Primer3 File - http://primer3.org
P3_FILE_TYPE=settings

PRIMER_FIRST_BASE_INDEX=1
PRIMER_TASK=generic
P3_FILE_ID=Settings for PCR amplification followed by Sanger sequencing on both strands using PCR primers
# 2012 01 29
PRIMER_MIN_THREE_PRIME_DISTANCE=3
PRIMER_EXPLAIN_FLAG=1

# Put something reasonable for PRIMER_MISPRIMING_LIBRARY depending
# on the species you are designing primers for.
PRIMER_MISPRIMING_LIBRARY=
PRIMER_MAX_LIBRARY_MISPRIMING=12.00
PRIMER_PAIR_MAX_LIBRARY_MISPRIMING=20.00

PRIMER_PRODUCT_SIZE_RANGE=300-400 401-500 501-600 601-700 701-850 851-1001
PRIMER_NUM_RETURN=5
PRIMER_MAX_END_STABILITY=9.0
#
PRIMER_MAX_SELF_ANY_TH=45.00
PRIMER_MAX_SELF_END_TH=35.00
PRIMER_PAIR_MAX_COMPL_ANY_TH=45.00
PRIMER_PAIR_MAX_COMPL_END_TH=35.00

PRIMER_MAX_HAIRPIN_TH=24.00
PRIMER_MAX_TEMPLATE_MISPRIMING_TH=40.00
PRIMER_PAIR_MAX_TEMPLATE_MISPRIMING_TH=70.00
PRIMER_MIN_SIZE=18
PRIMER_OPT_SIZE=20
PRIMER_MAX_SIZE=23
PRIMER_MIN_TM=57.0
PRIMER_OPT_TM=59.0
PRIMER_MAX_TM=62.0
PRIMER_PAIR_MAX_DIFF_TM=5.0

# PRIMER_TM_FORMULA=1 means use the SantaLucia parameters (Proc Natl Acad Sci 95:1460-65)
PRIMER_TM_FORMULA=1

# PRIMER_SALT_CORRECTIONS=1 means used the salt correction in SantaLucia et al 1998
PRIMER_SALT_CORRECTIONS=1

PRIMER_SALT_MONOVALENT=50.0
PRIMER_INTERNAL_SALT_MONOVALENT=50.0

# Millimolar conc of MgCl+2
PRIMER_SALT_DIVALENT=1.5
PRIMER_INTERNAL_SALT_DIVALENT=1.5

# Millimolar conc of dNTPs
PRIMER_DNTP_CONC=0.6

# Correct, 0, since we are assuming
# no dNTP's present when hybridizing.
PRIMER_INTERNAL_DNTP_CONC=0.0

PRIMER_DNA_CONC=50.0
PRIMER_INTERNAL_DNA_CONC=50.0

PRIMER_THERMODYNAMIC_OLIGO_ALIGNMENT=1
PRIMER_THERMODYNAMIC_TEMPLATE_ALIGNMENT=1
PRIMER_THERMODYNAMIC_PARAMETERS_PATH=/data/public/tools/primer3/primer3/trunk/src/primer3_config/
PRIMER_LOWERCASE_MASKING=0
#
PRIMER_MIN_GC=30.0
PRIMER_MAX_GC=70.0
PRIMER_MAX_NS_ACCEPTED=0
PRIMER_MAX_POLY_X=4
PRIMER_OUTSIDE_PENALTY=0
PRIMER_GC_CLAMP=0
PRIMER_LIBERAL_BASE=1
PRIMER_LIB_AMBIGUITY_CODES_CONSENSUS=0
PRIMER_PICK_ANYWAY=1

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
=
