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_LEFT_EXPLAIN=considered 2424, ok 2424
PRIMER_RIGHT_EXPLAIN=considered 2424, ok 2424
PRIMER_INTERNAL_EXPLAIN=considered 3555, GC content failed 92, ok 3463
PRIMER_PAIR_EXPLAIN=considered 94, unacceptable product size 90, ok 4
PRIMER_LEFT_NUM_RETURNED=1
PRIMER_RIGHT_NUM_RETURNED=1
PRIMER_INTERNAL_NUM_RETURNED=1
PRIMER_PAIR_NUM_RETURNED=1
PRIMER_PAIR_0_PENALTY=0.364612
PRIMER_LEFT_0_PENALTY=0.346766
PRIMER_RIGHT_0_PENALTY=0.017846
PRIMER_INTERNAL_0_PENALTY=0.339231
PRIMER_LEFT_0_SEQUENCE=CGACTCTAGAGGATCCCCCT
PRIMER_RIGHT_0_SEQUENCE=AGCCTGCCTTTGCAAACTTA
PRIMER_INTERNAL_0_SEQUENCE=GGAAGAGAGGGTCATGCAAC
PRIMER_LEFT_0=18,20
PRIMER_RIGHT_0=122,20
PRIMER_INTERNAL_0=72,20
PRIMER_LEFT_0_TM=59.653
PRIMER_RIGHT_0_TM=60.018
PRIMER_INTERNAL_0_TM=59.661
PRIMER_LEFT_0_GC_PERCENT=60.000
PRIMER_RIGHT_0_GC_PERCENT=45.000
PRIMER_INTERNAL_0_GC_PERCENT=55.000
PRIMER_LEFT_0_SELF_ANY=8.00
PRIMER_RIGHT_0_SELF_ANY=8.00
PRIMER_INTERNAL_0_SELF_ANY=4.00
PRIMER_LEFT_0_SELF_END=4.00
PRIMER_RIGHT_0_SELF_END=4.00
PRIMER_INTERNAL_0_SELF_END=2.00
PRIMER_LEFT_0_LIBRARY_MISPRIMING=9.00, L1 Human L1 interspersed repetitive sequence - full length copy
PRIMER_RIGHT_0_LIBRARY_MISPRIMING=10.00, reverse L1 Human L1 interspersed repetitive sequence - full length copy
PRIMER_PAIR_0_LIBRARY_MISPRIMING=18.00, reverse L1 Human L1 interspersed repetitive sequence - full length copy
PRIMER_LEFT_0_END_STABILITY=10.9000
PRIMER_RIGHT_0_END_STABILITY=5.7000
PRIMER_PAIR_0_COMPL_ANY=3.00
PRIMER_PAIR_0_COMPL_END=1.00
PRIMER_PAIR_0_PRODUCT_SIZE=105
PRIMER_PAIR_0_PRODUCT_TM=73.7
=
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
PRIMER_LEFT_EXPLAIN=considered 2424, ok 2424
PRIMER_RIGHT_EXPLAIN=considered 2424, ok 2424
PRIMER_INTERNAL_EXPLAIN=considered 3555, GC content failed 92, ok 3463
PRIMER_PAIR_EXPLAIN=considered 94, unacceptable product size 90, ok 4
PRIMER_LEFT_NUM_RETURNED=1
PRIMER_RIGHT_NUM_RETURNED=1
PRIMER_INTERNAL_NUM_RETURNED=1
PRIMER_PAIR_NUM_RETURNED=1
PRIMER_PAIR_0_PENALTY=0.364612
PRIMER_LEFT_0_PENALTY=0.346766
PRIMER_RIGHT_0_PENALTY=0.017846
PRIMER_INTERNAL_0_PENALTY=0.339231
PRIMER_LEFT_0_SEQUENCE=CGACTCTAGAGGATCCCCCT
PRIMER_RIGHT_0_SEQUENCE=AGCCTGCCTTTGCAAACTTA
PRIMER_INTERNAL_0_SEQUENCE=GGAAGAGAGGGTCATGCAAC
PRIMER_LEFT_0=18,20
PRIMER_RIGHT_0=122,20
PRIMER_INTERNAL_0=72,20
PRIMER_LEFT_0_TM=59.653
PRIMER_RIGHT_0_TM=60.018
PRIMER_INTERNAL_0_TM=59.661
PRIMER_LEFT_0_GC_PERCENT=60.000
PRIMER_RIGHT_0_GC_PERCENT=45.000
PRIMER_INTERNAL_0_GC_PERCENT=55.000
PRIMER_LEFT_0_SELF_ANY=8.00
PRIMER_RIGHT_0_SELF_ANY=8.00
PRIMER_INTERNAL_0_SELF_ANY=4.00
PRIMER_LEFT_0_SELF_END=4.00
PRIMER_RIGHT_0_SELF_END=4.00
PRIMER_INTERNAL_0_SELF_END=2.00
PRIMER_LEFT_0_LIBRARY_MISPRIMING=9.00, L1 Human L1 interspersed repetitive sequence - full length copy
PRIMER_RIGHT_0_LIBRARY_MISPRIMING=10.00, reverse L1 Human L1 interspersed repetitive sequence - full length copy
PRIMER_PAIR_0_LIBRARY_MISPRIMING=18.00, L1 Human L1 interspersed repetitive sequence - full length copy
PRIMER_LEFT_0_END_STABILITY=10.9000
PRIMER_RIGHT_0_END_STABILITY=5.7000
PRIMER_PAIR_0_COMPL_ANY=3.00
PRIMER_PAIR_0_COMPL_END=1.00
PRIMER_PAIR_0_PRODUCT_SIZE=105
PRIMER_PAIR_0_PRODUCT_TM=73.7
=
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
PRIMER_PAIR_EXPLAIN=considered 1, high mispriming library similarity 1, ok 1
PRIMER_LEFT_NUM_RETURNED=1
PRIMER_RIGHT_NUM_RETURNED=1
PRIMER_INTERNAL_NUM_RETURNED=1
PRIMER_PAIR_NUM_RETURNED=1
PRIMER_PAIR_0_PENALTY=0.364612
PRIMER_LEFT_0_PENALTY=0.346766
PRIMER_RIGHT_0_PENALTY=0.017846
PRIMER_INTERNAL_0_PENALTY=0.339231
PRIMER_LEFT_0_PROBLEMS= Similarity to non-template sequence too high;
PRIMER_RIGHT_0_PROBLEMS= Similarity to non-template sequence too high;
PRIMER_LEFT_0_SEQUENCE=CGACTCTAGAGGATCCCCCT
PRIMER_RIGHT_0_SEQUENCE=TAGCCTGCCTTTGCAAACTT
PRIMER_INTERNAL_0_SEQUENCE=GGAAGAGAGGGTCATGCAAC
PRIMER_LEFT_0=18,20
PRIMER_RIGHT_0=123,20
PRIMER_INTERNAL_0=72,20
PRIMER_LEFT_0_TM=59.653
PRIMER_RIGHT_0_TM=60.018
PRIMER_INTERNAL_0_TM=59.661
PRIMER_LEFT_0_GC_PERCENT=60.000
PRIMER_RIGHT_0_GC_PERCENT=45.000
PRIMER_INTERNAL_0_GC_PERCENT=55.000
PRIMER_LEFT_0_SELF_ANY=8.00
PRIMER_RIGHT_0_SELF_ANY=8.00
PRIMER_INTERNAL_0_SELF_ANY=4.00
PRIMER_LEFT_0_SELF_END=4.00
PRIMER_RIGHT_0_SELF_END=3.00
PRIMER_INTERNAL_0_SELF_END=2.00
PRIMER_LEFT_0_LIBRARY_MISPRIMING=20.00, L1 Human L1 interspersed repetitive sequence - full length copy
PRIMER_RIGHT_0_LIBRARY_MISPRIMING=20.00, L1 Human L1 interspersed repetitive sequence - full length copy
PRIMER_PAIR_0_LIBRARY_MISPRIMING=40.00, L1 Human L1 interspersed repetitive sequence - full length copy
PRIMER_LEFT_0_END_STABILITY=10.9000
PRIMER_RIGHT_0_END_STABILITY=6.7000
PRIMER_PAIR_0_COMPL_ANY=3.00
PRIMER_PAIR_0_COMPL_END=0.00
PRIMER_PAIR_0_PRODUCT_SIZE=106
PRIMER_PAIR_0_PRODUCT_TM=73.6
=
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
PRIMER_PAIR_EXPLAIN=considered 1, ok 1
PRIMER_LEFT_NUM_RETURNED=1
PRIMER_RIGHT_NUM_RETURNED=1
PRIMER_INTERNAL_NUM_RETURNED=1
PRIMER_PAIR_NUM_RETURNED=1
PRIMER_PAIR_0_PENALTY=0.364612
PRIMER_LEFT_0_PENALTY=0.346766
PRIMER_RIGHT_0_PENALTY=0.017846
PRIMER_INTERNAL_0_PENALTY=0.339231
PRIMER_LEFT_0_SEQUENCE=CGACTCTAGAGGATCCCCCT
PRIMER_RIGHT_0_SEQUENCE=TAGCCTGCCTTTGCAAACTT
PRIMER_INTERNAL_0_SEQUENCE=GGAAGAGAGGGTCATGCAAC
PRIMER_LEFT_0=18,20
PRIMER_RIGHT_0=123,20
PRIMER_INTERNAL_0=72,20
PRIMER_LEFT_0_TM=59.653
PRIMER_RIGHT_0_TM=60.018
PRIMER_INTERNAL_0_TM=59.661
PRIMER_LEFT_0_GC_PERCENT=60.000
PRIMER_RIGHT_0_GC_PERCENT=45.000
PRIMER_INTERNAL_0_GC_PERCENT=55.000
PRIMER_LEFT_0_SELF_ANY=8.00
PRIMER_RIGHT_0_SELF_ANY=8.00
PRIMER_INTERNAL_0_SELF_ANY=4.00
PRIMER_LEFT_0_SELF_END=4.00
PRIMER_RIGHT_0_SELF_END=3.00
PRIMER_INTERNAL_0_SELF_END=2.00
PRIMER_LEFT_0_LIBRARY_MISPRIMING=9.00, L1 Human L1 interspersed repetitive sequence - full length copy
PRIMER_RIGHT_0_LIBRARY_MISPRIMING=10.00, reverse L1 Human L1 interspersed repetitive sequence - full length copy
PRIMER_PAIR_0_LIBRARY_MISPRIMING=18.00, L1 Human L1 interspersed repetitive sequence - full length copy
PRIMER_LEFT_0_END_STABILITY=10.9000
PRIMER_RIGHT_0_END_STABILITY=6.7000
PRIMER_PAIR_0_COMPL_ANY=3.00
PRIMER_PAIR_0_COMPL_END=0.00
PRIMER_PAIR_0_PRODUCT_SIZE=106
PRIMER_PAIR_0_PRODUCT_TM=73.6
=
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.
PRIMER_LEFT_EXPLAIN=considered 2424, high end compl 27, high repeat similarity 2397, ok 0
PRIMER_RIGHT_EXPLAIN=considered 2424, ok 2424
PRIMER_INTERNAL_EXPLAIN=considered 3555, GC content failed 92, ok 3463
PRIMER_PAIR_EXPLAIN=considered 32248, unacceptable product size 32248, ok 0
PRIMER_LEFT_NUM_RETURNED=0
PRIMER_RIGHT_NUM_RETURNED=0
PRIMER_INTERNAL_NUM_RETURNED=0
PRIMER_PAIR_NUM_RETURNED=0
=
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
PRIMER_PAIR_EXPLAIN=considered 1, ok 1
PRIMER_LEFT_NUM_RETURNED=1
PRIMER_RIGHT_NUM_RETURNED=1
PRIMER_INTERNAL_NUM_RETURNED=1
PRIMER_PAIR_NUM_RETURNED=1
PRIMER_PAIR_0_PENALTY=0.364612
PRIMER_LEFT_0_PENALTY=0.346766
PRIMER_RIGHT_0_PENALTY=0.017846
PRIMER_INTERNAL_0_PENALTY=0.339231
PRIMER_INTERNAL_0_PROBLEMS= Similarity to non-template sequence too high;
PRIMER_LEFT_0_SEQUENCE=CGACTCTAGAGGATCCCCCT
PRIMER_RIGHT_0_SEQUENCE=TAGCCTGCCTTTGCAAACTT
PRIMER_INTERNAL_0_SEQUENCE=GGAAGAGAGGGTCATGCAAC
PRIMER_LEFT_0=18,20
PRIMER_RIGHT_0=123,20
PRIMER_INTERNAL_0=72,20
PRIMER_LEFT_0_TM=59.653
PRIMER_RIGHT_0_TM=60.018
PRIMER_INTERNAL_0_TM=59.661
PRIMER_LEFT_0_GC_PERCENT=60.000
PRIMER_RIGHT_0_GC_PERCENT=45.000
PRIMER_INTERNAL_0_GC_PERCENT=55.000
PRIMER_LEFT_0_SELF_ANY=8.00
PRIMER_RIGHT_0_SELF_ANY=8.00
PRIMER_INTERNAL_0_SELF_ANY=4.00
PRIMER_LEFT_0_SELF_END=4.00
PRIMER_RIGHT_0_SELF_END=3.00
PRIMER_INTERNAL_0_SELF_END=2.00
PRIMER_LEFT_0_LIBRARY_MISPRIMING=9.00, L1 Human L1 interspersed repetitive sequence - full length copy
PRIMER_RIGHT_0_LIBRARY_MISPRIMING=10.00, reverse L1 Human L1 interspersed repetitive sequence - full length copy
PRIMER_PAIR_0_LIBRARY_MISPRIMING=18.00, L1 Human L1 interspersed repetitive sequence - full length copy
PRIMER_INTERNAL_0_LIBRARY_MISHYB=20.00, L1 Human L1 interspersed repetitive sequence - full length copy
PRIMER_LEFT_0_END_STABILITY=10.9000
PRIMER_RIGHT_0_END_STABILITY=6.7000
PRIMER_PAIR_0_COMPL_ANY=3.00
PRIMER_PAIR_0_COMPL_END=0.00
PRIMER_PAIR_0_PRODUCT_SIZE=106
PRIMER_PAIR_0_PRODUCT_TM=73.6
=
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
PRIMER_LEFT_EXPLAIN=considered 2424, high end compl 27, high repeat similarity 63, ok 2334
PRIMER_RIGHT_EXPLAIN=considered 2424, high end compl 52, high repeat similarity 72, ok 2300
PRIMER_INTERNAL_EXPLAIN=considered 3555, GC content failed 92, high end compl 75, high repeat similarity 3028, ok 360
PRIMER_PAIR_EXPLAIN=considered 5374476, unacceptable product size 2713327, high end compl 966, no internal oligo 2660183, ok 0
PRIMER_LEFT_NUM_RETURNED=0
PRIMER_RIGHT_NUM_RETURNED=0
PRIMER_INTERNAL_NUM_RETURNED=0
PRIMER_PAIR_NUM_RETURNED=0
=
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
PRIMER_LEFT_EXPLAIN=considered 1712, high any compl 6, high end compl 24, high repeat similarity 26, ok 1656
PRIMER_RIGHT_EXPLAIN=considered 1712, high any compl 6, high end compl 25, high repeat similarity 28, ok 1653
PRIMER_INTERNAL_EXPLAIN=considered 2665, GC content failed 297, high any compl 15, high end compl 23, high repeat similarity 1970, ok 360
PRIMER_PAIR_EXPLAIN=considered 2737377, unacceptable product size 1340121, no internal oligo 1397256, ok 0
PRIMER_LEFT_NUM_RETURNED=0
PRIMER_RIGHT_NUM_RETURNED=0
PRIMER_INTERNAL_NUM_RETURNED=0
PRIMER_PAIR_NUM_RETURNED=0
=
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
PRIMER_WARNING=Unrecognized character (X) in mispriming library, entry L1 Human L1 interspersed repetitive sequence - full length copy
PRIMER_LEFT_EXPLAIN=considered 2424, ok 2424
PRIMER_RIGHT_EXPLAIN=considered 2424, ok 2424
PRIMER_INTERNAL_EXPLAIN=considered 3555, GC content failed 92, ok 3463
PRIMER_PAIR_EXPLAIN=considered 94, unacceptable product size 90, ok 4
PRIMER_LEFT_NUM_RETURNED=1
PRIMER_RIGHT_NUM_RETURNED=1
PRIMER_INTERNAL_NUM_RETURNED=1
PRIMER_PAIR_NUM_RETURNED=1
PRIMER_PAIR_0_PENALTY=0.364612
PRIMER_LEFT_0_PENALTY=0.346766
PRIMER_RIGHT_0_PENALTY=0.017846
PRIMER_INTERNAL_0_PENALTY=0.339231
PRIMER_LEFT_0_SEQUENCE=CGACTCTAGAGGATCCCCCT
PRIMER_RIGHT_0_SEQUENCE=AGCCTGCCTTTGCAAACTTA
PRIMER_INTERNAL_0_SEQUENCE=GGAAGAGAGGGTCATGCAAC
PRIMER_LEFT_0=18,20
PRIMER_RIGHT_0=122,20
PRIMER_INTERNAL_0=72,20
PRIMER_LEFT_0_TM=59.653
PRIMER_RIGHT_0_TM=60.018
PRIMER_INTERNAL_0_TM=59.661
PRIMER_LEFT_0_GC_PERCENT=60.000
PRIMER_RIGHT_0_GC_PERCENT=45.000
PRIMER_INTERNAL_0_GC_PERCENT=55.000
PRIMER_LEFT_0_SELF_ANY=8.00
PRIMER_RIGHT_0_SELF_ANY=8.00
PRIMER_INTERNAL_0_SELF_ANY=4.00
PRIMER_LEFT_0_SELF_END=4.00
PRIMER_RIGHT_0_SELF_END=4.00
PRIMER_INTERNAL_0_SELF_END=2.00
PRIMER_LEFT_0_LIBRARY_MISPRIMING=9.00, L1 Human L1 interspersed repetitive sequence - full length copy
PRIMER_RIGHT_0_LIBRARY_MISPRIMING=10.00, reverse L1 Human L1 interspersed repetitive sequence - full length copy
PRIMER_PAIR_0_LIBRARY_MISPRIMING=18.00, L1 Human L1 interspersed repetitive sequence - full length copy
PRIMER_INTERNAL_0_LIBRARY_MISHYB=11.00, L1 Human L1 interspersed repetitive sequence - full length copy
PRIMER_LEFT_0_END_STABILITY=10.9000
PRIMER_RIGHT_0_END_STABILITY=5.7000
PRIMER_PAIR_0_COMPL_ANY=3.00
PRIMER_PAIR_0_COMPL_END=1.00
PRIMER_PAIR_0_PRODUCT_SIZE=105
PRIMER_PAIR_0_PRODUCT_TM=73.7
=
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).
PRIMER_WARNING=Unrecognized character (X) in mispriming library, entry L1 Human L1 interspersed repetitive sequence - full length copy
PRIMER_LEFT_EXPLAIN=considered 2424, high end compl 27, high repeat similarity 2397, ok 0
PRIMER_RIGHT_EXPLAIN=considered 2424, ok 2424
PRIMER_INTERNAL_EXPLAIN=considered 3555, GC content failed 92, ok 3463
PRIMER_PAIR_EXPLAIN=considered 32248, unacceptable product size 32248, ok 0
PRIMER_LEFT_NUM_RETURNED=0
PRIMER_RIGHT_NUM_RETURNED=0
PRIMER_INTERNAL_NUM_RETURNED=0
PRIMER_PAIR_NUM_RETURNED=0
=
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).
PRIMER_WARNING=Unrecognized character (X) in internal oligo mishyb library, entry L1 Human L1 interspersed repetitive sequence - full length copy (for internal oligo)
PRIMER_LEFT_EXPLAIN=considered 2424, high end compl 27, ok 2397
PRIMER_RIGHT_EXPLAIN=considered 2424, high end compl 52, ok 2372
PRIMER_INTERNAL_EXPLAIN=considered 3555, GC content failed 92, high end compl 75, high repeat similarity 3028, ok 360
PRIMER_PAIR_EXPLAIN=considered 5691246, unacceptable product size 2862933, high end compl 994, no internal oligo 2827319, ok 0
PRIMER_LEFT_NUM_RETURNED=0
PRIMER_RIGHT_NUM_RETURNED=0
PRIMER_INTERNAL_NUM_RETURNED=0
PRIMER_PAIR_NUM_RETURNED=0
=
