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Viewing changes to test/primer_lib_amb_codes_input

  • Committer: Bazaar Package Importer
  • Author(s): Charles Plessy
  • Date: 2006-09-28 20:18:54 UTC
  • Revision ID: james.westby@ubuntu.com-20060928201854-45pwapz5e3a6d684
Tags: upstream-1.0b
Import upstream version 1.0b

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Lines of Context:
test/primer_lib_amb_codes_input
 
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PRIMER_EXPLAIN_FLAG=1
 
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PRIMER_NUM_RETURN=1
 
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PRIMER_OPT_SIZE=20
 
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PRIMER_PICK_INTERNAL_OLIGO=1
 
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PRIMER_INTERNAL_OLIGO_SELF_END=8
 
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PRIMER_INTERNAL_OLIGO_MAX_TM=100
 
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PRIMER_INTERNAL_OLIGO_MIN_TM=0
 
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PRIMER_MIN_SIZE=18
 
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PRIMER_MAX_SIZE=25
 
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PRIMER_OPT_TM=60.0
 
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PRIMER_MIN_TM=0.0
 
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PRIMER_MAX_TM=100.0
 
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PRIMER_MIN_GC=0.0
 
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PRIMER_MAX_GC=100.0
 
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PRIMER_MAX_POLY_X=100
 
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PRIMER_INTERNAL_OLIGO_MAX_POLY_X=100
 
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PRIMER_SALT_CONC=50.0
 
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PRIMER_DNA_CONC=50.0
 
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PRIMER_NUM_NS_ACCEPTED=0
 
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PRIMER_SELF_ANY=12
 
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PRIMER_SELF_END=8
 
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PRIMER_PRODUCT_SIZE_RANGE=75-500
 
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PRIMER_MISPRIMING_LIBRARY=not_for_production.lib
 
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MARKER_NAME=test_01
 
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SEQUENCE=GCTTGCATGCCTGCAGGTCGACTCTAGAGGATCCCCCTACATTTTAGCATCAGTGAGTACAGCATGCTTACTGGAAGAGAGGGTCATGCAACAGATTAGGAGGTAAGTTTGCAAAGGCAGGCTAAGGAGGAGACGCACTGAATGCCATGGTAAGAACTCTGGACATAAAAATATTGGAAGTTGTTGAGCAAGTAAAAAAATGTTTGGAAGTGTTACTTTAGCAATGGCAAGAATGATAGTATGGAATAGATTGGCAGAATGAAGGCAAAATGATTAGACATATTGCATTAAGGTAAAAAATGATAACTGAAGAATTATGTGCCACACTTATTAATAAGAAAGAATATGTGAACCTTGCAGATGTTTCCCTCTAGTAG
 
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PRIMER_COMMENT=Should succeed
 
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=
 
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PRIMER_MISPRIMING_LIBRARY=not_for_production.lib
 
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PRIMER_LIB_AMBIGUITY_CODES_CONSENSUS=0
 
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MARKER_NAME=test_02
 
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SEQUENCE=GCTTGCATGCCTGCAGGTCGACTCTAGAGGATCCCCCTACATTTTAGCATCAGTGAGTACAGCATGCTTACTGGAAGAGAGGGTCATGCAACAGATTAGGAGGTAAGTTTGCAAAGGCAGGCTAAGGAGGAGACGCACTGAATGCCATGGTAAGAACTCTGGACATAAAAATATTGGAAGTTGTTGAGCAAGTAAAAAAATGTTTGGAAGTGTTACTTTAGCAATGGCAAGAATGATAGTATGGAATAGATTGGCAGAATGAAGGCAAAATGATTAGACATATTGCATTAAGGTAAAAAATGATAACTGAAGAATTATGTGCCACACTTATTAATAAGAAAGAATATGTGAACCTTGCAGATGTTTCCCTCTAGTAG
 
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PRIMER_COMMENT=Should still succeed
 
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=
 
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MARKER_NAME=test_03
 
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PRIMER_LIB_AMBIGUITY_CODES_CONSENSUS=1
 
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PRIMER_MISPRIMING_LIBRARY=not_for_production_Ns.lib
 
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SEQUENCE=GCTTGCATGCCTGCAGGTCGACTCTAGAGGATCCCCCTACATTTTAGCATCAGTGAGTACAGCATGCTTACTGGAAGAGAGGGTCATGCAACAGATTAGGAGGTAAGTTTGCAAAGGCAGGCTAAGGAGGAGACGCACTGAATGCCATGGTAAGAACTCTGGACATAAAAATATTGGAAGTTGTTGAGCAAGTAAAAAAATGTTTGGAAGTGTTACTTTAGCAATGGCAAGAATGATAGTATGGAATAGATTGGCAGAATGAAGGCAAAATGATTAGACATATTGCATTAAGGTAAAAAATGATAACTGAAGAATTATGTGCCACACTTATTAATAAGAAAGAATATGTGAACCTTGCAGATGTTTCCCTCTAGTAG
 
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PRIMER_LEFT_INPUT=CGACTCTAGAGGATCCCCCT
 
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PRIMER_RIGHT_INPUT=TAGCCTGCCTTTGCAAACTT
 
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PRIMER_INTERNAL_OLIGO_INPUT=GGAAGAGAGGGTCATGCAAC
 
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PRIMER_PICK_ANYWAY=1
 
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PRIMER_COMMENT=Both primers should have high repeat similarity
 
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=
 
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MARKER_NAME=test_04
 
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PRIMER_LIB_AMBIGUITY_CODES_CONSENSUS=0
 
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PRIMER_MISPRIMING_LIBRARY=not_for_production_Ns.lib
 
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SEQUENCE=GCTTGCATGCCTGCAGGTCGACTCTAGAGGATCCCCCTACATTTTAGCATCAGTGAGTACAGCATGCTTACTGGAAGAGAGGGTCATGCAACAGATTAGGAGGTAAGTTTGCAAAGGCAGGCTAAGGAGGAGACGCACTGAATGCCATGGTAAGAACTCTGGACATAAAAATATTGGAAGTTGTTGAGCAAGTAAAAAAATGTTTGGAAGTGTTACTTTAGCAATGGCAAGAATGATAGTATGGAATAGATTGGCAGAATGAAGGCAAAATGATTAGACATATTGCATTAAGGTAAAAAATGATAACTGAAGAATTATGTGCCACACTTATTAATAAGAAAGAATATGTGAACCTTGCAGATGTTTCCCTCTAGTAG
 
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PRIMER_LEFT_INPUT=CGACTCTAGAGGATCCCCCT
 
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PRIMER_RIGHT_INPUT=TAGCCTGCCTTTGCAAACTT
 
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PRIMER_INTERNAL_OLIGO_INPUT=GGAAGAGAGGGTCATGCAAC
 
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PRIMER_PICK_ANYWAY=1
 
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PRIMER_COMMENT=Should succeed and both primers should have low repeat similarity
 
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=
 
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MARKER_NAME=test_05
 
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PRIMER_LIB_AMBIGUITY_CODES_CONSENSUS=1
 
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PRIMER_MISPRIMING_LIBRARY=not_for_production_Ns.lib
 
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SEQUENCE=GCTTGCATGCCTGCAGGTCGACTCTAGAGGATCCCCCTACATTTTAGCATCAGTGAGTACAGCATGCTTACTGGAAGAGAGGGTCATGCAACAGATTAGGAGGTAAGTTTGCAAAGGCAGGCTAAGGAGGAGACGCACTGAATGCCATGGTAAGAACTCTGGACATAAAAATATTGGAAGTTGTTGAGCAAGTAAAAAAATGTTTGGAAGTGTTACTTTAGCAATGGCAAGAATGATAGTATGGAATAGATTGGCAGAATGAAGGCAAAATGATTAGACATATTGCATTAAGGTAAAAAATGATAACTGAAGAATTATGTGCCACACTTATTAATAAGAAAGAATATGTGAACCTTGCAGATGTTTCCCTCTAGTAG
 
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PRIMER_COMMENT=Both primers should have high repeat similarity, but the explain line for right primers will not indicate this because mispriming is calculated "lazily" -- only if there are good left primers.
 
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=
 
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MARKER_NAME=test_06
 
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PRIMER_MISPRIMING_LIBRARY=not_for_production.lib
 
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PRIMER_INTERNAL_OLIGO_MISHYB_LIBRARY=not_for_production_Ns.lib
 
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SEQUENCE=GCTTGCATGCCTGCAGGTCGACTCTAGAGGATCCCCCTACATTTTAGCATCAGTGAGTACAGCATGCTTACTGGAAGAGAGGGTCATGCAACAGATTAGGAGGTAAGTTTGCAAAGGCAGGCTAAGGAGGAGACGCACTGAATGCCATGGTAAGAACTCTGGACATAAAAATATTGGAAGTTGTTGAGCAAGTAAAAAAATGTTTGGAAGTGTTACTTTAGCAATGGCAAGAATGATAGTATGGAATAGATTGGCAGAATGAAGGCAAAATGATTAGACATATTGCATTAAGGTAAAAAATGATAACTGAAGAATTATGTGCCACACTTATTAATAAGAAAGAATATGTGAACCTTGCAGATGTTTCCCTCTAGTAG
 
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PRIMER_LEFT_INPUT=CGACTCTAGAGGATCCCCCT
 
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PRIMER_RIGHT_INPUT=TAGCCTGCCTTTGCAAACTT
 
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PRIMER_INTERNAL_OLIGO_INPUT=GGAAGAGAGGGTCATGCAAC
 
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PRIMER_PICK_ANYWAY=1
 
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PRIMER_COMMENT=Primers should be ok, but not internal oligo
 
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=
 
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MARKER_NAME=test_07
 
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PRIMER_MISPRIMING_LIBRARY=not_for_production.lib
 
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PRIMER_INTERNAL_OLIGO_MISHYB_LIBRARY=not_for_production_Ns.lib
 
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SEQUENCE=GCTTGCATGCCTGCAGGTCGACTCTAGAGGATCCCCCTACATTTTAGCATCAGTGAGTACAGCATGCTTACTGGAAGAGAGGGTCATGCAACAGATTAGGAGGTAAGTTTGCAAAGGCAGGCTAAGGAGGAGACGCACTGAATGCCATGGTAAGAACTCTGGACATAAAAATATTGGAAGTTGTTGAGCAAGTAAAAAAATGTTTGGAAGTGTTACTTTAGCAATGGCAAGAATGATAGTATGGAATAGATTGGCAGAATGAAGGCAAAATGATTAGACATATTGCATTAAGGTAAAAAATGATAACTGAAGAATTATGTGCCACACTTATTAATAAGAAAGAATATGTGAACCTTGCAGATGTTTCCCTCTAGTAG
 
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PRIMER_PICK_ANYWAY=1
 
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PRIMER_COMMENT=Primers should be ok, but not internal oligo
 
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=
 
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MARKER_NAME=test_08
 
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PRIMER_LIB_AMBIGUITY_CODES_CONSENSUS=1
 
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PRIMER_MISPRIMING_LIBRARY=not_for_production.lib
 
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PRIMER_INTERNAL_OLIGO_MISHYB_LIBRARY=not_for_production_Ns.lib
 
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SEQUENCE=GCTTGCATGCCTGCAGGTCGACTCTAGAGGATCCCCCTCTGATCATCTTCTGATCCAAGACCCGTGCTAGTCTACTGTATTCTACATGTACCCTTCTACAAGCTTTGAATTCCATAATCATCAGAGAATCCAGAAATTATTCATTATCACATAATAACAACACTCAAATATTTAAAGTTTTATGGTTGAATCTTTATGATTGAACCCATTCTATCAGGTGGTTATTTTATATCTAATAGAATTCATTTCAGGGTTACACAAAGGTCCGAATCTATCCATTTTACTGAG
 
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PRIMER_COMMENT=Should fail because of high repeat similarity for all internal oligos
 
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=
 
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MARKER_NAME=test_09
 
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PRIMER_LIB_AMBIGUITY_CODES_CONSENSUS=0
 
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PRIMER_MISPRIMING_LIBRARY=not_for_production_Xs.lib
 
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SEQUENCE=GCTTGCATGCCTGCAGGTCGACTCTAGAGGATCCCCCTACATTTTAGCATCAGTGAGTACAGCATGCTTACTGGAAGAGAGGGTCATGCAACAGATTAGGAGGTAAGTTTGCAAAGGCAGGCTAAGGAGGAGACGCACTGAATGCCATGGTAAGAACTCTGGACATAAAAATATTGGAAGTTGTTGAGCAAGTAAAAAAATGTTTGGAAGTGTTACTTTAGCAATGGCAAGAATGATAGTATGGAATAGATTGGCAGAATGAAGGCAAAATGATTAGACATATTGCATTAAGGTAAAAAATGATAACTGAAGAATTATGTGCCACACTTATTAATAAGAAAGAATATGTGAACCTTGCAGATGTTTCCCTCTAGTAG
 
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PRIMER_COMMENT=Should succeed
 
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=
 
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MARKER_NAME=test_10
 
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PRIMER_LIB_AMBIGUITY_CODES_CONSENSUS=1
 
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PRIMER_MISPRIMING_LIBRARY=not_for_production_Xs.lib
 
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SEQUENCE=GCTTGCATGCCTGCAGGTCGACTCTAGAGGATCCCCCTACATTTTAGCATCAGTGAGTACAGCATGCTTACTGGAAGAGAGGGTCATGCAACAGATTAGGAGGTAAGTTTGCAAAGGCAGGCTAAGGAGGAGACGCACTGAATGCCATGGTAAGAACTCTGGACATAAAAATATTGGAAGTTGTTGAGCAAGTAAAAAAATGTTTGGAAGTGTTACTTTAGCAATGGCAAGAATGATAGTATGGAATAGATTGGCAGAATGAAGGCAAAATGATTAGACATATTGCATTAAGGTAAAAAATGATAACTGAAGAATTATGTGCCACACTTATTAATAAGAAAGAATATGTGAACCTTGCAGATGTTTCCCTCTAGTAG
 
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PRIMER_COMMENT=Should fail (Xs are treated as Ns).
 
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=
 
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MARKER_NAME=test_11
 
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PRIMER_LIB_AMBIGUITY_CODES_CONSENSUS=1
 
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PRIMER_MISPRIMING_LIBRARY=
 
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PRIMER_INTERNAL_OLIGO_MISHYB_LIBRARY=not_for_production_Xs.lib
 
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SEQUENCE=GCTTGCATGCCTGCAGGTCGACTCTAGAGGATCCCCCTACATTTTAGCATCAGTGAGTACAGCATGCTTACTGGAAGAGAGGGTCATGCAACAGATTAGGAGGTAAGTTTGCAAAGGCAGGCTAAGGAGGAGACGCACTGAATGCCATGGTAAGAACTCTGGACATAAAAATATTGGAAGTTGTTGAGCAAGTAAAAAAATGTTTGGAAGTGTTACTTTAGCAATGGCAAGAATGATAGTATGGAATAGATTGGCAGAATGAAGGCAAAATGATTAGACATATTGCATTAAGGTAAAAAATGATAACTGAAGAATTATGTGCCACACTTATTAATAAGAAAGAATATGTGAACCTTGCAGATGTTTCCCTCTAGTAG
 
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PRIMER_COMMENT=Should fail (Xs are treated as Ns).
 
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=