PRIMER_EXPLAIN_FLAG=1
PRIMER_NUM_RETURN=1
PRIMER_OPT_SIZE=20
PRIMER_PICK_INTERNAL_OLIGO=1
PRIMER_INTERNAL_MAX_SELF_END=8
PRIMER_INTERNAL_MAX_TM=100
PRIMER_INTERNAL_MIN_TM=0
PRIMER_MIN_SIZE=18
PRIMER_MAX_SIZE=25
PRIMER_OPT_TM=60.0
PRIMER_MIN_TM=0.0
PRIMER_MAX_TM=100.0
PRIMER_MIN_GC=0.0
PRIMER_MAX_GC=100.0
PRIMER_MAX_POLY_X=100
PRIMER_INTERNAL_MAX_POLY_X=100
PRIMER_SALT_MONOVALENT=50.0
PRIMER_DNA_CONC=50.0
PRIMER_MAX_NS_ACCEPTED=0
PRIMER_MAX_SELF_ANY=12
PRIMER_MAX_SELF_END=8
PRIMER_PAIR_MAX_COMPL_ANY=12
PRIMER_PAIR_MAX_COMPL_END=8
PRIMER_PRODUCT_SIZE_RANGE=75-500
PRIMER_MISPRIMING_LIBRARY=not_for_production.lib
SEQUENCE_ID=test_01
SEQUENCE_TEMPLATE=GCTTGCATGCCTGCAGGTCGACTCTAGAGGATCCCCCTACATTTTAGCATCAGTGAGTACAGCATGCTTACTGGAAGAGAGGGTCATGCAACAGATTAGGAGGTAAGTTTGCAAAGGCAGGCTAAGGAGGAGACGCACTGAATGCCATGGTAAGAACTCTGGACATAAAAATATTGGAAGTTGTTGAGCAAGTAAAAAAATGTTTGGAAGTGTTACTTTAGCAATGGCAAGAATGATAGTATGGAATAGATTGGCAGAATGAAGGCAAAATGATTAGACATATTGCATTAAGGTAAAAAATGATAACTGAAGAATTATGTGCCACACTTATTAATAAGAAAGAATATGTGAACCTTGCAGATGTTTCCCTCTAGTAG
P3_COMMENT=Should succeed
=
PRIMER_MISPRIMING_LIBRARY=not_for_production.lib
PRIMER_LIB_AMBIGUITY_CODES_CONSENSUS=0
SEQUENCE_ID=test_02
SEQUENCE_TEMPLATE=GCTTGCATGCCTGCAGGTCGACTCTAGAGGATCCCCCTACATTTTAGCATCAGTGAGTACAGCATGCTTACTGGAAGAGAGGGTCATGCAACAGATTAGGAGGTAAGTTTGCAAAGGCAGGCTAAGGAGGAGACGCACTGAATGCCATGGTAAGAACTCTGGACATAAAAATATTGGAAGTTGTTGAGCAAGTAAAAAAATGTTTGGAAGTGTTACTTTAGCAATGGCAAGAATGATAGTATGGAATAGATTGGCAGAATGAAGGCAAAATGATTAGACATATTGCATTAAGGTAAAAAATGATAACTGAAGAATTATGTGCCACACTTATTAATAAGAAAGAATATGTGAACCTTGCAGATGTTTCCCTCTAGTAG
P3_COMMENT=Should still succeed
=
SEQUENCE_ID=test_03
PRIMER_LIB_AMBIGUITY_CODES_CONSENSUS=1
PRIMER_MISPRIMING_LIBRARY=not_for_production_Ns.lib
SEQUENCE_TEMPLATE=GCTTGCATGCCTGCAGGTCGACTCTAGAGGATCCCCCTACATTTTAGCATCAGTGAGTACAGCATGCTTACTGGAAGAGAGGGTCATGCAACAGATTAGGAGGTAAGTTTGCAAAGGCAGGCTAAGGAGGAGACGCACTGAATGCCATGGTAAGAACTCTGGACATAAAAATATTGGAAGTTGTTGAGCAAGTAAAAAAATGTTTGGAAGTGTTACTTTAGCAATGGCAAGAATGATAGTATGGAATAGATTGGCAGAATGAAGGCAAAATGATTAGACATATTGCATTAAGGTAAAAAATGATAACTGAAGAATTATGTGCCACACTTATTAATAAGAAAGAATATGTGAACCTTGCAGATGTTTCCCTCTAGTAG
SEQUENCE_PRIMER=CGACTCTAGAGGATCCCCCT
SEQUENCE_PRIMER_REVCOMP=TAGCCTGCCTTTGCAAACTT
SEQUENCE_INTERNAL_OLIGO=GGAAGAGAGGGTCATGCAAC
PRIMER_PICK_ANYWAY=1
P3_COMMENT=Both primers should have high repeat similarity
=
SEQUENCE_ID=test_04
PRIMER_LIB_AMBIGUITY_CODES_CONSENSUS=0
PRIMER_MISPRIMING_LIBRARY=not_for_production_Ns.lib
SEQUENCE_TEMPLATE=GCTTGCATGCCTGCAGGTCGACTCTAGAGGATCCCCCTACATTTTAGCATCAGTGAGTACAGCATGCTTACTGGAAGAGAGGGTCATGCAACAGATTAGGAGGTAAGTTTGCAAAGGCAGGCTAAGGAGGAGACGCACTGAATGCCATGGTAAGAACTCTGGACATAAAAATATTGGAAGTTGTTGAGCAAGTAAAAAAATGTTTGGAAGTGTTACTTTAGCAATGGCAAGAATGATAGTATGGAATAGATTGGCAGAATGAAGGCAAAATGATTAGACATATTGCATTAAGGTAAAAAATGATAACTGAAGAATTATGTGCCACACTTATTAATAAGAAAGAATATGTGAACCTTGCAGATGTTTCCCTCTAGTAG
SEQUENCE_PRIMER=CGACTCTAGAGGATCCCCCT
SEQUENCE_PRIMER_REVCOMP=TAGCCTGCCTTTGCAAACTT
SEQUENCE_INTERNAL_OLIGO=GGAAGAGAGGGTCATGCAAC
PRIMER_PICK_ANYWAY=1
P3_COMMENT=Should succeed and both primers should have low repeat similarity
=
SEQUENCE_ID=test_05
PRIMER_LIB_AMBIGUITY_CODES_CONSENSUS=1
PRIMER_MISPRIMING_LIBRARY=not_for_production_Ns.lib
SEQUENCE_TEMPLATE=GCTTGCATGCCTGCAGGTCGACTCTAGAGGATCCCCCTACATTTTAGCATCAGTGAGTACAGCATGCTTACTGGAAGAGAGGGTCATGCAACAGATTAGGAGGTAAGTTTGCAAAGGCAGGCTAAGGAGGAGACGCACTGAATGCCATGGTAAGAACTCTGGACATAAAAATATTGGAAGTTGTTGAGCAAGTAAAAAAATGTTTGGAAGTGTTACTTTAGCAATGGCAAGAATGATAGTATGGAATAGATTGGCAGAATGAAGGCAAAATGATTAGACATATTGCATTAAGGTAAAAAATGATAACTGAAGAATTATGTGCCACACTTATTAATAAGAAAGAATATGTGAACCTTGCAGATGTTTCCCTCTAGTAG
P3_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.
=
SEQUENCE_ID=test_06
PRIMER_MISPRIMING_LIBRARY=not_for_production.lib
PRIMER_INTERNAL_MISHYB_LIBRARY=not_for_production_Ns.lib
SEQUENCE_TEMPLATE=GCTTGCATGCCTGCAGGTCGACTCTAGAGGATCCCCCTACATTTTAGCATCAGTGAGTACAGCATGCTTACTGGAAGAGAGGGTCATGCAACAGATTAGGAGGTAAGTTTGCAAAGGCAGGCTAAGGAGGAGACGCACTGAATGCCATGGTAAGAACTCTGGACATAAAAATATTGGAAGTTGTTGAGCAAGTAAAAAAATGTTTGGAAGTGTTACTTTAGCAATGGCAAGAATGATAGTATGGAATAGATTGGCAGAATGAAGGCAAAATGATTAGACATATTGCATTAAGGTAAAAAATGATAACTGAAGAATTATGTGCCACACTTATTAATAAGAAAGAATATGTGAACCTTGCAGATGTTTCCCTCTAGTAG
SEQUENCE_PRIMER=CGACTCTAGAGGATCCCCCT
SEQUENCE_PRIMER_REVCOMP=TAGCCTGCCTTTGCAAACTT
SEQUENCE_INTERNAL_OLIGO=GGAAGAGAGGGTCATGCAAC
PRIMER_PICK_ANYWAY=1
P3_COMMENT=Primers should be ok, but not internal oligo
=
SEQUENCE_ID=test_07
PRIMER_MISPRIMING_LIBRARY=not_for_production.lib
PRIMER_INTERNAL_MISHYB_LIBRARY=not_for_production_Ns.lib
SEQUENCE_TEMPLATE=GCTTGCATGCCTGCAGGTCGACTCTAGAGGATCCCCCTACATTTTAGCATCAGTGAGTACAGCATGCTTACTGGAAGAGAGGGTCATGCAACAGATTAGGAGGTAAGTTTGCAAAGGCAGGCTAAGGAGGAGACGCACTGAATGCCATGGTAAGAACTCTGGACATAAAAATATTGGAAGTTGTTGAGCAAGTAAAAAAATGTTTGGAAGTGTTACTTTAGCAATGGCAAGAATGATAGTATGGAATAGATTGGCAGAATGAAGGCAAAATGATTAGACATATTGCATTAAGGTAAAAAATGATAACTGAAGAATTATGTGCCACACTTATTAATAAGAAAGAATATGTGAACCTTGCAGATGTTTCCCTCTAGTAG
PRIMER_PICK_ANYWAY=1
P3_COMMENT=Primers should be ok, but not internal oligo
=
SEQUENCE_ID=test_08
PRIMER_LIB_AMBIGUITY_CODES_CONSENSUS=1
PRIMER_MISPRIMING_LIBRARY=not_for_production.lib
PRIMER_INTERNAL_MISHYB_LIBRARY=not_for_production_Ns.lib
SEQUENCE_TEMPLATE=GCTTGCATGCCTGCAGGTCGACTCTAGAGGATCCCCCTCTGATCATCTTCTGATCCAAGACCCGTGCTAGTCTACTGTATTCTACATGTACCCTTCTACAAGCTTTGAATTCCATAATCATCAGAGAATCCAGAAATTATTCATTATCACATAATAACAACACTCAAATATTTAAAGTTTTATGGTTGAATCTTTATGATTGAACCCATTCTATCAGGTGGTTATTTTATATCTAATAGAATTCATTTCAGGGTTACACAAAGGTCCGAATCTATCCATTTTACTGAG
P3_COMMENT=Should fail because of high repeat similarity for all internal oligos
=
SEQUENCE_ID=test_09
PRIMER_LIB_AMBIGUITY_CODES_CONSENSUS=0
PRIMER_MISPRIMING_LIBRARY=not_for_production_Xs.lib
SEQUENCE_TEMPLATE=GCTTGCATGCCTGCAGGTCGACTCTAGAGGATCCCCCTACATTTTAGCATCAGTGAGTACAGCATGCTTACTGGAAGAGAGGGTCATGCAACAGATTAGGAGGTAAGTTTGCAAAGGCAGGCTAAGGAGGAGACGCACTGAATGCCATGGTAAGAACTCTGGACATAAAAATATTGGAAGTTGTTGAGCAAGTAAAAAAATGTTTGGAAGTGTTACTTTAGCAATGGCAAGAATGATAGTATGGAATAGATTGGCAGAATGAAGGCAAAATGATTAGACATATTGCATTAAGGTAAAAAATGATAACTGAAGAATTATGTGCCACACTTATTAATAAGAAAGAATATGTGAACCTTGCAGATGTTTCCCTCTAGTAG
P3_COMMENT=Should succeed
=
SEQUENCE_ID=test_10
PRIMER_LIB_AMBIGUITY_CODES_CONSENSUS=1
PRIMER_MISPRIMING_LIBRARY=not_for_production_Xs.lib
SEQUENCE_TEMPLATE=GCTTGCATGCCTGCAGGTCGACTCTAGAGGATCCCCCTACATTTTAGCATCAGTGAGTACAGCATGCTTACTGGAAGAGAGGGTCATGCAACAGATTAGGAGGTAAGTTTGCAAAGGCAGGCTAAGGAGGAGACGCACTGAATGCCATGGTAAGAACTCTGGACATAAAAATATTGGAAGTTGTTGAGCAAGTAAAAAAATGTTTGGAAGTGTTACTTTAGCAATGGCAAGAATGATAGTATGGAATAGATTGGCAGAATGAAGGCAAAATGATTAGACATATTGCATTAAGGTAAAAAATGATAACTGAAGAATTATGTGCCACACTTATTAATAAGAAAGAATATGTGAACCTTGCAGATGTTTCCCTCTAGTAG
P3_COMMENT=Should fail (Xs are treated as Ns).
=
SEQUENCE_ID=test_11
PRIMER_LIB_AMBIGUITY_CODES_CONSENSUS=1
PRIMER_MISPRIMING_LIBRARY=
PRIMER_INTERNAL_MISHYB_LIBRARY=not_for_production_Xs.lib
SEQUENCE_TEMPLATE=GCTTGCATGCCTGCAGGTCGACTCTAGAGGATCCCCCTACATTTTAGCATCAGTGAGTACAGCATGCTTACTGGAAGAGAGGGTCATGCAACAGATTAGGAGGTAAGTTTGCAAAGGCAGGCTAAGGAGGAGACGCACTGAATGCCATGGTAAGAACTCTGGACATAAAAATATTGGAAGTTGTTGAGCAAGTAAAAAAATGTTTGGAAGTGTTACTTTAGCAATGGCAAGAATGATAGTATGGAATAGATTGGCAGAATGAAGGCAAAATGATTAGACATATTGCATTAAGGTAAAAAATGATAACTGAAGAATTATGTGCCACACTTATTAATAAGAAAGAATATGTGAACCTTGCAGATGTTTCCCTCTAGTAG
P3_COMMENT=Should fail (Xs are treated as Ns).
=
