGATAGACAAGGAACTGTATCCTTTAACTTCCCTCAGGTCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAGGAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAGTTTGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGATCAGATACTCATAGAAATCTGTGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACACCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTTTAAATTTTCCCATTAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGACTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGCAAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAACTCCTTAGAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACAATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACATGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCATAGTAGGAGCAGAAACCTTCTATGTAGATGGGGCAGCTAACAGGGAGACTAAATTAGGAAAAGCAGGATATGTTACTAATAGAGGAAGACAAAAAGTTGTCACCCTAACTGACACAACAAATCAGAAGACTGAGTTACAAGCAATTTATCTAGCTTTGCAGGATTCGGGATTAGAAGTAAACATAGTAACAGACTCACAATATGCATTAGGAATCATTCAAGCACAACCAGATCAAAGTGAATCAGAGTTAGTCAATCAAATAATAGAGCAGTTAATAAAAAAGGAAAAGGTCTATCTGGCATGGGTACCAGCACACAAAGGAATTGGAGGAAATGAACAAGTAGATAAATTAGTCAGTGCTGGAATCAGGAAAGTACTATTTTTAGATGGAATAGATAAGGCCCAAGATGAACATGAGAAATATCACAGTAATTGGAGAGCAATGGCTAGTGATTTTAACCTGCCACCTGTAGTAGCAAAAGAAATAGTAGCCAGCTGTGATAAATGTCAGCTAAAAGGAGAAGCCATGCATGGACAAGTAGACTGTAGTCCAGGAATATGGCAACTAGATTGTACACATTTAGAAGGAAAAGTTATCCTGGTAGCAGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCAGAAACAGGGCAGGAAACAGCATATTTTCTTTTAAAATTAGCAGGAAGATGGCCAGTAAAAACAATACATACTGACAATGGCAGCAATTTCACCGGTGCTACGGTTAGGGCCGCCTGTTGGTGGGCGGGAATCAAGCAGGAATTTGGAATTCCCTACAATCCCCAAAGTCAAGGAGTAGTAGAATCTATGAATAAAGAATTAAAGAAAATTATAGGACAGGTAAGAGATCAGGCTGAACATCTTAAGACAGCAGTACAAATGGCAGTATTCATCCACAATTTTAAAAGAAAAGGGGGGATTGGGGGGTACAGTGCAGGGGAAAGAATAGTAGACATAATAGCAACAGACATACAAACTAAAGAATTACAAAAACAAATTACAAAAATTCAAAATTTTCGGGTTTATTACAGGGACAGCAGAAATCCACTTTGGAAAGGACCAGCAAAGCTCCTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACATAAAAGTAGTGCCAAGAAGAAAAGCAAAGATCATTAGGGATTATGGAAAACAGATGGCAGGTGATGATTGTGTGGCAAGTAGACAGGATGAGGATTAGAACATGGAAAAGTTTAGTAAAACACCATATGTATGTTTCAGGGAAAGCTAGGGGATGGTTTTATAGACATCACTATGAAAGCCCTCATCCAAGAATAAGTTCAGAAGTACACATCCCACTAGGGGATGCTAGATTGGTAATAACAACATATTGGGGTCTGCATACAGGAGAAAGAGACTGGCATTTGGGTCAGGGAGTCTCCATAGAATGGAGGAAAAAGAGATATAGCACACAAGTAGACCCTGAACTAGCAGACCAACTAATTCATCTGTATTACTTTGACTGTTTTTCAGACTCTGCTATAAGAAAGGCCTTATTAGGACACATAGTTAGCCCTAGGTGTGAATATCAAGCAGGACATAACAAGGTAGGATCTCTACAATACTTGGCACTAGCAGCATTAATAACACCAAAAAAGATAAAGCCACCTTTGCCTAGTGTTACGAAACTGACAGAGGATAGATGGAACAAGCCCCAGAAGACCAAGGGCCACAGAGGGAGCCACACAATGAATGGACACTAGAGCTTTTAGAGGAGCTTAAGAATGAAGCTGTTAGACATTTTCCTAGGATTTGGCTCCATGGCTTAGGGCAACATATCTATGAAACTTATGGGGATACTTGGGCAGGAGTGGAAGCCATAATAAGAATTCTGCAACAACTGCTGTTTATCCATTTTCAGAATTGGGTGTCGACATAGCAGAATAGGCGTTACTCGACAGAGGAGAGCAAGAAATGGAGCCAGTAGATCCTAGACTAGAGCCCTGGAAGCATCCAGGAAGTCAGCCTAAAACTGCTTGTACCAATTGCTATTGTAAAAAGTGTTGCTTTCATTGCCAAGTTTGTTTCATAACAAAAGCCTTAGGCATCTCCTATGGCAGGAAGAAGCGGAGACAGCGACGAAGAGCTCATCAGAACAGTCAGACTCATCAAGCTTCTCTATCAAAGCAGTAAGTAGTACATGTAACGCAACCTATACCAATAGTAGCAATAGTAGCATTAGTAGTAGCAATAATAATAGCAATAGTTGTGTGGTCCATAGTAATCATAGAATATAGGAAAATATTAAGACAAAGAAAAATAGACAGGTTAATTGATAGACTAATAGAAAGAGCAGAAGACAGTGGCAATGAGAGTGAAGGAGAAATATCAGCACTTGTGGAGATGGGGGTGGAGATGGGGCACCATGCTCCTTGGGATGTTGATGATCTGTAGTGCTACAGAAAAATTGTGGGTCACAGTCTATTATGGGGTACCTGTGTGGAAGGAAGCAACCACCACTCTATTTTGTGCATCAGATGCTAAAGCATATGATACAGAGGTACATAATGTTTGGGCCACACATGCCTGTGTACCCACAGACCCCAACCCACAAGAAGTAGTATTGGTAAATGTGACAGAAAATTTTAACATGTGGAAAAATGACATGGTAGAACAGATGCATGAGGATATAATCAGTTTATGGGATCAAAGCCTAAAGCCATGTGTAAAATTAACCCCACTCTGTGTTAGTTTAAAGTGCACTGATTTGAAGAATGATACTAATACCAATAGTAGTAGCGGGAGAATGATAATGGAGAAAGGAGAGATAAAAAACTGCTCTTTCAATATCAGCACAAGCATAAGAGGTAAGGTGCAGAAAGAATATGCATTTTTTTATAAACTTGATATAATACCAATAGATAATGATACTACCAGCTATAAGTTGACAAGTTGTAACACCTCAGTCATTACACAGGCCTGTCCAAAGGTATCCTTTGAGCCAATTCCCATACATTATTGTGCCCCGGCTGGTTTTGCGATTCTAAAATGTAATAATAAGACGTTCAATGGAACAGGACCATGTACAAATGTCAGCACAGTACAATGTACACATGGAATTAGGCCAGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAGAGGTAGTAATTAGATCTGTCAATTTCACGGACAATGCTAAAACCATAATAGTACAGCTGAACACATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGAATCCGTATCCAGAGAGGACCAGGGAGAGCATTTGTTACAATAGGAAAAATAGGAAATATGAGACAAGCACATTGTAACATTAGTAGAGCAAAATGGAATAACACTTTAAAACAGATAGCTAGCAAATTAAGAGAACAATTTGGAAATAATAAAACAATAATCTTTAAGCAATCCTCAGGAGGGGACCCAGAAATTGTAACGCACAGTTTTAATTGTGGAGGGGAATTTTTCTACTGTAATTCAACACAACTGTTTAATAGTACTTGGTTTAATAGTACTTGGAGTACTGAAGGGTCAAATAACACTGAAGGAAGTGACACAATCACCCTCCCATGCAGAATAAAACAAATTATAAACATGTGGCAGAAAGTAGGAAAAGCAATGTATGCCCCTCCCATCAGTGGACAAATTAGATGTTCATCAAATATTACAGGGCTGCTATTAACAAGAGATGGTGGTAATAGCAACAATGAGTCCGAGATCTTCAGACCTGGAGGAGGAGATATGAGGGACAATTGGAGAAGTGAATTATATAAATATAAAGTAGTAAAAATTGAACCATTAGGAGTAGCACCCACCAAGGCAAAGAGAAGAGTGGTGCAGAGAGAAAAAAGAGCAGTGGGAATAGGAGCTTTGTTCCTTGGGTTCTTGGGAGCAGCAGGAAGCACTATGGGCGCAGCCTCAATGACGCTGACGGTACAGGCCAGACAATTATTGTCTGGTATAGTGCAGCAGCAGAACAATTTGCTGAGGGCTATTGAGGCGCAACAGCATCTGTTGCAACTCACAGTCTGGGGCATCAAGCAGCTCCAGGCAAGAATCCTGGCTGTGGAAAGATACCTAAAGGATCAACAGCTCCTGGGGATTTGGGGTTGCTCTGGAAAACTCATTTGCACCACTGCTGTGCCTTGGAATGCTAGTTGGAGTAATAAATCTCTGGAACAGATTTGGAATCACACGACCTGGATGGAGTGGGACAGAGAAATTAACAATTACACAAGCTTAATACACTCCTTAATTGAAGAATCGCAAAACCAGCAAGAAAAGAATGAACAAGAATTATTGGAATTAGATAAATGGGCAAGTTTGTGGAATTGGTTTAACATAACAAATTGGCTGTGGTATATAAAATTATTCATAATGATAGTAGGAGGCTTGGTAGGTTTAAGAATAGTTTTTGCTGTACTTTCTATAGTGAATAGAGTTAGGCAGGGATATTCACCATTATCGTTTCAGACCCACCTCCCAACCCCGAGGGGACCCGACAGGCCCGAAGGAATAGAAGAAGAAGGTGGAGAGAGAGACAGAGACAGATCCATTCGATTAGTGAACGGATCCTTGGCACTTATCTGGGACGATCTGCGGAGCCTGTGCCTCTTCAGCTACCACCGCTTGAGAGACTTACTCTTGATTGTAACGAGGATTGTGGAACTTCTGGGACGCAGGGGGTGGGAAGCCCTCAAATATTGGTGGAATCTCCTACAGTATTGGAGTCAGGAACTAAAGAATAGTGCTGTTAGCTTGCTCAATGCCACAGCCATAGCAGTAGCTGAGGGGACAGATAGGGTTATAGAAGTAGTACAAGGAGCTTGTAGAGCTATTCGCCACATACCTAGAAGAATAAGACAGGGCTTGGAAAGGATTTTGCTATAAGATGGGTGGCAAGTGGTCAAAAAGTAGTGTGATTGGATGGCCTACTGTAAGGGAAAGAATGAGACGAGCTGAGCCAGCAGCAGATAGGGTGGGAGCAGCATCTCGAGACCTGGAAAAACATGGAGCAATCACAAGTAGCAATACAGCAGCTACCAATGCTGCTTGTGCCTGGCTAGAAGCACAAGAGGAGGAGGAGGTGGGTTTTCCAGTCACACCTCAGGTACCTTTAAGACCAATGACTTACAAGGCAGCTGTAGATCTTAGCCACTTTTTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCACTCCCAAAGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTAGCAGAACTACACACCAGGGCCAGGGGTCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGATAAGATAGAAGAGGCCAATAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGGATGGATGACCCGGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACGTGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATCCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCA"
+
+  NL43 = "TGGAAGGGCTAATTTGGTCCCAAAAAAGACAAGAGATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTGGCAGAACTACACACCAGGGCCAGGGATCAGATATCCACTGACCTTTGGATGGTGCTTCAAGTTAGTACCAGTTGAACCAGAGCAAGTAGAAGAGGCCAAATAAGGAGAGAAGAACAGCTTGTTACACCCTATGAGCCAGCATGGGATGGAGGACCCGGAGGGAGAAGTATTAGTGTGGAAGTTTGACAGCCTCCTAGCATTTCGTCACATGGCCCGAGAGCTGCATCCGGAGTACTACAAAGACTGCTGACATCGAGCTTTCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGTGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATGCTACATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTCAAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCAGTGGCGCCCGAACAGGGACTTGAAAGCGAAAGTAAAGCCAGAGGAGATCTCTCGACGCAGGACTCGGCTTGCTGAAGCGCGCACGGCAAGAGGCGAGGGGCGGCGACTGGTGAGTACGCCAAAAATTTTGACTAGCGGAGGCTAGAAGGAGAGAGATGGGTGCGAGAGCGTCGGTATTAAGCGGGGGAGAATTAGATAAATGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAACAATATAAACTAAAACATATAGTATGGGCAAGCAGGGAGCTAGAACGATTCGCAGTTAATCCTGGCCTTTTAGAGACATCAGAAGGCTGTAGACAAATACTGGGACAGCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAGATCATTATATAATACAATAGCAGTCCTCTATTGTGTGCATCAAAGGATAGATGTAAAAGACACCAAGGAAGCCTTAGATAAGATAGAGGAAGAGCAAAACAAAAGTAAGAAAAAGGCACAGCAAGCAGCAGCTGACACAGGAAACAACAGCCAGGTCAGCCAAAATTACCCTATAGTGCAGAACCTCCAGGGGCAAATGGTACATCAGGCCATATCACCTAGAACTTTAAATGCATGGGTAAAAGTAGTAGAAGAGAAGGCTTTCAGCCCAGAAGTAATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACAAGATTTAAATACCATGCTAAACACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGAGACCATCAATGAGGAAGCTGCAGAATGGGATAGATTGCATCCAGTGCATGCAGGGCCTATTGCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTACTAGTACCCTTCAGGAACAAATAGGATGGATGACACATAATCCACCTATCCCAGTAGGAGAAATCTATAAAAGATGGATAATCCTGGGATTAAATAAAATAGTAAGAATGTATAGCCCTACCAGCATTCTGGACATAAGACAAGGACCAAAGGAACCCTTTAGAGACTATGTAGACCGATTCTATAAAACTCTAAGAGCCGAGCAAGCTTCACAAGAGGTAAAAAATTGGATGACAGAAACCTTGTTGGTCCAAAATGCGAACCCAGATTGTAAGACTATTTTAAAAGCATTGGGACCAGGAGCGACACTAGAAGAAATGATGACAGCATGTCAGGGAGTGGGGGGACCCGGCCATAAAGCAAGAGTTTTGGCTGAAGCAATGAGCCAAGTAACAAATCCAGCTACCATAATGATACAGAAAGGCAATTTTAGGAACCAAAGAAAGACTGTTAAGTGTTTCAATTGTGGCAAAGAAGGGCACATAGCCAAAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGAAAGGAAGGACACCAAATGAAAGATTGTACTGAGAGACAGGCTAATTTTTTAGGGAAGATCTGGCCTTCCCACAAGGGAAGGCCAGGGAATTTTCTTCAGAGCAGACCAGAGCCAACAGCCCCACCAGAAGAGAGCTTCAGGTTTGGGGAAGAGACAACAACTCCCTCTCAGAAGCAGGAGCCGATAGACAAGGAACTGTATCCTTTAGCTTCCCTCAGATCACTCTTTGGCAGCGACCCCTCGTCACAATAAAGATAGGGGGGCAATTAAAGGAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAATTTGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGATCAGATACTCATAGAAATCTGCGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACACCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGCTGCACTTTAAATTTTCCCATTAGTCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAAATGGAAAAGGAAGGAAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGATTTCTGGGAAGTTCAATTAGGAATACCACATCCTGCAGGGTTAAAACAGAAAAAATCAGTAACAGTACTGGATGTGGGCGATGCATATTTTTCAGTTCCCTTAGATAAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAGTGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTCATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAACTGAGACAACATCTGTTGAGGTGGGGATTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAGGACAGCTGGACTGTCAATGACATACAGAAATTAGTGGGAAAATTGAATTGGGCAAGTCAGATTTATGCAGGGATTAAAGTAAGGCAATTATGTAAACTTCTTAGGGGAACCAAAGCACTAACAGAAGTAGTACCACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGGGAGATTCTAAAAGAACCGGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAAGGGTGCCCACACTAATGATGTGAAACAATTAACAGAGGCAGTACAAAAAATAGCCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAATTACCCATACAAAAGGAAACATGGGAAGCATGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTCAATACCCCTCCCTTAGTGAAGTTATGGTACCAGTTAGAGAAAGAACCCATAATAGGAGCAGAAACTTTCTATGTAGATGGGGCAGCCAATAGGGAAACTAAATTAGGAAAAGCAGGATATGTAACTGACAGAGGAAGACAAAAAGTTGTCCCCCTAACGGACACAACAAATCAGAAGACTGAGTTACAAGCAATTCATCTAGCTTTGCAGGATTCGGGATTAGAAGTAAACATAGTGACAGACTCACAATATGCATTGGGAATCATTCAAGCACAACCAGATAAGAGTGAATCAGAGTTAGTCAGTCAAATAATAGAGCAGTTAATAAAAAAGGAAAAAGTCTACCTGGCATGGGTACCAGCACACAAAGGAATTGGAGGAAATGAACAAGTAGATGGGTTGGTCAGTGCTGGAATCAGGAAAGTACTATTTTTAGATGGAATAGATAAGGCCCAAGAAGAACATGAGAAATATCACAGTAATTGGAGAGCAATGGCTAGTGATTTTAACCTACCACCTGTAGTAGCAAAAGAAATAGTAGCCAGCTGTGATAAATGTCAGCTAAAAGGGGAAGCCATGCATGGACAAGTAGACTGTAGCCCAGGAATATGGCAGCTAGATTGTACACATTTAGAAGGAAAAGTTATCTTGGTAGCAGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTAATTCCAGCAGAGACAGGGCAAGAAACAGCATACTTCCTCTTAAAATTAGCAGGAAGATGGCCAGTAAAAACAGTACATACAGACAATGGCAGCAATTTCACCAGTACTACAGTTAAGGCCGCCTGTTGGTGGGCGGGGATCAAGCAGGAATTTGGCATTCCCTACAATCCCCAAAGTCAAGGAGTAATAGAATCTATGAATAAAGAATTAAAGAAAATTATAGGACAGGTAAGAGATCAGGCTGAACATCTTAAGACAGCAGTACAAATGGCAGTATTCATCCACAATTTTAAAAGAAAAGGGGGGATTGGGGGGTACAGTGCAGGGGAAAGAATAGTAGACATAATAGCAACAGACATACAAACTAAAGAATTACAAAAACAAATTACAAAAATTCAAAATTTTCGGGTTTATTACAGGGACAGCAGAGATCCAGTTTGGAAAGGACCAGCAAAGCTCCTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACATAAAAGTAGTGCCAAGAAGAAAAGCAAAGATCATCAGGGATTATGGAAAACAGATGGCAGGTGATGATTGTGTGGCAAGTAGACAGGATGAGGATTAACACATGGAAAAGATTAGTAAAACACCATATGTATATTTCAAGGAAAGCTAAGGACTGGTTTTATAGACATCACTATGAAAGTACTAATCCAAAAATAAGTTCAGAAGTACACATCCCACTAGGGGATGCTAAATTAGTAATAACAACATATTGGGGTCTGCATACAGGAGAAAGAGACTGGCATTTGGGTCAGGGAGTCTCCATAGAATGGAGGAAAAAGAGATATAGCACACAAGTAGACCCTGACCTAGCAGACCAACTAATTCATCTGCACTATTTTGATTGTTTTTCAGAATCTGCTATAAGAAATACCATATTAGGACGTATAGTTAGTCCTAGGTGTGAATATCAAGCAGGACATAACAAGGTAGGATCTCTACAGTACTTGGCACTAGCAGCATTAATAAAACCAAAACAGATAAAGCCACCTTTGCCTAGTGTTAGGAAACTGACAGAGGACAGATGGAACAAGCCCCAGAAGACCAAGGGCCACAGAGGGAGCCATACAATGAATGGACACTAGAGCTTTTAGAGGAACTTAAGAGTGAAGCTGTTAGACATTTTCCTAGGATATGGCTCCATAACTTAGGACAACATATCTATGAAACTTACGGGGATACTTGGGCAGGAGTGGAAGCCATAATAAGAATTCTGCAACAACTGCTGTTTATCCATTTCAGAATTGGGTGTCGACATAGCAGAATAGGCGTTACTCGACAGAGGAGAGCAAGAAATGGAGCCAGTAGATCCTAGACTAGAGCCCTGGAAGCATCCAGGAAGTCAGCCTAAAACTGCTTGTACCAATTGCTATTGTAAAAAGTGTTGCTTTCATTGCCAAGTTTGTTTCATGACAAAAGCCTTAGGCATCTCCTATGGCAGGAAGAAGCGGAGACAGCGACGAAGAGCTCATCAGAACAGTCAGACTCATCAAGCTTCTCTATCAAAGCAGTAAGTAGTACATGTAATGCAACCTATAATAGTAGCAATAGTAGCATTAGTAGTAGCAATAATAATAGCAATAGTTGTGTGGTCCATAGTAATCATAGAATATAGGAAAATATTAAGACAAAGAAAAATAGACAGGTTAATTGATAGACTAATAGAAAGAGCAGAAGACAGTGGCAATGAGAGTGAAGGAGAAGTATCAGCACTTGTGGAGATGGGGGTGGAAATGGGGCACCATGCTCCTTGGGATATTGATGATCTGTAGTGCTACAGAAAAATTGTGGGTCACAGTCTATTATGGGGTACCTGTGTGGAAGGAAGCAACCACCACTCTATTTTGTGCATCAGATGCTAAAGCATATGATACAGAGGTACATAATGTTTGGGCCACACATGCCTGTGTACCCACAGACCCCAACCCACAAGAAGTAGTATTGGTAAATGTGACAGAAAATTTTAACATGTGGAAAAATGACATGGTAGAACAGATGCATGAGGATATAATCAGTTTATGGGATCAAAGCCTAAAGCCATGTGTAAAATTAACCCCACTCTGTGTTAGTTTAAAGTGCACTGATTTGAAGAATGATACTAATACCAATAGTAGTAGCGGGAGAATGATAATGGAGAAAGGAGAGATAAAAAACTGCTCTTTCAATATCAGCACAAGCATAAGAGATAAGGTGCAGAAAGAATATGCATTCTTTTATAAACTTGATATAGTACCAATAGATAATACCAGCTATAGGTTGATAAGTTGTAACACCTCAGTCATTACACAGGCCTGTCCAAAGGTATCCTTTGAGCCAATTCCCATACATTATTGTGCCCCGGCTGGTTTTGCGATTCTAAAATGTAATAATAAGACGTTCAATGGAACAGGACCATGTACAAATGTCAGCACAGTACAATGTACACATGGAATCAGGCCAGTAGTATCAACTCAACTGCTGTTAAATGGCAGTCTAGCAGAAGAAGATGTAGTAATTAGATCTGCCAATTTCACAGACAATGCTAAAACCATAATAGTACAGCTGAACACATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATCCGTATCCAGAGGGGACCAGGGAGAGCATTTGTTACAATAGGAAAAATAGGAAATATGAGACAAGCACATTGTAACATTAGTAGAGCAAAATGGAATGCCACTTTAAAACAGATAGCTAGCAAATTAAGAGAACAATTTGGAAATAATAAAACAATAATCTTTAAGCAATCCTCAGGAGGGGACCCAGAAATTGTAACGCACAGTTTTAATTGTGGAGGGGAATTTTTCTACTGTAATTCAACACAACTGTTTAATAGTACTTGGTTTAATAGTACTTGGAGTACTGAAGGGTCAAATAACACTGAAGGAAGTGACACAATCACACTCCCATGCAGAATAAAACAATTTATAAACATGTGGCAGGAAGTAGGAAAAGCAATGTATGCCCCTCCCATCAGTGGACAAATTAGATGTTCATCAAATATTACTGGGCTGCTATTAACAAGAGATGGTGGTAATAACAACAATGGGTCCGAGATCTTCAGACCTGGAGGAGGCGATATGAGGGACAATTGGAGAAGTGAATTATATAAATATAAAGTAGTAAAAATTGAACCATTAGGAGTAGCACCCACCAAGGCAAAGAGAAGAGTGGTGCAGAGAGAAAAAAGAGCAGTGGGAATAGGAGCTTTGTTCCTTGGGTTCTTGGGAGCAGCAGGAAGCACTATGGGCTGCACGTCAATGACGCTGACGGTACAGGCCAGACAATTATTGTCTGATATAGTGCAGCAGCAGAACAATTTGCTGAGGGCTATTGAGGCGCAACAGCATCTGTTGCAACTCACAGTCTGGGGCATCAAACAGCTCCAGGCAAGAATCCTGGCTGTGGAAAGATACCTAAAGGATCAACAGCTCCTGGGGATTTGGGGTTGCTCTGGAAAACTCATTTGCACCACTGCTGTGCCTTGGAATGCTAGTTGGAGTAATAAATCTCTGGAACAGATTTGGAATAACATGACCTGGATGGAGTGGGACAGAGAAATTAACAATTACACAAGCTTAATACACTCCTTAATTGAAGAATCGCAAAACCAGCAAGAAAAGAATGAACAAGAATTATTGGAATTAGATAAATGGGCAAGTTTGTGGAATTGGTTTAACATAACAAATTGGCTGTGGTATATAAAATTATTCATAATGATAGTAGGAGGCTTGGTAGGTTTAAGAATAGTTTTTGCTGTACTTTCTATAGTGAATAGAGTTAGGCAGGGATATTCACCATTATCGTTTCAGACCCACCTCCCAATCCCGAGGGGACCCGACAGGCCCGAAGGAATAGAAGAAGAAGGTGGAGAGAGAGACAGAGACAGATCCATTCGATTAGTGAACGGATCCTTAGCACTTATCTGGGACGATCTGCGGAGCCTGTGCCTCTTCAGCTACCACCGCTTGAGAGACTTACTCTTGATTGTAACGAGGATTGTGGAACTTCTGGGACGCAGGGGGTGGGAAGCCCTCAAATATTGGTGGAATCTCCTACAGTATTGGAGTCAGGAACTAAAGAATAGTGCTGTTAACTTGCTCAATGCCACAGCCATAGCAGTAGCTGAGGGGACAGATAGGGTTATAGAAGTATTACAAGCAGCTTATAGAGCTATTCGCCACATACCTAGAAGAATAAGACAGGGCTTGGAAAGGATTTTGCTATAAGATGGGTGGCAAGTGGTCAAAAAGTAGTGTGATTGGATGGCCTGCTGTAAGGGAAAGAATGAGACGAGCTGAGCCAGCAGCAGATGGGGTGGGAGCAGTATCTCGAGACCTAGAAAAACATGGAGCAATCACAAGTAGCAATACAGCAGCTAACAATGCTGCTTGTGCCTGGCTAGAAGCACAAGAGGAGGAAGAGGTGGGTTTTCCAGTCACACCTCAGGTACCTTTAAGACCAATGACTTACAAGGCAGCTGTAGATCTTAGCCACTTTTTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCACTCCCAAAGAAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTGGCAGAACTACACACCAGGGCCAGGGGTCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGATAAGGTAGAAGAGGCCAATAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGAATGGATGACCCTGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACGTGGCCCGAGAGCTGCATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATGCTGCATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCA"
+
+  MAC239 = "GCATGCACATTTTAAAGGCTTTTGCTAAATATAGCCAAAAGTCCTTCTACAAATTTTCTAAGAGTTCTGATTCAAAGCAGTAACAGGCCTTGTCTCATCATGAACTTTGGCATTTCATCTACAGCTAAGTTTATATCATAAATAGTTCTTTACAGGCAGCACCAACTTATACCCTTATAGCATACTTTACTGTGTGAAAATTGCATCTTTCATTAAGCTTACTGTAAATTTACTGGCTGTCTTCCTTGCAGGTTTCTGGAAGGGATTTATTACAGTGCAAGAAGACATAGAATCTTAGACATATACTTAGAAAAGGAAGAAGGCATCATACCAGATTGGCAGGATTACACCTCAGGACCAGGAATTAGATACCCAAAGACATTTGGCTGGCTATGGAAATTAGTCCCTGTAAATGTATCAGATGAGGCACAGGAGGATGAGGAGCATTATTTAATGCATCCAGCTCAAACTTCCCAGTGGGATGACCCTTGGGGAGAGGTTCTAGCATGGAAGTTTGATCCAACTCTGGCCTACACTTATGAGGCATATGTTAGATACCCAGAAGAGTTTGGAAGCAAGTCAGGCCTGTCAGAGGAAGAGGTTAGAAGAAGGCTAACCGCAAGAGGCCTTCTTAACATGGCTGACAAGAAGGAAACTCGCTGAAACAGCAGGGACTTTCCACAAGGGGATGTTACGGGGAGGTACTGGGGAGGAGCCGGTCGGGAACGCCCACTTTCTTGATGTATAAATATCACTGCATTTCGCTCTGTATTCAGTCGCTCTGCGGAGAGGCTGGCAGATTGAGCCCTGGGAGGTTCTCTCCAGCACTAGCAGGTAGAGCCTGGGTGTTCCCTGCTAGACTCTCACCAGCACTTGGCCGGTGCTGGGCAGAGTGACTCCACGCTTGCTTGCTTAAAGCCCTCTTCAATAAAGCTGCCATTTTAGAAGTAAGCTAGTGTGTGTTCCCATCTCTCCTAGCCGCCGCCTGGTCAACTCGGTACTCAATAATAAGAAGACCCTGGTCTGTTAGGACCCTTTCTGCTTTGGGAAACCGAAGCAGGAAAATCCCTAGCAGATTGGCGCCTGAACAGGGACTTGAAGGAGAGTGAGAGACTCCTGAGTACGGCTGAGTGAAGGCAGTAAGGGCGGCAGGAACCAACCACGACGGAGTGCTCCTATAAAGGCGCGGGTCGGTACCAGACGGCGTGAGGAGCGGGAGAGGAAGAGGCCTCCGGTTGCAGGTAAGTGCAACACAAAAAAGAAATAGCTGTCTTTTATCCAGGAAGGGGTAATAAGATAGAGTGGGAGATGGGCGTGAGAAACTCCGTCTTGTCAGGGAAGAAAGCAGATGAATTAGAAAAAATTAGGCTACGACCCAACGGAAAGAAAAAGTACATGTTGAAGCATGTAGTATGGGCAGCAAATGAATTAGATAGATTTGGATTAGCAGAAAGCCTGTTGGAGAACAAAGAAGGATGTCAAAAAATACTTTCGGTCTTAGCTCCATTAGTGCCAACAGGCTCAGAAAATTTAAAAAGCCTTTATAATACTGTCTGCGTCATCTGGTGCATTCACGCAGAAGAGAAAGTGAAACACACTGAGGAAGCAAAACAGATAGTGCAGAGACACCTAGTGGTGGAAACAGGAACAACAGAAACTATGCCAAAAACAAGTAGACCAACAGCACCATCTAGCGGCAGAGGAGGAAATTACCCAGTACAACAAATAGGTGGTAACTATGTCCACCTGCCATTAAGCCCGAGAACATTAAATGCCTGGGTAAAATTGATAGAGGAAAAGAAATTTGGAGCAGAAGTAGTGCCAGGATTTCAGGCACTGTCAGAAGGTTGCACCCCCTATGACATTAATCAGATGTTAAATTGTGTGGGAGACCATCAAGCGGCTATGCAGATTATCAGAGATATTATAAACGAGGAGGCTGCAGATTGGGACTTGCAGCACCCACAACCAGCTCCACAACAAGGACAACTTAGGGAGCCGTCAGGATCAGATATTGCAGGAACAACTAGTTCAGTAGATGAACAAATCCAGTGGATGTACAGACAACAGAACCCCATACCAGTAGGCAACATTTACAGGAGATGGATCCAACTGGGGTTGCAAAAATGTGTCAGAATGTATAACCCAACAAACATTCTAGATGTAAAACAAGGGCCAAAAGAGCCATTTCAGAGCTATGTAGACAGGTTCTACAAAAGTTTAAGAGCAGAACAGACAGATGCAGCAGTAAAGAATTGGATGACTCAAACACTGCTGATTCAAAATGCTAACCCAGATTGCAAGCTAGTGCTGAAGGGGCTGGGTGTGAATCCCACCCTAGAAGAAATGCTGACGGCTTGTCAAGGAGTAGGGGGGCCGGGACAGAAGGCTAGATTAATGGCAGAAGCCCTGAAAGAGGCCCTCGCACCAGTGCCAATCCCTTTTGCAGCAGCCCAACAGAGGGGACCAAGAAAGCCAATTAAGTGTTGGAATTGTGGGAAAGAGGGACACTCTGCAAGGCAATGCAGAGCCCCAAGAAGACAGGGATGCTGGAAATGTGGAAAAATGGACCATGTTATGGCCAAATGCCCAGACAGACAGGCGGGTTTTTTAGGCCTTGGTCCATGGGGAAAGAAGCCCCGCAATTTCCCCATGGCTCAAGTGCATCAGGGGCTGATGCCAACTGCTCCCCCAGAGGACCCAGCTGTGGATCTGCTAAAGAACTACATGCAGTTGGGCAAGCAGCAGAGAGAAAAGCAGAGAGAAAGCAGAGAGAAGCCTTACAAGGAGGTGACAGAGGATTTGCTGCACCTCAATTCTCTCTTTGGAGGAGACCAGTAGTCACTGCTCATATTGAAGGACAGCCTGTAGAAGTATTACTGGATACAGGGGCTGATGATTCTATTGTAACAGGAATAGAGTTAGGTCCACATTATACCCCAAAAATAGTAGGAGGAATAGGAGGTTTTATTAATACTAAAGAATACAAAAATGTAGAAATAGAAGTTTTAGGCAAAAGGATTAAAGGGACAATCATGACAGGGGACACCCCGATTAACATTTTTGGTAGAAATTTGCTAACAGCTCTGGGGATGTCTCTAAATTTTCCCATAGCTAAAGTAGAGCCTGTAAAAGTCGCCTTAAAGCCAGGAAAGGATGGACCAAAATTGAAGCAGTGGCCATTATCAAAAGAAAAGATAGTTGCATTAAGAGAAATCTGTGAAAAGATGGAAAAGGATGGTCAGTTGGAGGAAGCTCCCCCGACCAATCCATACAACACCCCCACATTTGCTATAAAGAAAAAGGATAAGAACAAATGGAGAATGCTGATAGATTTTAGGGAACTAAATAGGGTCACTCAGGACTTTACGGAAGTCCAATTAGGAATACCACACCCTGCAGGACTAGCAAAAAGGAAAAGAATTACAGTACTGGATATAGGTGATGCATATTTCTCCATACCTCTAGATGAAGAATTTAGGCAGTACACTGCCTTTACTTTACCATCAGTAAATAATGCAGAGCCAGGAAAACGATACATTTATAAGGTTCTGCCTCAGGGATGGAAGGGGTCACCAGCCATCTTCCAATACACTATGAGACATGTGCTAGAACCCTTCAGGAAGGCAAATCCAGATGTGACCTTAGTCCAGTATATGGATGACATCTTAATAGCTAGTGACAGGACAGACCTGGAACATGACAGGGTAGTTTTACAGTCAAAGGAACTCTTGAATAGCATAGGGTTTTCTACCCCAGAAGAGAAATTCCAAAAAGATCCCCCATTTCAATGGATGGGGTACGAATTGTGGCCAACAAAATGGAAGTTGCAAAAGATAGAGTTGCCACAAAGAGAGACCTGGACAGTGAATGATATACAGAAGTTAGTAGGAGTATTAAATTGGGCAGCTCAAATTTATCCAGGTATAAAAACCAAACATCTCTGTAGGTTAATTAGAGGAAAAATGACTCTAACAGAGGAAGTTCAGTGGACTGAGATGGCAGAAGCAGAATATGAGGAAAATAAAATAATTCTCAGTCAGGAACAAGAAGGATGTTATTACCAAGAAGGCAAGCCATTAGAAGCCACGGTAATAAAGAGTCAGGACAATCAGTGGTCTTATAAAATTCACCAAGAAGACAAAATACTGAAAGTAGGAAAATTTGCAAAGATAAAGAATACACATACCAATGGAGTGAGACTATTAGCACATGTAATACAGAAAATAGGAAAGGAAGCAATAGTGATCTGGGGACAGGTCCCAAAATTCCACTTACCAGTTGAGAAGGATGTATGGGAACAGTGGTGGACAGACTATTGGCAGGTAACCTGGATACCGGAATGGGATTTTATCTCAACACCACCGCTAGTAAGATTAGTCTTCAATCTAGTGAAGGACCCTATAGAGGGAGAAGAAACCTATTATACAGATGGATCATGTAATAAACAGTCAAAAGAAGGGAAAGCAGGATATATCACAGATAGGGGCAAAGACAAAGTAAAAGTGTTAGAACAGACTACTAATCAACAAGCAGAATTGGAAGCATTTCTCATGGCATTGACAGACTCAGGGCCAAAGGCAAATATTATAGTAGATTCACAATATGTTATGGGAATAATAACAGGATGCCCTACAGAATCAGAGAGCAGGCTAGTTAATCAAATAATAGAAGAAATGATTAAAAAGTCAGAAATTTATGTAGCATGGGTACCAGCACACAAAGGTATAGGAGGAAACCAAGAAATAGACCACCTAGTTAGTCAAGGGATTAGACAAGTTCTCTTCTTGGAAAAGATAGAGCCAGCACAAGAAGAACATGATAAATACCATAGTAATGTAAAAGAATTGGTATTCAAATTTGGATTACCCAGAATAGTGGCCAGACAGATAGTAGACACCTGTGATAAATGTCATCAGAAAGGAGAGGCTATACATGGGCAGGCAAATTCAGATCTAGGGACTTGGCAAATGGATTGTACCCATCTAGAGGGAAAAATAATCATAGTTGCAGTACATGTAGCTAGTGGATTCATAGAAGCAGAGGTAATTCCACAAGAGACAGGAAGACAGACAGCACTATTTCTGTTAAAATTGGCAGGCAGATGGCCTATTACACATCTACACACAGATAATGGTGCTAACTTTGCTTCGCAAGAAGTAAAGATGGTTGCATGGTGGGCAGGGATAGAGCACACCTTTGGGGTACCATACAATCCACAGAGTCAGGGAGTAGTGGAAGCAATGAATCACCACCTGAAAAATCAAATAGATAGAATCAGGGAACAAGCAAATTCAGTAGAAACCATAGTATTAATGGCAGTTCATTGCATGAATTTTAAAAGAAGGGGAGGAATAGGGGATATGACTCCAGCAGAAAGATTAATTAACATGATCACTACAGAACAAGAGATACAATTTCAACAATCAAAAAACTCAAAATTTAAAAATTTTCGGGTCTATTACAGAGAAGGCAGAGATCAACTGTGGAAGGGACCCGGTGAGCTATTGTGGAAAGGGGAAGGAGCAGTCATCTTAAAGGTAGGGACAGACATTAAGGTAGTACCCAGAAGAAAGGCTAAAATTATCAAAGATTATGGAGGAGGAAAAGAGGTGGATAGCAGTTCCCACATGGAGGATACCGGAGAGGCTAGAGAGGTGGCATAGCCTCATAAAATATCTGAAATATAAAACTAAAGATCTACAAAAGGTTTGCTATGTGCCCCATTTTAAGGTCGGATGGGCATGGTGGACCTGCAGCAGAGTAATCTTCCCACTACAGGAAGGAAGCCATTTAGAAGTACAAGGGTATTGGCATTTGACACCAGAAAAAGGGTGGCTCAGTACTTATGCAGTGAGGATAACCTGGTACTCAAAGAACTTTTGGACAGATGTAACACCAAACTATGCAGACATTTTACTGCATAGCACTTATTTCCCTTGCTTTACAGCGGGAGAAGTGAGAAGGGCCATCAGGGGAGAACAACTGCTGTCTTGCTGCAGGTTCCCGAGAGCTCATAAGTACCAGGTACCAAGCCTACAGTACTTAGCACTGAAAGTAGTAAGCGATGTCAGATCCCAGGGAGAGAATCCCACCTGGAAACAGTGGAGAAGAGACAATAGGAGAGGCCTTCGAATGGCTAAACAGAACAGTAGAGGAGATAAACAGAGAGGCGGTAAACCACCTACCAAGGGAGCTAATTTTCCAGGTTTGGCAAAGGTCTTGGGAATACTGGCATGATGAACAAGGGATGTCACCAAGCTATGTAAAATACAGATACTTGTGTTTAATACAAAAGGCTTTATTTATGCATTGCAAGAAAGGCTGTAGATGTCTAGGGGAAGGACATGGGGCAGGGGGATGGAGACCAGGACCTCCTCCTCCTCCCCCTCCAGGACTAGCATAAATGGAAGAAAGACCTCCAGAAAATGAAGGACCACAAAGGGAACCATGGGATGAATGGGTAGTGGAGGTTCTGGAAGAACTGAAAGAAGAAGCTTTAAAACATTTTGATCCTCGCTTGCTAACTGCACTTGGTAATCATATCTATAATAGACATGGAGACACCCTTGAGGGAGCAGGAGAACTCATTAGAATCCTCCAACGAGCGCTCTTCATGCATTTCAGAGGCGGATGCATCCACTCCAGAATCGGCCAACCTGGGGGAGGAAATCCTCTCTCAGCTATACCGCCCTCTAGAAGCATGCTATAACACATGCTATTGTAAAAAGTGTTGCTACCATTGCCAGTTTTGTTTTCTTAAAAAAGGCTTGGGGATATGTTATGAGCAATCACGAAAGAGAAGAAGAACTCCGAAAAAGGCTAAGGCTAATACATCTTCTGCATCAAACAAGTAAGTATGGGATGTCTTGGGAATCAGCTGCTTATCGCCATCTTGCTTTTAAGTGTCTATGGGATCTATTGTACTCTATATGTCACAGTCTTTTATGGTGTACCAGCTTGGAGGAATGCGACAATTCCCCTCTTTTGTGCAACCAAGAATAGGGATACTTGGGGAACAACTCAGTGCCTACCAGATAATGGTGATTATTCAGAAGTGGCCCTTAATGTTACAGAAAGCTTTGATGCCTGGAATAATACAGTCACAGAACAGGCAATAGAGGATGTATGGCAACTCTTTGAGACCTCAATAAAGCCTTGTGTAAAATTATCCCCATTATGCATTACTATGAGATGCAATAAAAGTGAGACAGATAGATGGGGATTGACAAAATCAATAACAACAACAGCATCAACAACATCAACGACAGCATCAGCAAAAGTAGACATGGTCAATGAGACTAGTTCTTGTATAGCCCAGGATAATTGCACAGGCTTGGAACAAGAGCAAATGATAAGCTGTAAATTCAACATGACAGGGTTAAAAAGAGACAAGAAAAAAGAGTACAATGAAACTTGGTACTCTGCAGATTTGGTATGTGAACAAGGGAATAACACTGGTAATGAAAGTAGATGTTACATGAACCACTGTAACACTTCTGTTATCCAAGAGTCTTGTGACAAACATTATTGGGATGCTATTAGATTTAGGTATTGTGCACCTCCAGGTTATGCTTTGCTTAGATGTAATGACACAAATTATTCAGGCTTTATGCCTAAATGTTCTAAGGTGGTGGTCTCTTCATGCACAAGGATGATGGAGACACAGACTTCTACTTGGTTTGGCTTTAATGGAACTAGAGCAGAAAATAGAACTTATATTTACTGGCATGGTAGGGATAATAGGACTATAATTAGTTTAAATAAGTATTATAATCTAACAATGAAATGTAGAAGACCAGGAAATAAGACAGTTTTACCAGTCACCATTATGTCTGGATTGGTTTTCCACTCACAACCAATCAATGATAGGCCAAAGCAGGCATGGTGTTGGTTTGGAGGAAAATGGAAGGATGCAATAAAAGAGGTGAAGCAGACCATTGTCAAACATCCCAGGTATACTGGAACTAACAATACTGATAAAATCAATTTGACGGCTCCTGGAGGAGGAGATCCGGAAGTTACCTTCATGTGGACAAATTGCAGAGGAGAGTTCCTCTACTGTAAAATGAATTGGTTTCTAAATTGGGTAGAAGATAGGAATACAGCTAACCAGAAGCCAAAGGAACAGCATAAAAGGAATTACGTGCCATGTCATATTAGACAAATAATCAACACTTGGCATAAAGTAGGCAAAAATGTTTATTTGCCTCCAAGAGAGGGAGACCTCACGTGTAACTCCACAGTGACCAGTCTCATAGCAAACATAGATTGGATTGATGGAAACCAAACTAATATCACCATGAGTGCAGAGGTGGCAGAACTGTATCGATTGGAATTGGGAGATTATAAATTAGTAGAGATCACTCCAATTGGCTTGGCCCCCACAGATGTGAAGAGGTACACTACTGGTGGCACCTCAAGAAATAAAAGAGGGGTCTTTGTGCTAGGGTTCTTGGGTTTTCTCGCAACGGCAGGTTCTGCAATGGGCGCGGCGTCGTTGACGCTGACCGCTCAGTCCCGAACTTTATTGGCTGGGATAGTGCAGCAACAGCAACAGCTGTTGGACGTGGTCAAGAGACAACAAGAATTGTTGCGACTGACCGTCTGGGGAACAAAGAACCTCCAGACTAGGGTCACTGCCATCGAGAAGTACTTAAAGGACCAGGCGCAGCTGAATGCTTGGGGATGTGCGTTTAGACAAGTCTGCCACACTACTGTACCATGGCCAAATGCAAGTCTAACACCAAAGTGGAACAATGAGACTTGGCAAGAGTGGGAGCGAAAGGTTGACTTCTTGGAAGAAAATATAACAGCCCTCCTAGAGGAGGCACAAATTCAACAAGAGAAGAACATGTATGAATTACAAAAGTTGAATAGCTGGGATGTGTTTGGCAATTGGTTTGACCTTGCTTCTTGGATAAAGTATATACAATATGGAGTTTATATAGTTGTAGGAGTAATACTGTTAAGAATAGTGATCTATATAGTACAAATGCTAGCTAAGTTAAGGCAGGGGTATAGGCCAGTGTTCTCTTCCCCACCCTCTTATTTCCAGCAGACCCATATCCAACAGGACCCGGCACTGCCAACCAGAGAAGGCAAAGAAAGAGACGGTGGAGAAGGCGGTGGCAACAGCTCCTGGCCTTGGCAGATAGAATATATTCATTTCCTGATCCGCCAACTGATACGCCTCTTGACTTGGCTATTCAGCAACTGCAGAACCTTGCTATCGAGAGTATACCAGATCCTCCAACCAATACTCCAGAGGCTCTCTGCGACCCTACAGAGGATTCGAGAAGTCCTCAGGACTGAACTGACCTACCTACAATATGGGTGGAGCTATTTCCATGAGGCGGTCCAGGCCGTCTGGAGATCTGCGACAGAGACTCTTGCGGGCGCGTGGGGAGACTTATGGGAGACTCTTAGGAGAGGTGGAAGATGGATACTCGCAATCCCCAGGAGGATTAGACAAGGGCTTGAGCTCACTCTCTTGTGAGGGACAGAAATACAATCAGGGACAGTATATGAATACTCCATGGAGAAACCCAGCTGAAGAGAGAGAAAAATTAGCATACAGAAAACAAAATATGGATGATATAGATGAGTAAGATGATGACTTGGTAGGGGTATCAGTGAGGCCAAAAGTTCCCCTAAGAACAATGAGTTACAAATTGGCAATAGACATGTCTCATTTTATAAAAGAAAAGGGGGGACTGGAAGGGATTTATTACAGTGCAAGAAGACATAGAATCTTAGACATATACTTAGAAAAGGAAGAAGGCATCATACCAGATTGGCAGGATTACACCTCAGGACCAGGAATTAGATACCCAAAGACATTTGGCTGGCTATGGAAATTAGTCCCTGTAAATGTATCAGATGAGGCACAGGAGGATGAGGAGCATTATTTAATGCATCCAGCTCAAACTTCCCAGTGGGATGACCCTTGGGGAGAGGTTCTAGCATGGAAGTTTGATCCAACTCTGGCCTACACTTATGAGGCATATGTTAGATACCCAGAAGAGTTTGGAAGCAAGTCAGGCCTGTCAGAGGAAGAGGTTAGAAGAAGGCTAACCGCAAGAGGCCTTCTTAACATGGCTGACAAGAAGGAAACTCGCTGAAACAGCAGGGACTTTCCACAAGGGGATGTTACGGGGAGGTACTGGGGAGGAGCCGGTCGGGAACGCCCACTTTCTTGATGTATAAATATCACTGCATTTCGCTCTGTATTCAGTCGCTCTGCGGAGAGGCTGGCAGATTGAGCCCTGGGAGGTTCTCTCCAGCACTAGCAGGTAGAGCCTGGGTGTTCCCTGCTAGACTCTCACCAGCACTTGGCCGGTGCTGGGCAGAGTGACTCCACGCTTGCTTGCTTAAAGCCCTCTTCAATAAAGCTGCCATTTTAGAAGTAAGCTAGTGTGTGTTCCCATCTCTCCTAGCCGCCGCCTGGTCAACTCGGTACTCAATAATAAGAAGACCCTGGTCTGTTAGGACCCTTTCTGCTTTGGGAAACCGAAGCAGGAAAATCCCTAGCA"
+
+
+  # check if reference option is correct, return chosen 'ref_option'
+  def self.check_ref(ref_option)
+    begin
+      case ref_option
+      when :HXB2
+        HXB2.dup
+      when :NL43
+        NL43.dup
+      when :MAC239
+        MAC239.dup
+      else
+        raise StandardError.new("reference sequence not recognized, choose from 'HXB2' (default), 'NL43', or 'MAC239'.")
+      end
+    rescue StandardError => e
+      puts e.message
+      return nil
+    end
+  end
+
+end