PRIMER_SECONDARY_STRUCTURE_ALIGNMENT=1
PRIMER_FIRST_BASE_INDEX=1
PRIMER_EXPLAIN_FLAG=1
PRIMER_MISPRIMING_LIBRARY=../src/humrep_and_simple.txt
PRIMER_PRODUCT_SIZE_RANGE=300-400 401-500 200-299 501-600 100-199 601-700 701-850 851-1001
PRIMER_NUM_RETURN=5
PRIMER_MAX_END_STABILITY=9.0
PRIMER_MAX_LIBRARY_MISPRIMING=12.00
PRIMER_PAIR_MAX_LIBRARY_MISPRIMING=20.00
PRIMER_MAX_SELF_ANY_TH=47.00
PRIMER_MAX_SELF_END_TH=47.00
PRIMER_MAX_HAIRPIN_TH=47.0
PRIMER_PAIR_MAX_COMPL_ANY_TH=47.00
PRIMER_PAIR_MAX_COMPL_END_TH=47.00
PRIMER_MAX_TEMPLATE_MISPRIMING_TH=47.00
PRIMER_PAIR_MAX_TEMPLATE_MISPRIMING_TH=80.00
PRIMER_MIN_TM=57.0
PRIMER_OPT_TM=59.0
PRIMER_MAX_TM=63.0
PRIMER_PAIR_MAX_DIFF_TM=5.0
PRIMER_TM_FORMULA=1
PRIMER_SALT_MONOVALENT=50.0
PRIMER_SALT_CORRECTIONS=1
PRIMER_SALT_DIVALENT=1.5
PRIMER_DNTP_CONC=0.6
PRIMER_DNA_CONC=50.0
PRIMER_THERMODYNAMIC_OLIGO_ALIGNMENT=1
PRIMER_THERMODYNAMIC_TEMPLATE_ALIGNMENT=1
PRIMER_LOWERCASE_MASKING=0
PRIMER_MIN_GC=20.0
PRIMER_MAX_GC=80.0
PRIMER_MAX_NS_ACCEPTED=0
PRIMER_MAX_POLY_X=5
PRIMER_OUTSIDE_PENALTY=0
PRIMER_GC_CLAMP=0
PRIMER_LIBERAL_BASE=1
PRIMER_LIB_AMBIGUITY_CODES_CONSENSUS=0
PRIMER_WT_TM_LT=1.0
PRIMER_WT_TM_GT=1.0
PRIMER_WT_SIZE_LT=1.0
PRIMER_WT_SIZE_GT=1.0
PRIMER_WT_GC_PERCENT_LT=0.0
PRIMER_WT_GC_PERCENT_GT=0.0
PRIMER_WT_SELF_ANY_TH=0.0
PRIMER_WT_SELF_END_TH=0.0
PRIMER_WT_HAIRPIN_TH=0.0
PRIMER_WT_NUM_NS=0.0
PRIMER_WT_LIBRARY_MISPRIMING=0.0
PRIMER_WT_SEQ_QUAL=0.0
PRIMER_WT_END_QUAL=0.0
PRIMER_WT_POS_PENALTY=0.0
PRIMER_WT_END_STABILITY=0.0
PRIMER_WT_TEMPLATE_MISPRIMING_TH=0.0
PRIMER_PAIR_WT_PRODUCT_SIZE_LT=0.0
PRIMER_PAIR_WT_PRODUCT_SIZE_GT=0.0
PRIMER_PAIR_WT_PRODUCT_TM_LT=0.0
PRIMER_PAIR_WT_PRODUCT_TM_GT=0.0
PRIMER_PAIR_WT_DIFF_TM=0.0
PRIMER_PAIR_WT_COMPL_ANY_TH=0.0
PRIMER_PAIR_WT_COMPL_END_TH=0.0
PRIMER_PAIR_WT_LIBRARY_MISPRIMING=0.0
PRIMER_PAIR_WT_PR_PENALTY=1.0
PRIMER_PAIR_WT_IO_PENALTY=0.0
PRIMER_PAIR_WT_TEMPLATE_MISPRIMING=0.0
PRIMER_PICK_ANYWAY=0
PRIMER_TASK=generic
PRIMER_OPT_SIZE=20
PRIMER_MIN_SIZE=19
PRIMER_MAX_SIZE=21
SEQUENCE_ID=start_up
SEQUENCE_TEMPLATE=GTAGTCAGTAGACATGACACTGACGATGCAGACNACACACACACACACAGCACACAGGTATTAGTGGGCCATTCGATCCCGACCCAAATCGATAGCTACGATGACG
SEQUENCE_TARGET=37,21
=
PRIMER_NUM_RETURN=1
PRIMER_MAX_SELF_ANY_TH=47.00
PRIMER_MAX_SELF_END_TH=47.00
PRIMER_MAX_HAIRPIN_TH=47.0
PRIMER_PAIR_MAX_COMPL_ANY_TH=47.00
PRIMER_PAIR_MAX_COMPL_END_TH=47.00
PRIMER_MAX_TEMPLATE_MISPRIMING_TH=47.00
PRIMER_PAIR_MAX_TEMPLATE_MISPRIMING_TH=80.00
PRIMER_PRODUCT_SIZE_RANGE=75-200
SEQUENCE_INTERNAL_EXCLUDED_REGION=37,21
PRIMER_EXPLAIN_FLAG=1
SEQUENCE_ID=pick_detection_primers_th_1
SEQUENCE_TEMPLATE=GTAGTCAGTAGACATGACACTGACGATGCAGACNACACACACACACACAGCACACAGGTATTAGTGGGCCATTCGATCCCGACCCAAATCGATAGCTACGATGACG
SEQUENCE_TARGET=37,21
=
PRIMER_PRODUCT_SIZE_RANGE=75-100
SEQUENCE_ID=pick_detection_primers_th_2
SEQUENCE_TEMPLATE=GANAATGCAGTAATGAGTTGGCAAATTATGAATCGCAATCAAATTTTTTCTATGACCTGATAGAAACGCCAACTCACTGTATGAGTCTGTTGTCAAAGTCTAACGTTGTCAAAGTCTATTCCAAAACGCAAAGCACGCTCCCGATC
=
PRIMER_TASK=pick_left_only
PRIMER_PRODUCT_SIZE_RANGE=75-200
SEQUENCE_ID=pick_left_only_th_1
SEQUENCE_TEMPLATE=GTAGTCAGTAGACATGACACTGACGATGCAGACNACACACACACACACAGCACACAGGTATTAGTGGGCCATTCGATCCCGACCCAAATCGATAGCTACGATGACG
SEQUENCE_TARGET=37,21
=
PRIMER_PRODUCT_SIZE_RANGE=75-100
SEQUENCE_ID=pick_left_only_th_2
SEQUENCE_TEMPLATE=GANAATGCAGTAATGAGTTGGCAAATTATGAATCGCAATCAAATTTTTTCTATGACCTGATAGAAACGCCAACTCACTGTATGAGTCTGTTGTCAAAGTCTAACGTTGTCAAAGTCTATTCCAAAACGCAAAGCACGCTCCCGATC
=
PRIMER_TASK=pick_right_only
PRIMER_PRODUCT_SIZE_RANGE=75-200
SEQUENCE_ID=pick_right_only_th_1
SEQUENCE_TEMPLATE=GTAGTCAGTAGACATGACACTGACGATGCAGACNACACACACACACACAGCACACAGGTATTAGTGGGCCATTCGATCCCGACCCAAATCGATAGCTACGATGACG
SEQUENCE_TARGET=37,21
=
PRIMER_PRODUCT_SIZE_RANGE=75-100
SEQUENCE_ID=pick_right_only_th_2
SEQUENCE_TEMPLATE=GANAATGCAGTAATGAGTTGGCAAATTATGAATCGCAATCAAATTTTTTCTATGACCTGATAGAAACGCCAACTCACTGTATGAGTCTGTTGTCAAAGTCTAACGTTGTCAAAGTCTATTCCAAAACGCAAAGCACGCTCCCGATC
=
PRIMER_TASK=pick_hyb_probe_only
PRIMER_PRODUCT_SIZE_RANGE=75-200
SEQUENCE_ID=pick_hyb_probe_only_th_1
SEQUENCE_TEMPLATE=GTAGTCAGTAGACATGACACTGACGATGCAGACNACACACACACACACAGCACACAGGTATTAGTGGGCCATTCGATCCCGACCCAAATCGATAGCTACGATGACG
SEQUENCE_TARGET=37,21
=
PRIMER_PRODUCT_SIZE_RANGE=75-100
SEQUENCE_ID=pick_hyb_probe_only_th_2
SEQUENCE_TEMPLATE=GANAATGCAGTAATGAGTTGGCAAATTATGAATCGCAATCAAATTTTTTCTATGACCTGATAGAAACGCCAACTCACTGTATGAGTCTGTTGTCAAAGTCTAACGTTGTCAAAGTCTATTCCAAAACGCAAAGCACGCTCCCGATC
=
PRIMER_TASK=pick_primer_list
PRIMER_NUM_RETURN=30
PRIMER_PRODUCT_SIZE_RANGE=75-200
SEQUENCE_ID=pick_primer_list_th_1
SEQUENCE_TEMPLATE=GTAGTCAGTAGACATGACACTGACGATGCAGACNACACACACACACACAGCACACAGGTATTAGTGGGCCATTCGATCCCGACCCAAATCGATAGCTACGATGACG
SEQUENCE_TARGET=37,21
=
PRIMER_PICK_LEFT_PRIMER=1
PRIMER_PICK_RIGHT_PRIMER=1
PRIMER_PICK_INTERNAL_OLIGO=1
PRIMER_PRODUCT_SIZE_RANGE=75-100
SEQUENCE_ID=pick_pick_primer_list_th_2
SEQUENCE_TEMPLATE=GANAATGCAGTAATGAGTTGGCAAATTATGAATCGCAATCAAATTTTTTCTATGACCTGATAGAAACGCCAACTCACTGTATGAGTCTGTTGTCAAAGTCTAACGTTGTCAAAGTCTATTCCAAAACGCAAAGCACGCTCCCGATC
=
PRIMER_TASK=pick_primer_list
PRIMER_PRODUCT_SIZE_RANGE=75-200
SEQUENCE_ID=pick_primer_list_and_file_flag_th_1
SEQUENCE_TEMPLATE=GTAGTCAGTAGACATGACACTGACGATGCAGACNACACACACACACACAGCACACAGGTATTAGTGGGCCATTCGATCCCGACCCAAATCGATAGCTACGATGACG
SEQUENCE_TARGET=37,21
=
PRIMER_PRODUCT_SIZE_RANGE=75-100
SEQUENCE_ID=pick_primer_list_and_file_flag_th_2
SEQUENCE_TEMPLATE=GANAATGCAGTAATGAGTTGGCAAATTATGAATCGCAATCAAATTTTTTCTATGACCTGATAGAAACGCCAACTCACTGTATGAGTCTGTTGTCAAAGTCTAACGTTGTCAAAGTCTATTCCAAAACGCAAAGCACGCTCCCGATC
=
PRIMER_TASK=pick_primer_list
PRIMER_PRODUCT_SIZE_RANGE=75-200
PRIMER_MIN_LEFT_THREE_PRIME_DISTANCE=4
PRIMER_MIN_RIGHT_THREE_PRIME_DISTANCE=4
SEQUENCE_ID=pick_primer_list_and_file_flag_th_3
SEQUENCE_TEMPLATE=GTAGTCAGTAGACATGACACTGACGATGCAGACNACACACACACACACAGCACACAGGTATTAGTGGGCCATTCGATCCCGACCCAAATCGATAGCTACGATGACG
SEQUENCE_TARGET=37,21
=
PRIMER_PRODUCT_SIZE_RANGE=75-100
SEQUENCE_ID=pick_primer_list_and_file_flag_th_4
SEQUENCE_TEMPLATE=GANAATGCAGTAATGAGTTGGCAAATTATGAATCGCAATCAAATTTTTTCTATGACCTGATAGAAACGCCAACTCACTGTATGAGTCTGTTGTCAAAGTCTAACGTTGTCAAAGTCTATTCCAAAACGCAAAGCACGCTCCCGATC
=
PRIMER_TASK=pick_sequencing_primers
PRIMER_PICK_LEFT_PRIMER=0
PRIMER_PICK_RIGHT_PRIMER=0
PRIMER_PICK_INTERNAL_OLIGO=0
PRIMER_NUM_RETURN=1
PRIMER_MIN_LEFT_THREE_PRIME_DISTANCE=-1
PRIMER_MIN_RIGHT_THREE_PRIME_DISTANCE=-1
PRIMER_PRODUCT_SIZE_RANGE=75-200
SEQUENCE_ID=pick_sequencing_primers_th_1
SEQUENCE_TEMPLATE=GTAGTCAGTAGACATGACACTGACGATGCAGACNACACACACACACACAGCACACAGGTATTAGTGGGCCATTCGATCCCGACCCAAATCGATAGCTACGATGACG
SEQUENCE_TARGET=37,21
=
PRIMER_PRODUCT_SIZE_RANGE=75-100
PRIMER_PICK_LEFT_PRIMER=1
SEQUENCE_ID=pick_sequencing_primers_th_2
SEQUENCE_TEMPLATE=GANAATGCAGTAATGAGTTGGCAAATTATGAATCGCAATCAAATTTTTTCTATGACCTGATAGAAACGCCAACTCACTGTATGAGTCTGTTGTCAAAGTCTAACGTTGTCAAAGTCTATTCCAAAACGCAAAGCACGCTCCCGATC
=
PRIMER_PRODUCT_SIZE_RANGE=75-100
PRIMER_PICK_RIGHT_PRIMER=1
SEQUENCE_ID=pick_sequencing_primers_th_3
SEQUENCE_TEMPLATE=GANAATGCAGTAATGAGTTGGCAAATTATGAATCGCAATCAAATTTTTTCTATGACCTGATAGAAACGCCAACTCACTGTATGAGTCTGTTGTCAAAGTCTAACGTTGTCAAAGTCTATTCCAAAACGCAAAGCACGCTCCCGATC
=
PRIMER_TASK=check_primers
PRIMER_PRODUCT_SIZE_RANGE=75-200
SEQUENCE_ID=check_primers_th_1
SEQUENCE_TEMPLATE=GTAGTCAGTAGACATGACACTGACGATGCAGACNACACACACACACACAGCACACAGGTATTAGTGGGCCATTCGATCCCGACCCAAATCGATAGCTACGATGACG
SEQUENCE_TARGET=37,21
SEQUENCE_PRIMER=GACATGACACTGACGATGCA
SEQUENCE_PRIMER_REVCOMP=TAGCTATCGATTTGGGTCGG
=
PRIMER_PRODUCT_SIZE_RANGE=75-100
SEQUENCE_ID=check_primers_th_2
SEQUENCE_TEMPLATE=GANAATGCAGTAATGAGTTGGCAAATTATGAATCGCAATCAAATTTTTTCTATGACCTGATAGAAACGCCAACTCACTGTATGAGTCTGTTGTCAAAGTCTAACGTTGTCAAAGTCTATTCCAAAACGCAAAGCACGCTCCCGATC
SEQUENCE_PRIMER=TGACCTGATAGAAACGCCAA
SEQUENCE_PRIMER_REVCOMP=TGCTTTGCGTTTTGGAATAG
=
PRIMER_TASK=pick_discriminative_primers
PRIMER_PRODUCT_SIZE_RANGE=75-200
SEQUENCE_ID=pick_disc_th_1
SEQUENCE_TEMPLATE=GTAGTCAGTAGACATGACACTGACGATGCAGACNACACACACACACACAGCACACAGGTATTAGTGGGCCATTCGATCCCGACCCAAATCGATAGCTACGATGACG
SEQUENCE_TARGET=37,21
PRIMER_PICK_ANYWAY=1
=
PRIMER_PRODUCT_SIZE_RANGE=75-100
SEQUENCE_ID=pick_disc_primer_th_2
SEQUENCE_TEMPLATE=GANAATGCAGTAATGAGTTGGCAAATTATGAATCGCAATCAAATTTTTTCTATGACCTGATAGAAACGCCAACTCACTGTATGAGTCTGTTGTCAAAGTCTAACGTTGTCAAAGTCTATTCCAAAACGCAAAGCACGCTCCCGATC
SEQUENCE_TARGET=37,21
=
PRIMER_TASK=pick_cloning_primers
PRIMER_PRODUCT_SIZE_RANGE=200-300
SEQUENCE_ID=pick_disc_th_1
SEQUENCE_TEMPLATE=GTAGTCAGTAGACATGACACTGACGATGCAGACNACACACACACACACAGCACACAGGTATTAGTGGGCCATTCGATCCCGACCCAAATCGATAGCTACGATGACG
SEQUENCE_TARGET=2,100
=
PRIMER_PRODUCT_SIZE_RANGE=200-300
SEQUENCE_ID=pick_disc_primer_th_2
SEQUENCE_TEMPLATE=GANAATGCAGTAATGAGTTGGCAAATTATGAATCGCAATCAAATTTTTTCTATGACCTGATAGAAACGCCAACTCACTGTATGAGTCTGTTGTCAAAGTCTAACGTTGTCAAAGTCTATTCCAAAACGCAAAGCACGCTCCCGATC
SEQUENCE_TARGET=2,120
=
