bio-alignment 0.0.8 → 0.0.9

checksums.yaml

@@ -0,0 +1,7 @@
+---
+SHA1:
+  metadata.gz: f485c3fa56f81dd8913f1d069611a6b3322c9826
+  data.tar.gz: 71987f39b8dbf6d1b3317395ea2b9eb427370280
+SHA512:
+  metadata.gz: 5defd20690fdd472763e04cfa8abfd1056e046474097dc1eee088773a5e575cac11dd92558bf9b0664ab6012ad8c3096938ed76572ecc5ee217267327159babf
+  data.tar.gz: b27cf7bb277b44f12b4ed8110b695c5abc0f4234fe87060c41e82d7d2c78f5907283d81de7fa7a925c6529016fd36a7c4d1cc330c9b59e37766707b9e9a2176c

data/.travis.yml

@@ -1,12 +1,3 @@
 language: ruby
 rvm:
-  - 1.9.2
-  - jruby-19mode # JRuby in 1.9 mode
-#  - 1.8.7
-#  - 1.9.3
-#  - rbx-19mode
-#  - jruby-18mode # JRuby in 1.8 mode
-#  - rbx-18mode
-
-# uncomment this line if your project needs to run something other than `rake`:
-# script: bundle exec rspec spec
+  - 2.3.1

data/Gemfile

@@ -1,14 +1,12 @@
 source "http://rubygems.org"
 gem "bio-logger"
-gem "bio", ">= 1.4.2"      # for translation tables, BioRuby compat and Newick parser
+gem "bio", ">= 1.5.0"      # for translation tables, BioRuby compat and Newick parser
 
 # Add dependencies to develop your gem here.
 # Include everything needed to run rake, tests, features, etc.
 group :development do
   gem "rake"
-  gem "bio-bigbio", "> 0.1.3"         # for reading FASTA files in tests
-  gem "cucumber", ">= 0"
-  gem "rspec", "~> 2.10.0"
-  gem "bundler", ">= 1.0.21"
-  gem "jeweler"
+  gem "bio-bigbio"         # for reading FASTA files in tests
+  gem "cucumber"
+  gem "rspec"
 end

data/LICENSE.txt

@@ -1,4 +1,4 @@
-Copyright (c) 2012 Pjotr Prins
+Copyright (c) 2012-2016 Pjotr Prins
 
 Permission is hereby granted, free of charge, to any person obtaining
 a copy of this software and associated documentation files (the

data/README.md

@@ -47,7 +47,7 @@ Remove bridges (columns with mostly gaps) from an alignment
 
     bio-alignment aa-alignment.fa --type aminoacid --edit bridges
 
-Mask islands (short misaligned 'floating' parts in a sequence) 
+Mask islands (short misaligned 'floating' parts in a sequence)
 
     coming soon...
 
@@ -56,7 +56,7 @@ Mask serial mutations
     coming soon...
 
 Remove all sequences consisting of mostly gaps (30% informative) and output to FASTA
- 
+
     bio-alignment codon-alignment.fa --type codon --edit info --out fasta
 
 or output codon style
@@ -167,7 +167,7 @@ labeled 'id?'. In the second case BioRuby's FlatFile returns a
 FastaFormat object, this time with ID, but FastaFormat does not
 support indexing. In general, it is recommended to stay with the
 bio-alignment Sequence classes (or roll your own, as long as they are
-Enumerable). 
+Enumerable).
 
 ### Pal2nal
 
@@ -228,12 +228,12 @@ alignment, and traversing the tree using an intuitive interface
   newick_tree = Bio::Newick.new(string).tree  # use BioRuby's tree parser
   tree = aln.attach_tree(newick_tree)         # attach the tree
   # now do stuff with the tree, which has improved bio-alignment support
-  root = tree.root 
+  root = tree.root
   children = root.children
   children.map { |n| n.name }.sort.should == ["","seq7"]
   seq7 = children.last
   seq4 = tree.find("seq4")
-  seq4.distance(seq7).should == 19.387756600000003 
+  seq4.distance(seq7).should == 19.387756600000003
   # find the sequence in the alignment belonging to the node
   print seq4.sequence
   print tree.output_newick                  # BioRuby Newick output
@@ -244,7 +244,7 @@ based on the tree, and locating sequences on the same branch. More
 examples can be found in the tests and features.  The underlying
 implementation of Bio::Tree is that of BioRuby. We have added an OOP
 layer for traversing the tree by injecting methods into the BioRuby
-object itself. 
+object itself.
 
 ### Alignment marking/masking/editing
 
@@ -288,7 +288,7 @@ marking columns looks much the same
   mark_columns { |colstate,col|  # for every column
     num = col.count { |e| e.gap? }
     if (num.to_f/col.length) > 0.5
-      colstate.delete! 
+      colstate.delete!
     end
     colstate
   }
@@ -313,7 +313,7 @@ and, here we remove every marked element by turning it into a gap
 ```
 
 ''update_each_element'' visits every element in the MSA, and replaces
-the old with the new. 
+the old with the new.
 
 It is important to note that, instead of directly editing alignments
 in place, bio-alignment always makes it a two step process. First items
@@ -334,7 +334,7 @@ An edit feature is added at runtime(!) Example:
 ```ruby
   require 'bio-alignment/edit/del_bridges'
 
-  aln.extend DelBridges         # mix the module into the object 
+  aln.extend DelBridges         # mix the module into the object
   aln2 = aln.del_bridges        # execute the alignment editor
 ```
 
@@ -358,7 +358,7 @@ The API documentation can be found
 ## Cite
 
 If you use this software, please cite one of
-  
+
 * [BioRuby: bioinformatics software for the Ruby programming language](http://dx.doi.org/10.1093/bioinformatics/btq475)
 * [Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics](http://dx.doi.org/10.1093/bioinformatics/bts080)
 
@@ -368,5 +368,4 @@ This Biogem is published at [#bio-alignment](http://biogems.info/index.html)
 
 ## Copyright
 
-Copyright (c) 2012 Pjotr Prins. See LICENSE.txt for further details.
-
+Copyright (c) 2012-2016 Pjotr Prins. See LICENSE.txt for further details.

data/Rakefile

@@ -1,30 +1,16 @@
 # encoding: utf-8
 
 require 'rubygems'
-require 'bundler'
-begin
-  Bundler.setup(:default, :development)
-rescue Bundler::BundlerError => e
-  $stderr.puts e.message
-  $stderr.puts "Run `bundle install` to install missing gems"
-  exit e.status_code
-end
+# require 'bundler'
+# begin
+#   Bundler.setup(:default, :development)
+# rescue Bundler::BundlerError => e
+#   $stderr.puts e.message
+#   $stderr.puts "Run `bundle install` to install missing gems"
+#   exit e.status_code
+# end
 require 'rake'
 
-require 'jeweler'
-Jeweler::Tasks.new do |gem|
-  # gem is a Gem::Specification... see http://docs.rubygems.org/read/chapter/20 for more options
-  gem.name = "bio-alignment"
-  gem.homepage = "http://github.com/pjotrp/bioruby-alignment"
-  gem.license = "MIT"
-  gem.summary = %Q{Support for multiple sequence alignments (MSA)}
-  gem.description = %Q{Alignment handler for multiple sequence alignments (MSA)}
-  gem.email = "pjotr.public01@thebird.nl"
-  gem.authors = ["Pjotr Prins"]
-  # dependencies defined in Gemfile
-end
-Jeweler::RubygemsDotOrgTasks.new
-
 require 'rspec/core'
 require 'rspec/core/rake_task'
 RSpec::Core::RakeTask.new(:spec) do |spec|
@@ -33,9 +19,10 @@ end
 
 require 'cucumber/rake/task'
 Cucumber::Rake::Task.new do |features|
+  # features.cucumber_opts = "--bundler false"
 end
 
-task :test => [ :spec, :cucumber ] 
+task :test => [ :spec, :cucumber ]
 task :default => [ :test ]
 
 require 'rdoc/task'

data/VERSION

@@ -1 +1 @@
-0.0.8
+0.0.9

data/bin/bio-alignment

@@ -2,7 +2,7 @@
 #
 # BioRuby bio-alignment Plugin
 # Author:: Pjotr Prins
-# Copyright:: 2012
+# Copyright:: 2012-2016
 # License:: The Ruby License
 
 rootpath = File.dirname(File.dirname(__FILE__))
@@ -10,7 +10,7 @@ $: << File.join(rootpath,'lib')
 
 _VERSION = File.new(File.join(rootpath,'VERSION')).read.chomp
 
-$stderr.print "bio-alignment "+_VERSION+" Copyright (C) 2012 Pjotr Prins <pjotr.prins@thebird.nl>\n\n"
+$stderr.print "bio-alignment "+_VERSION+" Copyright (C) 2012-2016 Pjotr Prins <pjotr.prins@thebird.nl>\n\n"
 
 USAGE =<<EOU
 
@@ -61,19 +61,19 @@ opts = OptionParser.new do |o|
   o.on("--logger filename",String,"Log to file (default stderr)") do | name |
     Bio::Log::CLI.logger(name)
   end
-  
+
   o.on("--trace options",String,"Set log level (default INFO, see bio-logger)") do | s |
     Bio::Log::CLI.trace(s)
   end
-  
+
   o.on("-q", "--quiet", "Run quietly") do |q|
     Bio::Log::CLI.trace('error')
   end
-  
+
   o.on("-v", "--verbose", "Run verbosely") do |v|
     Bio::Log::CLI.trace('info')
   end
-  
+
   o.on("--debug", "Show debug messages") do |v|
     Bio::Log::CLI.trace('debug')
   end
@@ -88,7 +88,7 @@ end
 begin
   opts.parse!(ARGV)
 
-  if options[:show_help] 
+  if options[:show_help]
     print opts
     print USAGE
   end
@@ -107,7 +107,7 @@ ARGV.each do |fn|
     case options[:type]
       when :codon
         aln << CodonSequence.new(entry.entry_id,entry.seq)
-      when :nucleotide 
+      when :nucleotide
         aln << Sequence.new(entry.entry_id,entry.seq)
       when :aminoacid
         aln << Sequence.new(entry.entry_id,entry.seq)
@@ -138,7 +138,7 @@ ARGV.each do |fn|
       aln.each { |seq| seq.extend(State) }
       aln2 = aln.del_non_informative_sequences(options[:perc])
       aln = aln2
-    else 
+    else
       # do nothing
   end
   case options[:out]

data/features/codon-feature.rb

@@ -35,7 +35,7 @@ Then /^it should write a nucleotide alignment$/ do
   # Writing is actually handles by a different library
   fasta = FastaWriter.new('test/data/regression/nt-aln.fa')
   @aln.rows.each do | row |
-    fasta.write(row)
+    fasta.write(row.id, row.to_s)
   end
 end
 
@@ -45,4 +45,3 @@ Then /^it should write an amino acid alignment$/ do
     fasta.write(row.id, row.to_aa.to_s)
   end
 end
-

data/features/columns-feature.rb

@@ -17,19 +17,18 @@ When /^I inject column state$/ do
 end
 
 Then /^I should be able to get the column state$/ do
-  column.state.deleted?.should be_true
+  column.state.deleted?.should be true
 end
 
 list = []
 When /^I iterate a column$/ do
   column10 = @aln.columns[10]
-  column10.each do | element | 
+  column10.each do | element |
     list << element.to_s
   end
 end
 
 Then /^I should get the column elements$/ do
-  list[0..10].should == 
+  list[0..10].should ==
   ["ctt", "gcg", "ctt", "ttt", "gcg", "ttt", "ttt", "agt", "ttt", "atg", "agt"]
 end
-

data/features/rows-feature.rb

@@ -11,19 +11,22 @@ end
 
 When /^I inject row state$/ do
   # tell row to handle state
+  # row = @aln.rows[3]
   row.extend(State)
   row.state = RowState.new
   row.state.deleted = true
+  row.state.deleted?.should be true
 end
 
 Then /^I should be able to get the row state$/ do
-  row.state.deleted?.should be_true
+  row.state.deleted?.should be true
 end
 
+
 list = []
 When /^I iterate a row$/ do
   row10 = @aln.rows[10]
-  row10.each do | element | 
+  row10.each do | element |
     list << element.to_s
   end
 end
@@ -32,4 +35,3 @@ Then /^I should get the row elements$/ do
   list[0..10].should == ["---", "---", "---", "---", "---", "---", "---", "atg", "tcg", "tcc", "agt"]
 
 end
-

data/features/support/env.rb

@@ -1,11 +1,11 @@
-require 'bundler'
-begin
-  Bundler.setup(:default, :development)
-rescue Bundler::BundlerError => e
-  $stderr.puts e.message
-  $stderr.puts "Run `bundle install` to install missing gems"
-  exit e.status_code
-end
+# require 'bundler'
+# begin
+#   Bundler.setup(:default, :development)
+# rescue Bundler::BundlerError => e
+#   $stderr.puts e.message
+#   $stderr.puts "Run `bundle install` to install missing gems"
+#   exit e.status_code
+# end
 
 $LOAD_PATH.unshift(File.dirname(__FILE__) + '/../../lib')
 require 'bio-alignment'
@@ -16,4 +16,3 @@ log = Bio::Log::LoggerPlus.new 'bio-alignment'
 
 Bio::Log::CLI.logger('stderr')
 Bio::Log::CLI.trace('info')
-

data/test/data/regression/nt-aln.fa

@@ -1,24 +1,24 @@
 >ZK909.2e
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+atg ccc act cga ttg gat att gtt gga aac ctt cag ttc tct agc tca act gat aac gga gat gaa gac cag gaa gct gac gtg aca gcc tgc ttt gtg ctt cct tct cca tcg agt ttt tct aaa ttg agc atc ttg gat gat cct gtg gag gat ttc aaa gaa ttc ctg gac aag gca cgc gaa gac ttc aaa caa cga tgg gag aat ccg gct cag aac acg gcg tgt ctt gac gac ttt gat agg ata aaa acc ctt gga acc gga tca ttc ggg cgc gtg atg ctt gtg aag cat aag cag tcg ggc aac tat tat gcc atg aaa att cta gac aaa caa aag gtt gta aaa ctc aag caa gtg gag cac acg ttg aac gaa aag cgc att ctc cag gct atc gat ttt ccg ttt ttg gtg aac atg acg ttc tct ttc aag gac aac tcc aac ttg tac atg gtg ctc gaa ttc atc tcg gga ggt gag atg ttc tca cat tta cgc cga atc gga cgt ttc tcc gag ccc cac tcg cgt ttc tac gcc gct caa att gtg ctt gcc ttt gag tac ctt cac tcc tta gat ctc atc tat cgt gat ctg aaa ccc gag aac ttg ctt atc gat tcc act gga tat cta aag atc acc gat ttc gga ttt gcg aaa cgt gtc aaa gga cga acg tgg aca ttg tgc ggc aca cca gaa tac ttg gca ccc gag att att ttg tca aaa gga tac aat aag gct gtc gat tgg tgg gca ctt ggt gtg ttg atc tac gaa atg gcc gcc ggt tat ccg ccg ttc ttt gcc gat cag ccg att caa att tat gag aag att gtg tca gga aaa gtg aaa ttc ccg tcg cac ttc tcg aat gag ttg aaa gac ttg ctg aag aat ttg ctc caa gtt gat ctt aca aag cga tac ggt aac ctg aaa aat gga gtt gcc gat atc aaa aat cac aag tgg ttt gga agt acc gac tgg att gcc atc tat cag aag aag atc aca ccg ccc tcg ttc tcc aaa gga gaa tcc aat ggt cga ctg ttc gag gct ctg tat cca cgt gtc gat ggt ccc gcc gac aca cgt cat ttt gtg gaa gag gtg caa gag ccg act gag ttt gtg atc gcc gcg act cca cag ttg gaa gag ctg ttc gtc gag ttt
 >ZK909.2j
-[---, ---, ---, ---, ---, ---, ---, atg, gga, aat, gcg, gca, tct, ggc, gga, tct, tct, gga, ggt, ggg, gga, tcg, gca, cga, cgt, gga, aac, ggt, ggc, gga, aac, aac, ggt, agt, gac, tat, aac, aat, gcg, atg, gtt, ttc, tcg, aat, gga, cgt, tta, gcc, gcg, gca, gag, aca, atc, aaa, gaa, ttc, ctg, gac, aag, gca, cgc, gaa, gac, ttc, aaa, caa, cga, tgg, gag, aat, ccg, gct, cag, aac, acg, gcg, tgt, ctt, gac, gac, ttt, gat, agg, ata, aaa, acc, ctt, gga, acc, gga, tca, ttc, ggg, cgc, gtg, atg, ctt, gtg, aag, cat, aag, cag, tcg, ggc, aac, tat, tat, gcc, atg, aaa, att, cta, gac, aaa, caa, aag, gtt, gta, aaa, ctc, aag, caa, gtg, gag, cac, acg, ttg, aac, gaa, aag, cgc, att, ctc, cag, gct, atc, gat, ttt, ccg, ttt, ttg, gtg, aac, atg, acg, ttc, tct, ttc, aag, gac, aac, tcc, aac, ttg, tac, atg, gtg, ctc, gaa, ttc, atc, tcg, gga, ggt, gag, atg, ttc, tca, cat, tta, cgc, cga, atc, gga, cgt, ttc, tcc, gag, ccc, cac, tcg, cgt, ttc, tac, gcc, gct, caa, att, gtg, ctt, gcc, ttt, gag, tac, ctt, cac, tcc, tta, gat, ctc, atc, tat, cgt, gat, ctg, aaa, ccc, gag, aac, ttg, ctt, atc, gat, tcc, act, gga, tat, cta, aag, atc, acc, gat, ttc, gga, ttt, gcg, aaa, cgt, gtc, aaa, gga, cga, acg, tgg, aca, ttg, tgc, ggc, aca, cca, gaa, tac, ttg, gca, ccc, gag, att, att, ttg, tca, aaa, gga, tac, aat, aag, gct, gtc, gat, tgg, tgg, gca, ctt, ggt, gtg, ttg, atc, tac, gaa, atg, gcc, gcc, ggt, tat, ccg, ccg, ttc, ttt, gcc, gat, cag, ccg, att, caa, att, tat, gag, aag, att, gtg, tca, gga, aaa, gtg, aaa, ttc, ccg, tcg, cac, ttc, tcg, aat, gag, ttg, aaa, gac, ttg, ctg, aag, aat, ttg, ctc, caa, gtt, gat, ctt, aca, aag, cga, tac, ggt, aac, ctg, aaa, aat, gga, gtt, gcc, gat, atc, aaa, aat, cac, aag, tgg, ttt, gga, agt, acc, gac, tgg, att, gcc, atc, tat, cag, aag, aag, atc, aca, ccg, ccc, tcg, ttc, tcc, aaa, gga, gaa, tcc, aat, ggt, cga, ctg, ttc, gag, gct, ctg, tat, cca, cgt, gtc, gat, ggt, ccc, gcc, gac, aca, cgt, cat, ttt, gtg, gaa, gag, gtg, caa, gag, ccg, act, gag, ttt, gtg, atc, gcc, gcg, act, cca, cag, ttg, gaa, gag, ctg, ttc, gtc, gag, ttt]
+--- --- --- --- --- --- --- atg gga aat gcg gca tct ggc gga tct tct gga ggt ggg gga tcg gca cga cgt gga aac ggt ggc gga aac aac ggt agt gac tat aac aat gcg atg gtt ttc tcg aat gga cgt tta gcc gcg gca gag aca atc aaa gaa ttc ctg gac aag gca cgc gaa gac ttc aaa caa cga tgg gag aat ccg gct cag aac acg gcg tgt ctt gac gac ttt gat agg ata aaa acc ctt gga acc gga tca ttc ggg cgc gtg atg ctt gtg aag cat aag cag tcg ggc aac tat tat gcc atg aaa att cta gac aaa caa aag gtt gta aaa ctc aag caa gtg gag cac acg ttg aac gaa aag cgc att ctc cag gct atc gat ttt ccg ttt ttg gtg aac atg acg ttc tct ttc aag gac aac tcc aac ttg tac atg gtg ctc gaa ttc atc tcg gga ggt gag atg ttc tca cat tta cgc cga atc gga cgt ttc tcc gag ccc cac tcg cgt ttc tac gcc gct caa att gtg ctt gcc ttt gag tac ctt cac tcc tta gat ctc atc tat cgt gat ctg aaa ccc gag aac ttg ctt atc gat tcc act gga tat cta aag atc acc gat ttc gga ttt gcg aaa cgt gtc aaa gga cga acg tgg aca ttg tgc ggc aca cca gaa tac ttg gca ccc gag att att ttg tca aaa gga tac aat aag gct gtc gat tgg tgg gca ctt ggt gtg ttg atc tac gaa atg gcc gcc ggt tat ccg ccg ttc ttt gcc gat cag ccg att caa att tat gag aag att gtg tca gga aaa gtg aaa ttc ccg tcg cac ttc tcg aat gag ttg aaa gac ttg ctg aag aat ttg ctc caa gtt gat ctt aca aag cga tac ggt aac ctg aaa aat gga gtt gcc gat atc aaa aat cac aag tgg ttt gga agt acc gac tgg att gcc atc tat cag aag aag atc aca ccg ccc tcg ttc tcc aaa gga gaa tcc aat ggt cga ctg ttc gag gct ctg tat cca cgt gtc gat ggt ccc gcc gac aca cgt cat ttt gtg gaa gag gtg caa gag ccg act gag ttt gtg atc gcc gcg act cca cag ttg gaa gag ctg ttc gtc gag ttt
 >ZK909.2l
-[atg, ccc, act, cga, ttg, gat, att, gtt, gga, aac, ctt, cag, ttc, tct, agc, tca, act, gat, aac, gga, gat, gaa, gac, cag, gaa, gct, gac, gtg, aca, gcc, tgc, ttt, gtg, ctt, cct, tct, cca, tcg, agt, ttt, tct, aaa, ttg, agc, atc, ttg, gat, gat, cct, gtg, gag, gat, ttc, aaa, gaa, ttc, ctg, gac, aag, gca, cgc, gaa, gac, ttc, aaa, caa, cga, tgg, gag, aat, ccg, gct, cag, aac, acg, gcg, tgt, ctt, gac, gac, ttt, gat, agg, ata, aaa, acc, ctt, gga, acc, gga, tca, ttc, ggg, cgc, gtg, atg, ctt, gtg, aag, cat, aag, cag, tcg, ggc, aac, tat, tat, gcc, atg, aaa, att, cta, gac, aaa, caa, aag, gtt, gta, aaa, ctc, aag, caa, gtg, gag, cac, acg, ttg, aac, gaa, aag, cgc, att, ctc, cag, gct, atc, gat, ttt, ccg, ttt, ttg, gtg, aac, atg, acg, ttc, tct, ttc, aag, gac, aac, tcc, aac, ttg, tac, atg, gtg, ctc, gaa, ttc, atc, tcg, gga, ggt, gag, atg, ttc, tca, cat, tta, cgc, cga, atc, gga, cgt, ttc, tcc, gag, ccc, cac, tcg, cgt, ttc, tac, gcc, gct, caa, att, gtg, ctt, gcc, ttt, gag, tac, ctt, cac, tcc, tta, gat, ctc, atc, tat, cgt, gat, ctg, aaa, ccc, gag, aac, ttg, ctt, atc, gat, tcc, act, gga, tat, cta, aag, atc, acc, gat, ttc, gga, ttt, gcg, aaa, cgt, gtc, aaa, gga, cga, acg, tgg, aca, ttg, tgc, ggc, aca, cca, gaa, tac, ttg, gca, ccc, gag, att, att, ttg, tca, aaa, gga, tac, aat, aag, gct, gtc, gat, tgg, tgg, gca, ctt, ggt, gtg, ttg, atc, tac, gaa, atg, gcc, gcc, ggt, tat, ccg, ccg, ttc, ttt, gcc, gat, cag, ccg, att, caa, att, tat, gag, aag, att, gtg, tca, gga, aaa, gtg, aaa, ttc, ccg, tcg, cac, ttc, tcg, aat, gag, ttg, aaa, gac, ttg, ctg, aag, aat, ttg, ctc, caa, gtt, gat, ctt, aca, aag, cga, tac, ggt, aac, ctg, aaa, aat, gga, gtt, gcc, gat, atc, aaa, aat, cac, aag, tgg, ttt, gga, agt, acc, gac, tgg, att, gcc, atc, tat, cag, aag, aag, atc, gaa, gca, ccg, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ttc, ctt, cca, aaa, tgc, cgt, ggc, cct, ggc, gac, gca, tct, aac, ttt, gac, gac, tac, gag, gaa, gag, ccg, ---, ---, ctt, cgt, atc, tcg, ggc, acc, gag, aaa, tgc, gcc, aaa, gag, ttt, gcc, gag, ttt]
+atg ccc act cga ttg gat att gtt gga aac ctt cag ttc tct agc tca act gat aac gga gat gaa gac cag gaa gct gac gtg aca gcc tgc ttt gtg ctt cct tct cca tcg agt ttt tct aaa ttg agc atc ttg gat gat cct gtg gag gat ttc aaa gaa ttc ctg gac aag gca cgc gaa gac ttc aaa caa cga tgg gag aat ccg gct cag aac acg gcg tgt ctt gac gac ttt gat agg ata aaa acc ctt gga acc gga tca ttc ggg cgc gtg atg ctt gtg aag cat aag cag tcg ggc aac tat tat gcc atg aaa att cta gac aaa caa aag gtt gta aaa ctc aag caa gtg gag cac acg ttg aac gaa aag cgc att ctc cag gct atc gat ttt ccg ttt ttg gtg aac atg acg ttc tct ttc aag gac aac tcc aac ttg tac atg gtg ctc gaa ttc atc tcg gga ggt gag atg ttc tca cat tta cgc cga atc gga cgt ttc tcc gag ccc cac tcg cgt ttc tac gcc gct caa att gtg ctt gcc ttt gag tac ctt cac tcc tta gat ctc atc tat cgt gat ctg aaa ccc gag aac ttg ctt atc gat tcc act gga tat cta aag atc acc gat ttc gga ttt gcg aaa cgt gtc aaa gga cga acg tgg aca ttg tgc ggc aca cca gaa tac ttg gca ccc gag att att ttg tca aaa gga tac aat aag gct gtc gat tgg tgg gca ctt ggt gtg ttg atc tac gaa atg gcc gcc ggt tat ccg ccg ttc ttt gcc gat cag ccg att caa att tat gag aag att gtg tca gga aaa gtg aaa ttc ccg tcg cac ttc tcg aat gag ttg aaa gac ttg ctg aag aat ttg ctc caa gtt gat ctt aca aag cga tac ggt aac ctg aaa aat gga gtt gcc gat atc aaa aat cac aag tgg ttt gga agt acc gac tgg att gcc atc tat cag aag aag atc gaa gca ccg --- --- --- --- --- --- --- --- --- --- --- --- --- --- ttc ctt cca aaa tgc cgt ggc cct ggc gac gca tct aac ttt gac gac tac gag gaa gag ccg --- --- ctt cgt atc tcg ggc acc gag aaa tgc gcc aaa gag ttt gcc gag ttt
 >ZK909.2k
-[---, ---, ---, ---, ---, atg, ctg, tcc, tcg, tcg, ttt, ttc, cgc, ggc, agt, atg, aaa, gaa, cgg, aag, aat, gag, gcg, ttg, aag, aat, cac, aaa, agt, aaa, tac, ata, tca, gga, ggt, tat, tta, gaa, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, act, gtc, aaa, gaa, ttc, ctg, gac, aag, gca, cgc, gaa, gac, ttc, aaa, caa, cga, tgg, gag, aat, ccg, gct, cag, aac, acg, gcg, tgt, ctt, gac, gac, ttt, gat, agg, ata, aaa, acc, ctt, gga, acc, gga, tca, ttc, ggg, cgc, gtg, atg, ctt, gtg, aag, cat, aag, cag, tcg, ggc, aac, tat, tat, gcc, atg, aaa, att, cta, gac, aaa, caa, aag, gtt, gta, aaa, ctc, aag, caa, gtg, gag, cac, acg, ttg, aac, gaa, aag, cgc, att, ctc, cag, gct, atc, gat, ttt, ccg, ttt, ttg, gtg, aac, atg, acg, ttc, tct, ttc, aag, gac, aac, tcc, aac, ttg, tac, atg, gtg, ctc, gaa, ttc, atc, tcg, gga, ggt, gag, atg, ttc, tca, cat, tta, cgc, cga, atc, gga, cgt, ttc, tcc, gag, ccc, cac, tcg, cgt, ttc, tac, gcc, gct, caa, att, gtg, ctt, gcc, ttt, gag, tac, ctt, cac, tcc, tta, gat, ctc, atc, tat, cgt, gat, ctg, aaa, ccc, gag, aac, ttg, ctt, atc, gat, tcc, act, gga, tat, cta, aag, atc, acc, gat, ttc, gga, ttt, gcg, aaa, cgt, gtc, aaa, gga, cga, acg, tgg, aca, ttg, tgc, ggc, aca, cca, gaa, tac, ttg, gca, ccc, gag, att, att, ttg, tca, aaa, gga, tac, aat, aag, gct, gtc, gat, tgg, tgg, gca, ctt, ggt, gtg, ttg, atc, tac, gaa, atg, gcc, gcc, ggt, tat, ccg, ccg, ttc, ttt, gcc, gat, cag, ccg, att, caa, att, tat, gag, aag, att, gtg, tca, gga, aaa, gtg, aaa, ttc, ccg, tcg, cac, ttc, tcg, aat, gag, ttg, aaa, gac, ttg, ctg, aag, aat, ttg, ctc, caa, gtt, gat, ctt, aca, aag, cga, tac, ggt, aac, ctg, aaa, aat, gga, gtt, gcc, gat, atc, aaa, aat, cac, aag, tgg, ttt, gga, agt, acc, gac, tgg, att, gcc, atc, tat, cag, aag, aag, atc, aca, ccg, ccc, tcg, ttc, tcc, aaa, gga, gaa, tcc, aat, ggt, cga, ctg, ttc, gag, gct, ctg, tat, cca, cgt, gtc, gat, ggt, ccc, gcc, gac, aca, cgt, cat, ttt, gtg, gaa, gag, gtg, caa, gag, ccg, act, gag, ttt, gtg, atc, gcc, gcg, act, cca, cag, ttg, gaa, gag, ctg, ttc, gtc, gag, ttt]
+--- --- --- --- --- atg ctg tcc tcg tcg ttt ttc cgc ggc agt atg aaa gaa cgg aag aat gag gcg ttg aag aat cac aaa agt aaa tac ata tca gga ggt tat tta gaa --- --- --- --- --- --- --- --- --- --- --- --- --- act gtc aaa gaa ttc ctg gac aag gca cgc gaa gac ttc aaa caa cga tgg gag aat ccg gct cag aac acg gcg tgt ctt gac gac ttt gat agg ata aaa acc ctt gga acc gga tca ttc ggg cgc gtg atg ctt gtg aag cat aag cag tcg ggc aac tat tat gcc atg aaa att cta gac aaa caa aag gtt gta aaa ctc aag caa gtg gag cac acg ttg aac gaa aag cgc att ctc cag gct atc gat ttt ccg ttt ttg gtg aac atg acg ttc tct ttc aag gac aac tcc aac ttg tac atg gtg ctc gaa ttc atc tcg gga ggt gag atg ttc tca cat tta cgc cga atc gga cgt ttc tcc gag ccc cac tcg cgt ttc tac gcc gct caa att gtg ctt gcc ttt gag tac ctt cac tcc tta gat ctc atc tat cgt gat ctg aaa ccc gag aac ttg ctt atc gat tcc act gga tat cta aag atc acc gat ttc gga ttt gcg aaa cgt gtc aaa gga cga acg tgg aca ttg tgc ggc aca cca gaa tac ttg gca ccc gag att att ttg tca aaa gga tac aat aag gct gtc gat tgg tgg gca ctt ggt gtg ttg atc tac gaa atg gcc gcc ggt tat ccg ccg ttc ttt gcc gat cag ccg att caa att tat gag aag att gtg tca gga aaa gtg aaa ttc ccg tcg cac ttc tcg aat gag ttg aaa gac ttg ctg aag aat ttg ctc caa gtt gat ctt aca aag cga tac ggt aac ctg aaa aat gga gtt gcc gat atc aaa aat cac aag tgg ttt gga agt acc gac tgg att gcc atc tat cag aag aag atc aca ccg ccc tcg ttc tcc aaa gga gaa tcc aat ggt cga ctg ttc gag gct ctg tat cca cgt gtc gat ggt ccc gcc gac aca cgt cat ttt gtg gaa gag gtg caa gag ccg act gag ttt gtg atc gcc gcg act cca cag ttg gaa gag ctg ttc gtc gag ttt
 >ZK909.2h
-[---, ---, ---, ---, ---, ---, ---, atg, gga, aat, gcg, gca, tct, ggc, gga, tct, tct, gga, ggt, ggg, gga, tcg, gca, cga, cgt, gga, aac, ggt, ggc, gga, aac, aac, ggt, agt, gac, tat, aac, aat, gcg, atg, gtt, ttc, tcg, aat, gga, cgt, tta, gcc, gcg, gca, gag, aca, atc, aaa, gaa, ttc, ctg, gac, aag, gca, cgc, gaa, gac, ttc, aaa, caa, cga, tgg, gag, aat, ccg, gct, cag, aac, acg, gcg, tgt, ctt, gac, gac, ttt, gat, agg, ata, aaa, acc, ctt, gga, acc, gga, tca, ttc, ggg, cgc, gtg, atg, ctt, gtg, aag, cat, aag, cag, tcg, ggc, aac, tat, tat, gcc, atg, aaa, att, cta, gac, aaa, caa, aag, gtt, gta, aaa, ctc, aag, caa, gtg, gag, cac, acg, ttg, aac, gaa, aag, cgc, att, ctc, cag, gct, atc, gat, ttt, ccg, ttt, ttg, gtg, aac, atg, acg, ttc, tct, ttc, aag, gac, aac, tcc, aac, ttg, tac, atg, gtg, ctc, gaa, ttc, atc, tcg, gga, ggt, gag, atg, ttc, tca, cat, tta, cgc, cga, atc, gga, cgt, ttc, tcc, gag, ccc, cac, tcg, cgt, ttc, tac, gcc, gct, caa, att, gtg, ctt, gcc, ttt, gag, tac, ctt, cac, tcc, tta, gat, ctc, atc, tat, cgt, gat, ctg, aaa, ccc, gag, aac, ttg, ctt, atc, gat, tcc, act, gga, tat, cta, aag, atc, acc, gat, ttc, gga, ttt, gcg, aaa, cgt, gtc, aaa, gga, cga, acg, tgg, aca, ttg, tgc, ggc, aca, cca, gaa, tac, ttg, gca, ccc, gag, att, att, ttg, tca, aaa, gga, tac, aat, aag, gct, gtc, gat, tgg, tgg, gca, ctt, ggt, gtg, ttg, atc, tac, gaa, atg, gcc, gcc, ggt, tat, ccg, ccg, ttc, ttt, gcc, gat, cag, ccg, att, caa, att, tat, gag, aag, att, gtg, tca, gga, aaa, gtg, aaa, ttc, ccg, tcg, cac, ttc, tcg, aat, gag, ttg, aaa, gac, ttg, ctg, aag, aat, ttg, ctc, caa, gtt, gat, ctt, aca, aag, cga, tac, ggt, aac, ctg, aaa, aat, gga, gtt, gcc, gat, atc, aaa, aat, cac, aag, tgg, ttt, gga, agt, acc, gac, tgg, att, gcc, atc, tat, cag, aag, aag, atc, gaa, gca, ccg, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ttc, ctt, cca, aaa, tgc, cgt, ggc, cct, ggc, gac, gca, tct, aac, ttt, gac, gac, tac, gag, gaa, gag, ccg, ---, ---, ctt, cgt, atc, tcg, ggc, acc, gag, aaa, tgc, gcc, aaa, gag, ttt, gcc, gag, ttt]
+--- --- --- --- --- --- --- atg gga aat gcg gca tct ggc gga tct tct gga ggt ggg gga tcg gca cga cgt gga aac ggt ggc gga aac aac ggt agt gac tat aac aat gcg atg gtt ttc tcg aat gga cgt tta gcc gcg gca gag aca atc aaa gaa ttc ctg gac aag gca cgc gaa gac ttc aaa caa cga tgg gag aat ccg gct cag aac acg gcg tgt ctt gac gac ttt gat agg ata aaa acc ctt gga acc gga tca ttc ggg cgc gtg atg ctt gtg aag cat aag cag tcg ggc aac tat tat gcc atg aaa att cta gac aaa caa aag gtt gta aaa ctc aag caa gtg gag cac acg ttg aac gaa aag cgc att ctc cag gct atc gat ttt ccg ttt ttg gtg aac atg acg ttc tct ttc aag gac aac tcc aac ttg tac atg gtg ctc gaa ttc atc tcg gga ggt gag atg ttc tca cat tta cgc cga atc gga cgt ttc tcc gag ccc cac tcg cgt ttc tac gcc gct caa att gtg ctt gcc ttt gag tac ctt cac tcc tta gat ctc atc tat cgt gat ctg aaa ccc gag aac ttg ctt atc gat tcc act gga tat cta aag atc acc gat ttc gga ttt gcg aaa cgt gtc aaa gga cga acg tgg aca ttg tgc ggc aca cca gaa tac ttg gca ccc gag att att ttg tca aaa gga tac aat aag gct gtc gat tgg tgg gca ctt ggt gtg ttg atc tac gaa atg gcc gcc ggt tat ccg ccg ttc ttt gcc gat cag ccg att caa att tat gag aag att gtg tca gga aaa gtg aaa ttc ccg tcg cac ttc tcg aat gag ttg aaa gac ttg ctg aag aat ttg ctc caa gtt gat ctt aca aag cga tac ggt aac ctg aaa aat gga gtt gcc gat atc aaa aat cac aag tgg ttt gga agt acc gac tgg att gcc atc tat cag aag aag atc gaa gca ccg --- --- --- --- --- --- --- --- --- --- --- --- --- --- ttc ctt cca aaa tgc cgt ggc cct ggc gac gca tct aac ttt gac gac tac gag gaa gag ccg --- --- ctt cgt atc tcg ggc acc gag aaa tgc gcc aaa gag ttt gcc gag ttt
 >ZK909.2b
-[---, ---, ---, ---, ---, ---, ---, atg, ctc, aag, ttt, ctg, aaa, cca, aaa, tcg, tcg, gac, gag, gga, agc, tcg, aag, gac, aac, aag, aac, tcg, gcg, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, tcg, ctc, aaa, gaa, ttc, ctg, gac, aag, gca, cgc, gaa, gac, ttc, aaa, caa, cga, tgg, gag, aat, ccg, gct, cag, aac, acg, gcg, tgt, ctt, gac, gac, ttt, gat, agg, ata, aaa, acc, ctt, gga, acc, gga, tca, ttc, ggg, cgc, gtg, atg, ctt, gtg, aag, cat, aag, cag, tcg, ggc, aac, tat, tat, gcc, atg, aaa, att, cta, gac, aaa, caa, aag, gtt, gta, aaa, ctc, aag, caa, gtg, gag, cac, acg, ttg, aac, gaa, aag, cgc, att, ctc, cag, gct, atc, gat, ttt, ccg, ttt, ttg, gtg, aac, atg, acg, ttc, tct, ttc, aag, gac, aac, tcc, aac, ttg, tac, atg, gtg, ctc, gaa, ttc, atc, tcg, gga, ggt, gag, atg, ttc, tca, cat, tta, cgc, cga, atc, gga, cgt, ttc, tcc, gag, ccc, cac, tcg, cgt, ttc, tac, gcc, gct, caa, att, gtg, ctt, gcc, ttt, gag, tac, ctt, cac, tcc, tta, gat, ctc, atc, tat, cgt, gat, ctg, aaa, ccc, gag, aac, ttg, ctt, atc, gat, tcc, act, gga, tat, cta, aag, atc, acc, gat, ttc, gga, ttt, gcg, aaa, cgt, gtc, aaa, gga, cga, acg, tgg, aca, ttg, tgc, ggc, aca, cca, gaa, tac, ttg, gca, ccc, gag, att, att, ttg, tca, aaa, gga, tac, aat, aag, gct, gtc, gat, tgg, tgg, gca, ctt, ggt, gtg, ttg, atc, tac, gaa, atg, gcc, gcc, ggt, tat, ccg, ccg, ttc, ttt, gcc, gat, cag, ccg, att, caa, att, tat, gag, aag, att, gtg, tca, gga, aaa, gtg, aaa, ttc, ccg, tcg, cac, ttc, tcg, aat, gag, ttg, aaa, gac, ttg, ctg, aag, aat, ttg, ctc, caa, gtt, gat, ctt, aca, aag, cga, tac, ggt, aac, ctg, aaa, aat, gga, gtt, gcc, gat, atc, aaa, aat, cac, aag, tgg, ttt, gga, agt, acc, gac, tgg, att, gcc, atc, tat, cag, aag, aag, atc, aca, ccg, ccc, tcg, ttc, tcc, aaa, gga, gaa, tcc, aat, ggt, cga, ctg, ttc, gag, gct, ctg, tat, cca, cgt, gtc, gat, ggt, ccc, gcc, gac, aca, cgt, cat, ttt, gtg, gaa, gag, gtg, caa, gag, ccg, act, gag, ttt, gtg, atc, gcc, gcg, act, cca, cag, ttg, gaa, gag, ctg, ttc, gtc, gag, ttt]
+--- --- --- --- --- --- --- atg ctc aag ttt ctg aaa cca aaa tcg tcg gac gag gga agc tcg aag gac aac aag aac tcg gcg --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- tcg ctc aaa gaa ttc ctg gac aag gca cgc gaa gac ttc aaa caa cga tgg gag aat ccg gct cag aac acg gcg tgt ctt gac gac ttt gat agg ata aaa acc ctt gga acc gga tca ttc ggg cgc gtg atg ctt gtg aag cat aag cag tcg ggc aac tat tat gcc atg aaa att cta gac aaa caa aag gtt gta aaa ctc aag caa gtg gag cac acg ttg aac gaa aag cgc att ctc cag gct atc gat ttt ccg ttt ttg gtg aac atg acg ttc tct ttc aag gac aac tcc aac ttg tac atg gtg ctc gaa ttc atc tcg gga ggt gag atg ttc tca cat tta cgc cga atc gga cgt ttc tcc gag ccc cac tcg cgt ttc tac gcc gct caa att gtg ctt gcc ttt gag tac ctt cac tcc tta gat ctc atc tat cgt gat ctg aaa ccc gag aac ttg ctt atc gat tcc act gga tat cta aag atc acc gat ttc gga ttt gcg aaa cgt gtc aaa gga cga acg tgg aca ttg tgc ggc aca cca gaa tac ttg gca ccc gag att att ttg tca aaa gga tac aat aag gct gtc gat tgg tgg gca ctt ggt gtg ttg atc tac gaa atg gcc gcc ggt tat ccg ccg ttc ttt gcc gat cag ccg att caa att tat gag aag att gtg tca gga aaa gtg aaa ttc ccg tcg cac ttc tcg aat gag ttg aaa gac ttg ctg aag aat ttg ctc caa gtt gat ctt aca aag cga tac ggt aac ctg aaa aat gga gtt gcc gat atc aaa aat cac aag tgg ttt gga agt acc gac tgg att gcc atc tat cag aag aag atc aca ccg ccc tcg ttc tcc aaa gga gaa tcc aat ggt cga ctg ttc gag gct ctg tat cca cgt gtc gat ggt ccc gcc gac aca cgt cat ttt gtg gaa gag gtg caa gag ccg act gag ttt gtg atc gcc gcg act cca cag ttg gaa gag ctg ttc gtc gag ttt
 >ZK909.2f
-[---, ---, ---, ---, ---, atg, ctg, tcc, tcg, tcg, ttt, ttc, cgc, ggc, agt, atg, aaa, gaa, cgg, aag, aat, gag, gcg, ttg, aag, aat, cac, aaa, agt, aaa, tac, ata, tca, gga, ggt, tat, tta, gaa, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, act, gtc, aaa, gaa, ttc, ctg, gac, aag, gca, cgc, gaa, gac, ttc, aaa, caa, cga, tgg, gag, aat, ccg, gct, cag, aac, acg, gcg, tgt, ctt, gac, gac, ttt, gat, agg, ata, aaa, acc, ctt, gga, acc, gga, tca, ttc, ggg, cgc, gtg, atg, ctt, gtg, aag, cat, aag, cag, tcg, ggc, aac, tat, tat, gcc, atg, aaa, att, cta, gac, aaa, caa, aag, gtt, gta, aaa, ctc, aag, caa, gtg, gag, cac, acg, ttg, aac, gaa, aag, cgc, att, ctc, cag, gct, atc, gat, ttt, ccg, ttt, ttg, gtg, aac, atg, acg, ttc, tct, ttc, aag, gac, aac, tcc, aac, ttg, tac, atg, gtg, ctc, gaa, ttc, atc, tcg, gga, ggt, gag, atg, ttc, tca, cat, tta, cgc, cga, atc, gga, cgt, ttc, tcc, gag, ccc, cac, tcg, cgt, ttc, tac, gcc, gct, caa, att, gtg, ctt, gcc, ttt, gag, tac, ctt, cac, tcc, tta, gat, ctc, atc, tat, cgt, gat, ctg, aaa, ccc, gag, aac, ttg, ctt, atc, gat, tcc, act, gga, tat, cta, aag, atc, acc, gat, ttc, gga, ttt, gcg, aaa, cgt, gtc, aaa, gga, cga, acg, tgg, aca, ttg, tgc, ggc, aca, cca, gaa, tac, ttg, gca, ccc, gag, att, att, ttg, tca, aaa, gga, tac, aat, aag, gct, gtc, gat, tgg, tgg, gca, ctt, ggt, gtg, ttg, atc, tac, gaa, atg, gcc, gcc, ggt, tat, ccg, ccg, ttc, ttt, gcc, gat, cag, ccg, att, caa, att, tat, gag, aag, att, gtg, tca, gga, aaa, gtg, aaa, ttc, ccg, tcg, cac, ttc, tcg, aat, gag, ttg, aaa, gac, ttg, ctg, aag, aat, ttg, ctc, caa, gtt, gat, ctt, aca, aag, cga, tac, ggt, aac, ctg, aaa, aat, gga, gtt, gcc, gat, atc, aaa, aat, cac, aag, tgg, ttt, gga, agt, acc, gac, tgg, att, gcc, atc, tat, cag, aag, aag, atc, gaa, gca, ccg, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ttc, ctt, cca, aaa, tgc, cgt, ggc, cct, ggc, gac, gca, tct, aac, ttt, gac, gac, tac, gag, gaa, gag, ccg, ---, ---, ctt, cgt, atc, tcg, ggc, acc, gag, aaa, tgc, gcc, aaa, gag, ttt, gcc, gag, ttt]
+--- --- --- --- --- atg ctg tcc tcg tcg ttt ttc cgc ggc agt atg aaa gaa cgg aag aat gag gcg ttg aag aat cac aaa agt aaa tac ata tca gga ggt tat tta gaa --- --- --- --- --- --- --- --- --- --- --- --- --- act gtc aaa gaa ttc ctg gac aag gca cgc gaa gac ttc aaa caa cga tgg gag aat ccg gct cag aac acg gcg tgt ctt gac gac ttt gat agg ata aaa acc ctt gga acc gga tca ttc ggg cgc gtg atg ctt gtg aag cat aag cag tcg ggc aac tat tat gcc atg aaa att cta gac aaa caa aag gtt gta aaa ctc aag caa gtg gag cac acg ttg aac gaa aag cgc att ctc cag gct atc gat ttt ccg ttt ttg gtg aac atg acg ttc tct ttc aag gac aac tcc aac ttg tac atg gtg ctc gaa ttc atc tcg gga ggt gag atg ttc tca cat tta cgc cga atc gga cgt ttc tcc gag ccc cac tcg cgt ttc tac gcc gct caa att gtg ctt gcc ttt gag tac ctt cac tcc tta gat ctc atc tat cgt gat ctg aaa ccc gag aac ttg ctt atc gat tcc act gga tat cta aag atc acc gat ttc gga ttt gcg aaa cgt gtc aaa gga cga acg tgg aca ttg tgc ggc aca cca gaa tac ttg gca ccc gag att att ttg tca aaa gga tac aat aag gct gtc gat tgg tgg gca ctt ggt gtg ttg atc tac gaa atg gcc gcc ggt tat ccg ccg ttc ttt gcc gat cag ccg att caa att tat gag aag att gtg tca gga aaa gtg aaa ttc ccg tcg cac ttc tcg aat gag ttg aaa gac ttg ctg aag aat ttg ctc caa gtt gat ctt aca aag cga tac ggt aac ctg aaa aat gga gtt gcc gat atc aaa aat cac aag tgg ttt gga agt acc gac tgg att gcc atc tat cag aag aag atc gaa gca ccg --- --- --- --- --- --- --- --- --- --- --- --- --- --- ttc ctt cca aaa tgc cgt ggc cct ggc gac gca tct aac ttt gac gac tac gag gaa gag ccg --- --- ctt cgt atc tcg ggc acc gag aaa tgc gcc aaa gag ttt gcc gag ttt
 >ZK909.2d
-[---, ---, ---, ---, ---, ---, ---, atg, tcg, tcc, agt, agc, aat, aaa, aaa, gtg, caa, gtc, aag, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ttt, ttc, aaa, gaa, ttc, ctg, gac, aag, gca, cgc, gaa, gac, ttc, aaa, caa, cga, tgg, gag, aat, ccg, gct, cag, aac, acg, gcg, tgt, ctt, gac, gac, ttt, gat, agg, ata, aaa, acc, ctt, gga, acc, gga, tca, ttc, ggg, cgc, gtg, atg, ctt, gtg, aag, cat, aag, cag, tcg, ggc, aac, tat, tat, gcc, atg, aaa, att, cta, gac, aaa, caa, aag, gtt, gta, aaa, ctc, aag, caa, gtg, gag, cac, acg, ttg, aac, gaa, aag, cgc, att, ctc, cag, gct, atc, gat, ttt, ccg, ttt, ttg, gtg, aac, atg, acg, ttc, tct, ttc, aag, gac, aac, tcc, aac, ttg, tac, atg, gtg, ctc, gaa, ttc, atc, tcg, gga, ggt, gag, atg, ttc, tca, cat, tta, cgc, cga, atc, gga, cgt, ttc, tcc, gag, ccc, cac, tcg, cgt, ttc, tac, gcc, gct, caa, att, gtg, ctt, gcc, ttt, gag, tac, ctt, cac, tcc, tta, gat, ctc, atc, tat, cgt, gat, ctg, aaa, ccc, gag, aac, ttg, ctt, atc, gat, tcc, act, gga, tat, cta, aag, atc, acc, gat, ttc, gga, ttt, gcg, aaa, cgt, gtc, aaa, gga, cga, acg, tgg, aca, ttg, tgc, ggc, aca, cca, gaa, tac, ttg, gca, ccc, gag, att, att, ttg, tca, aaa, gga, tac, aat, aag, gct, gtc, gat, tgg, tgg, gca, ctt, ggt, gtg, ttg, atc, tac, gaa, atg, gcc, gcc, ggt, tat, ccg, ccg, ttc, ttt, gcc, gat, cag, ccg, att, caa, att, tat, gag, aag, att, gtg, tca, gga, aaa, gtg, aaa, ttc, ccg, tcg, cac, ttc, tcg, aat, gag, ttg, aaa, gac, ttg, ctg, aag, aat, ttg, ctc, caa, gtt, gat, ctt, aca, aag, cga, tac, ggt, aac, ctg, aaa, aat, gga, gtt, gcc, gat, atc, aaa, aat, cac, aag, tgg, ttt, gga, agt, acc, gac, tgg, att, gcc, atc, tat, cag, aag, aag, atc, aca, ccg, ccc, tcg, ttc, tcc, aaa, gga, gaa, tcc, aat, ggt, cga, ctg, ttc, gag, gct, ctg, tat, cca, cgt, gtc, gat, ggt, ccc, gcc, gac, aca, cgt, cat, ttt, gtg, gaa, gag, gtg, caa, gag, ccg, act, gag, ttt, gtg, atc, gcc, gcg, act, cca, cag, ttg, gaa, gag, ctg, ttc, gtc, gag, ttt]
+--- --- --- --- --- --- --- atg tcg tcc agt agc aat aaa aaa gtg caa gtc aag --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- ttt ttc aaa gaa ttc ctg gac aag gca cgc gaa gac ttc aaa caa cga tgg gag aat ccg gct cag aac acg gcg tgt ctt gac gac ttt gat agg ata aaa acc ctt gga acc gga tca ttc ggg cgc gtg atg ctt gtg aag cat aag cag tcg ggc aac tat tat gcc atg aaa att cta gac aaa caa aag gtt gta aaa ctc aag caa gtg gag cac acg ttg aac gaa aag cgc att ctc cag gct atc gat ttt ccg ttt ttg gtg aac atg acg ttc tct ttc aag gac aac tcc aac ttg tac atg gtg ctc gaa ttc atc tcg gga ggt gag atg ttc tca cat tta cgc cga atc gga cgt ttc tcc gag ccc cac tcg cgt ttc tac gcc gct caa att gtg ctt gcc ttt gag tac ctt cac tcc tta gat ctc atc tat cgt gat ctg aaa ccc gag aac ttg ctt atc gat tcc act gga tat cta aag atc acc gat ttc gga ttt gcg aaa cgt gtc aaa gga cga acg tgg aca ttg tgc ggc aca cca gaa tac ttg gca ccc gag att att ttg tca aaa gga tac aat aag gct gtc gat tgg tgg gca ctt ggt gtg ttg atc tac gaa atg gcc gcc ggt tat ccg ccg ttc ttt gcc gat cag ccg att caa att tat gag aag att gtg tca gga aaa gtg aaa ttc ccg tcg cac ttc tcg aat gag ttg aaa gac ttg ctg aag aat ttg ctc caa gtt gat ctt aca aag cga tac ggt aac ctg aaa aat gga gtt gcc gat atc aaa aat cac aag tgg ttt gga agt acc gac tgg att gcc atc tat cag aag aag atc aca ccg ccc tcg ttc tcc aaa gga gaa tcc aat ggt cga ctg ttc gag gct ctg tat cca cgt gtc gat ggt ccc gcc gac aca cgt cat ttt gtg gaa gag gtg caa gag ccg act gag ttt gtg atc gcc gcg act cca cag ttg gaa gag ctg ttc gtc gag ttt
 >ZK909.2a
-[---, ---, ---, ---, ---, ---, ---, atg, ctc, aag, ttt, ctg, aaa, cca, aaa, tcg, tcg, gac, gag, gga, agc, tcg, aag, gac, aac, aag, aac, tcg, gcg, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, tcg, ctc, aaa, gaa, ttc, ctg, gac, aag, gca, cgc, gaa, gac, ttc, aaa, caa, cga, tgg, gag, aat, ccg, gct, cag, aac, acg, gcg, tgt, ctt, gac, gac, ttt, gat, agg, ata, aaa, acc, ctt, gga, acc, gga, tca, ttc, ggg, cgc, gtg, atg, ctt, gtg, aag, cat, aag, cag, tcg, ggc, aac, tat, tat, gcc, atg, aaa, att, cta, gac, aaa, caa, aag, gtt, gta, aaa, ctc, aag, caa, gtg, gag, cac, acg, ttg, aac, gaa, aag, cgc, att, ctc, cag, gct, atc, gat, ttt, ccg, ttt, ttg, gtg, aac, atg, acg, ttc, tct, ttc, aag, gac, aac, tcc, aac, ttg, tac, atg, gtg, ctc, gaa, ttc, atc, tcg, gga, ggt, gag, atg, ttc, tca, cat, tta, cgc, cga, atc, gga, cgt, ttc, tcc, gag, ccc, cac, tcg, cgt, ttc, tac, gcc, gct, caa, att, gtg, ctt, gcc, ttt, gag, tac, ctt, cac, tcc, tta, gat, ctc, atc, tat, cgt, gat, ctg, aaa, ccc, gag, aac, ttg, ctt, atc, gat, tcc, act, gga, tat, cta, aag, atc, acc, gat, ttc, gga, ttt, gcg, aaa, cgt, gtc, aaa, gga, cga, acg, tgg, aca, ttg, tgc, ggc, aca, cca, gaa, tac, ttg, gca, ccc, gag, att, att, ttg, tca, aaa, gga, tac, aat, aag, gct, gtc, gat, tgg, tgg, gca, ctt, ggt, gtg, ttg, atc, tac, gaa, atg, gcc, gcc, ggt, tat, ccg, ccg, ttc, ttt, gcc, gat, cag, ccg, att, caa, att, tat, gag, aag, att, gtg, tca, gga, aaa, gtg, aaa, ttc, ccg, tcg, cac, ttc, tcg, aat, gag, ttg, aaa, gac, ttg, ctg, aag, aat, ttg, ctc, caa, gtt, gat, ctt, aca, aag, cga, tac, ggt, aac, ctg, aaa, aat, gga, gtt, gcc, gat, atc, aaa, aat, cac, aag, tgg, ttt, gga, agt, acc, gac, tgg, att, gcc, atc, tat, cag, aag, aag, atc, gaa, gca, ccg, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ttc, ctt, cca, aaa, tgc, cgt, ggc, cct, ggc, gac, gca, tct, aac, ttt, gac, gac, tac, gag, gaa, gag, ccg, ---, ---, ctt, cgt, atc, tcg, ggc, acc, gag, aaa, tgc, gcc, aaa, gag, ttt, gcc, gag, ttt]
+--- --- --- --- --- --- --- atg ctc aag ttt ctg aaa cca aaa tcg tcg gac gag gga agc tcg aag gac aac aag aac tcg gcg --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- tcg ctc aaa gaa ttc ctg gac aag gca cgc gaa gac ttc aaa caa cga tgg gag aat ccg gct cag aac acg gcg tgt ctt gac gac ttt gat agg ata aaa acc ctt gga acc gga tca ttc ggg cgc gtg atg ctt gtg aag cat aag cag tcg ggc aac tat tat gcc atg aaa att cta gac aaa caa aag gtt gta aaa ctc aag caa gtg gag cac acg ttg aac gaa aag cgc att ctc cag gct atc gat ttt ccg ttt ttg gtg aac atg acg ttc tct ttc aag gac aac tcc aac ttg tac atg gtg ctc gaa ttc atc tcg gga ggt gag atg ttc tca cat tta cgc cga atc gga cgt ttc tcc gag ccc cac tcg cgt ttc tac gcc gct caa att gtg ctt gcc ttt gag tac ctt cac tcc tta gat ctc atc tat cgt gat ctg aaa ccc gag aac ttg ctt atc gat tcc act gga tat cta aag atc acc gat ttc gga ttt gcg aaa cgt gtc aaa gga cga acg tgg aca ttg tgc ggc aca cca gaa tac ttg gca ccc gag att att ttg tca aaa gga tac aat aag gct gtc gat tgg tgg gca ctt ggt gtg ttg atc tac gaa atg gcc gcc ggt tat ccg ccg ttc ttt gcc gat cag ccg att caa att tat gag aag att gtg tca gga aaa gtg aaa ttc ccg tcg cac ttc tcg aat gag ttg aaa gac ttg ctg aag aat ttg ctc caa gtt gat ctt aca aag cga tac ggt aac ctg aaa aat gga gtt gcc gat atc aaa aat cac aag tgg ttt gga agt acc gac tgg att gcc atc tat cag aag aag atc gaa gca ccg --- --- --- --- --- --- --- --- --- --- --- --- --- --- ttc ctt cca aaa tgc cgt ggc cct ggc gac gca tct aac ttt gac gac tac gag gaa gag ccg --- --- ctt cgt atc tcg ggc acc gag aaa tgc gcc aaa gag ttt gcc gag ttt
 >ZK909.2i
-[---, ---, ---, ---, ---, ---, ---, atg, gga, tcc, atg, gtg, ttc, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, att, gtc, aaa, gaa, ttc, ctg, gac, aag, gca, cgc, gaa, gac, ttc, aaa, caa, cga, tgg, gag, aat, ccg, gct, cag, aac, acg, gcg, tgt, ctt, gac, gac, ttt, gat, agg, ata, aaa, acc, ctt, gga, acc, gga, tca, ttc, ggg, cgc, gtg, atg, ctt, gtg, aag, cat, aag, cag, tcg, ggc, aac, tat, tat, gcc, atg, aaa, att, cta, gac, aaa, caa, aag, gtt, gta, aaa, ctc, aag, caa, gtg, gag, cac, acg, ttg, aac, gaa, aag, cgc, att, ctc, cag, gct, atc, gat, ttt, ccg, ttt, ttg, gtg, aac, atg, acg, ttc, tct, ttc, aag, gac, aac, tcc, aac, ttg, tac, atg, gtg, ctc, gaa, ttc, atc, tcg, gga, ggt, gag, atg, ttc, tca, cat, tta, cgc, cga, atc, gga, cgt, ttc, tcc, gag, ccc, cac, tcg, cgt, ttc, tac, gcc, gct, caa, att, gtg, ctt, gcc, ttt, gag, tac, ctt, cac, tcc, tta, gat, ctc, atc, tat, cgt, gat, ctg, aaa, ccc, gag, aac, ttg, ctt, atc, gat, tcc, act, gga, tat, cta, aag, atc, acc, gat, ttc, gga, ttt, gcg, aaa, cgt, gtc, aaa, gga, cga, acg, tgg, aca, ttg, tgc, ggc, aca, cca, gaa, tac, ttg, gca, ccc, gag, att, att, ttg, tca, aaa, gga, tac, aat, aag, gct, gtc, gat, tgg, tgg, gca, ctt, ggt, gtg, ttg, atc, tac, gaa, atg, gcc, gcc, ggt, tat, ccg, ccg, ttc, ttt, gcc, gat, cag, ccg, att, caa, att, tat, gag, aag, att, gtg, tca, gga, aaa, gtg, aaa, ttc, ccg, tcg, cac, ttc, tcg, aat, gag, ttg, aaa, gac, ttg, ctg, aag, aat, ttg, ctc, caa, gtt, gat, ctt, aca, aag, cga, tac, ggt, aac, ctg, aaa, aat, gga, gtt, gcc, gat, atc, aaa, aat, cac, aag, tgg, ttt, gga, agt, acc, gac, tgg, att, gcc, atc, tat, cag, aag, aag, atc, aca, ccg, ccc, tcg, ttc, tcc, aaa, gga, gaa, tcc, aat, ggt, cga, ctg, ttc, gag, gct, ctg, tat, cca, cgt, gtc, gat, ggt, ccc, gcc, gac, aca, cgt, cat, ttt, gtg, gaa, gag, gtg, caa, gag, ccg, act, gag, ttt, gtg, atc, gcc, gcg, act, cca, cag, ttg, gaa, gag, ctg, ttc, gtc, gag, ttt]
+--- --- --- --- --- --- --- atg gga tcc atg gtg ttc --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- att gtc aaa gaa ttc ctg gac aag gca cgc gaa gac ttc aaa caa cga tgg gag aat ccg gct cag aac acg gcg tgt ctt gac gac ttt gat agg ata aaa acc ctt gga acc gga tca ttc ggg cgc gtg atg ctt gtg aag cat aag cag tcg ggc aac tat tat gcc atg aaa att cta gac aaa caa aag gtt gta aaa ctc aag caa gtg gag cac acg ttg aac gaa aag cgc att ctc cag gct atc gat ttt ccg ttt ttg gtg aac atg acg ttc tct ttc aag gac aac tcc aac ttg tac atg gtg ctc gaa ttc atc tcg gga ggt gag atg ttc tca cat tta cgc cga atc gga cgt ttc tcc gag ccc cac tcg cgt ttc tac gcc gct caa att gtg ctt gcc ttt gag tac ctt cac tcc tta gat ctc atc tat cgt gat ctg aaa ccc gag aac ttg ctt atc gat tcc act gga tat cta aag atc acc gat ttc gga ttt gcg aaa cgt gtc aaa gga cga acg tgg aca ttg tgc ggc aca cca gaa tac ttg gca ccc gag att att ttg tca aaa gga tac aat aag gct gtc gat tgg tgg gca ctt ggt gtg ttg atc tac gaa atg gcc gcc ggt tat ccg ccg ttc ttt gcc gat cag ccg att caa att tat gag aag att gtg tca gga aaa gtg aaa ttc ccg tcg cac ttc tcg aat gag ttg aaa gac ttg ctg aag aat ttg ctc caa gtt gat ctt aca aag cga tac ggt aac ctg aaa aat gga gtt gcc gat atc aaa aat cac aag tgg ttt gga agt acc gac tgg att gcc atc tat cag aag aag atc aca ccg ccc tcg ttc tcc aaa gga gaa tcc aat ggt cga ctg ttc gag gct ctg tat cca cgt gtc gat ggt ccc gcc gac aca cgt cat ttt gtg gaa gag gtg caa gag ccg act gag ttt gtg atc gcc gcg act cca cag ttg gaa gag ctg ttc gtc gag ttt
 >ZK909.2m
-[---, ---, ---, ---, ---, ---, ---, atg, tcg, tcc, agt, agc, aat, aaa, aaa, gtg, caa, gtc, aag, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ttt, ttc, aaa, gaa, ttc, ctg, gac, aag, gca, cgc, gaa, gac, ttc, aaa, caa, cga, tgg, gag, aat, ccg, gct, cag, aac, acg, gcg, tgt, ctt, gac, gac, ttt, gat, agg, ata, aaa, acc, ctt, gga, acc, gga, tca, ttc, ggg, cgc, gtg, atg, ctt, gtg, aag, cat, aag, cag, tcg, ggc, aac, tat, tat, gcc, atg, aaa, att, cta, gac, aaa, caa, aag, gtt, gta, aaa, ctc, aag, caa, gtg, gag, cac, acg, ttg, aac, gaa, aag, cgc, att, ctc, cag, gct, atc, gat, ttt, ccg, ttt, ttg, gtg, aac, atg, acg, ttc, tct, ttc, aag, gac, aac, tcc, aac, ttg, tac, atg, gtg, ctc, gaa, ttc, atc, tcg, gga, ggt, gag, atg, ttc, tca, cat, tta, cgc, cga, atc, gga, cgt, ttc, tcc, gag, ccc, cac, tcg, cgt, ttc, tac, gcc, gct, caa, att, gtg, ctt, gcc, ttt, gag, tac, ctt, cac, tcc, tta, gat, ctc, atc, tat, cgt, gat, ctg, aaa, ccc, gag, aac, ttg, ctt, atc, gat, tcc, act, gga, tat, cta, aag, atc, acc, gat, ttc, gga, ttt, gcg, aaa, cgt, gtc, aaa, gga, cga, acg, tgg, aca, ttg, tgc, ggc, aca, cca, gaa, tac, ttg, gca, ccc, gag, att, att, ttg, tca, aaa, gga, tac, aat, aag, gct, gtc, gat, tgg, tgg, gca, ctt, ggt, gtg, ttg, atc, tac, gaa, atg, gcc, gcc, ggt, tat, ccg, ccg, ttc, ttt, gcc, gat, cag, ccg, att, caa, att, tat, gag, aag, att, gtg, tca, gga, aaa, gtg, aaa, ttc, ccg, tcg, cac, ttc, tcg, aat, gag, ttg, aaa, gac, ttg, ctg, aag, aat, ttg, ctc, caa, gtt, gat, ctt, aca, aag, cga, tac, ggt, aac, ctg, aaa, aat, gga, gtt, gcc, gat, atc, aaa, aat, cac, aag, tgg, ttt, gga, agt, acc, gac, tgg, att, gcc, atc, tat, cag, aag, aag, atc, gaa, gca, ccg, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ttc, ctt, cca, aaa, tgc, cgt, ggc, cct, ggc, gac, gca, tct, aac, ttt, gac, gac, tac, gag, gaa, gag, ccg, ---, ---, ctt, cgt, atc, tcg, ggc, acc, gag, aaa, tgc, gcc, aaa, gag, ttt, gcc, gag, ttt]
+--- --- --- --- --- --- --- atg tcg tcc agt agc aat aaa aaa gtg caa gtc aag --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- ttt ttc aaa gaa ttc ctg gac aag gca cgc gaa gac ttc aaa caa cga tgg gag aat ccg gct cag aac acg gcg tgt ctt gac gac ttt gat agg ata aaa acc ctt gga acc gga tca ttc ggg cgc gtg atg ctt gtg aag cat aag cag tcg ggc aac tat tat gcc atg aaa att cta gac aaa caa aag gtt gta aaa ctc aag caa gtg gag cac acg ttg aac gaa aag cgc att ctc cag gct atc gat ttt ccg ttt ttg gtg aac atg acg ttc tct ttc aag gac aac tcc aac ttg tac atg gtg ctc gaa ttc atc tcg gga ggt gag atg ttc tca cat tta cgc cga atc gga cgt ttc tcc gag ccc cac tcg cgt ttc tac gcc gct caa att gtg ctt gcc ttt gag tac ctt cac tcc tta gat ctc atc tat cgt gat ctg aaa ccc gag aac ttg ctt atc gat tcc act gga tat cta aag atc acc gat ttc gga ttt gcg aaa cgt gtc aaa gga cga acg tgg aca ttg tgc ggc aca cca gaa tac ttg gca ccc gag att att ttg tca aaa gga tac aat aag gct gtc gat tgg tgg gca ctt ggt gtg ttg atc tac gaa atg gcc gcc ggt tat ccg ccg ttc ttt gcc gat cag ccg att caa att tat gag aag att gtg tca gga aaa gtg aaa ttc ccg tcg cac ttc tcg aat gag ttg aaa gac ttg ctg aag aat ttg ctc caa gtt gat ctt aca aag cga tac ggt aac ctg aaa aat gga gtt gcc gat atc aaa aat cac aag tgg ttt gga agt acc gac tgg att gcc atc tat cag aag aag atc gaa gca ccg --- --- --- --- --- --- --- --- --- --- --- --- --- --- ttc ctt cca aaa tgc cgt ggc cct ggc gac gca tct aac ttt gac gac tac gag gaa gag ccg --- --- ctt cgt atc tcg ggc acc gag aaa tgc gcc aaa gag ttt gcc gag ttt
 >ZK909.2g
-[---, ---, ---, ---, ---, ---, ---, atg, gga, tcc, atg, gtg, ttc, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, att, gtc, aaa, gaa, ttc, ctg, gac, aag, gca, cgc, gaa, gac, ttc, aaa, caa, cga, tgg, gag, aat, ccg, gct, cag, aac, acg, gcg, tgt, ctt, gac, gac, ttt, gat, agg, ata, aaa, acc, ctt, gga, acc, gga, tca, ttc, ggg, cgc, gtg, atg, ctt, gtg, aag, cat, aag, cag, tcg, ggc, aac, tat, tat, gcc, atg, aaa, att, cta, gac, aaa, caa, aag, gtt, gta, aaa, ctc, aag, caa, gtg, gag, cac, acg, ttg, aac, gaa, aag, cgc, att, ctc, cag, gct, atc, gat, ttt, ccg, ttt, ttg, gtg, aac, atg, acg, ttc, tct, ttc, aag, gac, aac, tcc, aac, ttg, tac, atg, gtg, ctc, gaa, ttc, atc, tcg, gga, ggt, gag, atg, ttc, tca, cat, tta, cgc, cga, atc, gga, cgt, ttc, tcc, gag, ccc, cac, tcg, cgt, ttc, tac, gcc, gct, caa, att, gtg, ctt, gcc, ttt, gag, tac, ctt, cac, tcc, tta, gat, ctc, atc, tat, cgt, gat, ctg, aaa, ccc, gag, aac, ttg, ctt, atc, gat, tcc, act, gga, tat, cta, aag, atc, acc, gat, ttc, gga, ttt, gcg, aaa, cgt, gtc, aaa, gga, cga, acg, tgg, aca, ttg, tgc, ggc, aca, cca, gaa, tac, ttg, gca, ccc, gag, att, att, ttg, tca, aaa, gga, tac, aat, aag, gct, gtc, gat, tgg, tgg, gca, ctt, ggt, gtg, ttg, atc, tac, gaa, atg, gcc, gcc, ggt, tat, ccg, ccg, ttc, ttt, gcc, gat, cag, ccg, att, caa, att, tat, gag, aag, att, gtg, tca, gga, aaa, gtg, aaa, ttc, ccg, tcg, cac, ttc, tcg, aat, gag, ttg, aaa, gac, ttg, ctg, aag, aat, ttg, ctc, caa, gtt, gat, ctt, aca, aag, cga, tac, ggt, aac, ctg, aaa, aat, gga, gtt, gcc, gat, atc, aaa, aat, cac, aag, tgg, ttt, gga, agt, acc, gac, tgg, att, gcc, atc, tat, cag, aag, aag, atc, gaa, gca, ccg, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ---, ttc, ctt, cca, aaa, tgc, cgt, ggc, cct, ggc, gac, gca, tct, aac, ttt, gac, gac, tac, gag, gaa, gag, ccg, ---, ---, ctt, cgt, atc, tcg, ggc, acc, gag, aaa, tgc, gcc, aaa, gag, ttt, gcc, gag, ttt]
+--- --- --- --- --- --- --- atg gga tcc atg gtg ttc --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- --- att gtc aaa gaa ttc ctg gac aag gca cgc gaa gac ttc aaa caa cga tgg gag aat ccg gct cag aac acg gcg tgt ctt gac gac ttt gat agg ata aaa acc ctt gga acc gga tca ttc ggg cgc gtg atg ctt gtg aag cat aag cag tcg ggc aac tat tat gcc atg aaa att cta gac aaa caa aag gtt gta aaa ctc aag caa gtg gag cac acg ttg aac gaa aag cgc att ctc cag gct atc gat ttt ccg ttt ttg gtg aac atg acg ttc tct ttc aag gac aac tcc aac ttg tac atg gtg ctc gaa ttc atc tcg gga ggt gag atg ttc tca cat tta cgc cga atc gga cgt ttc tcc gag ccc cac tcg cgt ttc tac gcc gct caa att gtg ctt gcc ttt gag tac ctt cac tcc tta gat ctc atc tat cgt gat ctg aaa ccc gag aac ttg ctt atc gat tcc act gga tat cta aag atc acc gat ttc gga ttt gcg aaa cgt gtc aaa gga cga acg tgg aca ttg tgc ggc aca cca gaa tac ttg gca ccc gag att att ttg tca aaa gga tac aat aag gct gtc gat tgg tgg gca ctt ggt gtg ttg atc tac gaa atg gcc gcc ggt tat ccg ccg ttc ttt gcc gat cag ccg att caa att tat gag aag att gtg tca gga aaa gtg aaa ttc ccg tcg cac ttc tcg aat gag ttg aaa gac ttg ctg aag aat ttg ctc caa gtt gat ctt aca aag cga tac ggt aac ctg aaa aat gga gtt gcc gat atc aaa aat cac aag tgg ttt gga agt acc gac tgg att gcc atc tat cag aag aag atc gaa gca ccg --- --- --- --- --- --- --- --- --- --- --- --- --- --- ttc ctt cca aaa tgc cgt ggc cct ggc gac gca tct aac ttt gac gac tac gag gaa gag ccg --- --- ctt cgt atc tcg ggc acc gag aaa tgc gcc aaa gag ttt gcc gag ttt

metadata

@@ -1,145 +1,16 @@
 --- !ruby/object:Gem::Specification
 name: bio-alignment
 version: !ruby/object:Gem::Version
-  version: 0.0.8
-  prerelease: 
+  version: 0.0.9
 platform: ruby
 authors:
 - Pjotr Prins
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-05-15 00:00:00.000000000 Z
-dependencies:
-- !ruby/object:Gem::Dependency
-  name: bio-logger
-  requirement: !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - ! '>='
-      - !ruby/object:Gem::Version
-        version: '0'
-  type: :runtime
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - ! '>='
-      - !ruby/object:Gem::Version
-        version: '0'
-- !ruby/object:Gem::Dependency
-  name: bio
-  requirement: !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - ! '>='
-      - !ruby/object:Gem::Version
-        version: 1.4.2
-  type: :runtime
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - ! '>='
-      - !ruby/object:Gem::Version
-        version: 1.4.2
-- !ruby/object:Gem::Dependency
-  name: rake
-  requirement: !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - ! '>='
-      - !ruby/object:Gem::Version
-        version: '0'
-  type: :development
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - ! '>='
-      - !ruby/object:Gem::Version
-        version: '0'
-- !ruby/object:Gem::Dependency
-  name: bio-bigbio
-  requirement: !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - ! '>'
-      - !ruby/object:Gem::Version
-        version: 0.1.3
-  type: :development
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - ! '>'
-      - !ruby/object:Gem::Version
-        version: 0.1.3
-- !ruby/object:Gem::Dependency
-  name: cucumber
-  requirement: !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - ! '>='
-      - !ruby/object:Gem::Version
-        version: '0'
-  type: :development
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - ! '>='
-      - !ruby/object:Gem::Version
-        version: '0'
-- !ruby/object:Gem::Dependency
-  name: rspec
-  requirement: !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - ~>
-      - !ruby/object:Gem::Version
-        version: 2.10.0
-  type: :development
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - ~>
-      - !ruby/object:Gem::Version
-        version: 2.10.0
-- !ruby/object:Gem::Dependency
-  name: bundler
-  requirement: !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - ! '>='
-      - !ruby/object:Gem::Version
-        version: 1.0.21
-  type: :development
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - ! '>='
-      - !ruby/object:Gem::Version
-        version: 1.0.21
-- !ruby/object:Gem::Dependency
-  name: jeweler
-  requirement: !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - ! '>='
-      - !ruby/object:Gem::Version
-        version: '0'
-  type: :development
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - ! '>='
-      - !ruby/object:Gem::Version
-        version: '0'
-description: Alignment handler for multiple sequence alignments (MSA)
+date: 2016-10-11 00:00:00.000000000 Z
+dependencies: []
+description: 
 email: pjotr.public01@thebird.nl
 executables:
 - bio-alignment
@@ -149,9 +20,9 @@ extra_rdoc_files:
 - README.md
 - TODO
 files:
-- .document
-- .rspec
-- .travis.yml
+- ".document"
+- ".rspec"
+- ".travis.yml"
 - Gemfile
 - LICENSE.txt
 - README.md
@@ -221,29 +92,25 @@ files:
 homepage: http://github.com/pjotrp/bioruby-alignment
 licenses:
 - MIT
+metadata: {}
 post_install_message: 
 rdoc_options: []
 require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
-  - - ! '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: '0'
-      segments:
-      - 0
-      hash: 3021753307968946034
 required_rubygems_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
-  - - ! '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 1.8.23
+rubygems_version: 2.5.1
 signing_key: 
-specification_version: 3
+specification_version: 4
 summary: Support for multiple sequence alignments (MSA)
 test_files: []