P3_SETTINGS_FILE_USED=../settings_files/primer3_v1_1_4_default_settings.txt
P3_FILE_TYPE=settings
P3_FILE_ID=Default settings of primer3 version 1.1.4
PRIMER_TASK=pick_detection_primers
PRIMER_PICK_LEFT_PRIMER=1
PRIMER_PICK_INTERNAL_OLIGO=0
PRIMER_PICK_RIGHT_PRIMER=1
PRIMER_NUM_RETURN=5
PRIMER_MIN_5_PRIME_OVERLAP_OF_JUNCTION=5
PRIMER_PRODUCT_SIZE_RANGE=100-300
PRIMER_PRODUCT_OPT_SIZE=0
PRIMER_PAIR_WT_PRODUCT_SIZE_LT=0.0
PRIMER_PAIR_WT_PRODUCT_SIZE_GT=0.0
PRIMER_MIN_SIZE=18
PRIMER_INTERNAL_MIN_SIZE=18
PRIMER_OPT_SIZE=20
PRIMER_INTERNAL_OPT_SIZE=20
PRIMER_MAX_SIZE=27
PRIMER_INTERNAL_MAX_SIZE=27
PRIMER_WT_SIZE_LT=1.0
PRIMER_INTERNAL_WT_SIZE_LT=1.0
PRIMER_WT_SIZE_GT=1.0
PRIMER_INTERNAL_WT_SIZE_GT=1.0
PRIMER_MIN_GC=20.0
PRIMER_INTERNAL_MIN_GC=20.0
PRIMER_OPT_GC_PERCENT=50.0
PRIMER_MAX_GC=80.0
PRIMER_INTERNAL_MAX_GC=80.0
PRIMER_WT_GC_PERCENT_LT=0.0
PRIMER_INTERNAL_WT_GC_PERCENT_LT=0.0
PRIMER_WT_GC_PERCENT_GT=0.0
PRIMER_INTERNAL_WT_GC_PERCENT_GT=0.0
PRIMER_GC_CLAMP=0
PRIMER_MAX_END_GC=5
PRIMER_MIN_TM=57.0
PRIMER_INTERNAL_MIN_TM=57.0
PRIMER_OPT_TM=60.0
PRIMER_INTERNAL_OPT_TM=60.0
PRIMER_MAX_TM=63.0
PRIMER_INTERNAL_MAX_TM=63.0
PRIMER_PAIR_MAX_DIFF_TM=100.0
PRIMER_WT_TM_LT=1.0
PRIMER_INTERNAL_WT_TM_LT=1.0
PRIMER_WT_TM_GT=1.0
PRIMER_INTERNAL_WT_TM_GT=1.0
PRIMER_PAIR_WT_DIFF_TM=0.0
PRIMER_PRODUCT_MIN_TM=-1000000.0
PRIMER_PRODUCT_OPT_TM=0.0
PRIMER_PRODUCT_MAX_TM=1000000.0
PRIMER_PAIR_WT_PRODUCT_TM_LT=0.0
PRIMER_PAIR_WT_PRODUCT_TM_GT=0.0
PRIMER_TM_FORMULA=0
PRIMER_SALT_MONOVALENT=50.0
PRIMER_INTERNAL_SALT_MONOVALENT=50.0
PRIMER_SALT_DIVALENT=0.0
PRIMER_INTERNAL_SALT_DIVALENT=0.0
PRIMER_DNTP_CONC=0.0
PRIMER_INTERNAL_DNTP_CONC=0.0
PRIMER_SALT_CORRECTIONS=0
PRIMER_DNA_CONC=50.0
PRIMER_INTERNAL_DNA_CONC=50.0
PRIMER_MAX_SELF_ANY=8.00
PRIMER_INTERNAL_MAX_SELF_ANY=12.00
PRIMER_PAIR_MAX_COMPL_ANY=8.00
PRIMER_WT_SELF_ANY=0.0
PRIMER_INTERNAL_WT_SELF_ANY=0.0
PRIMER_PAIR_WT_COMPL_ANY=0.0
PRIMER_MAX_SELF_END=3.00
PRIMER_INTERNAL_MAX_SELF_END=12.00
PRIMER_PAIR_MAX_COMPL_END=3.00
PRIMER_WT_SELF_END=0.0
PRIMER_INTERNAL_WT_SELF_END=0.0
PRIMER_PAIR_WT_COMPL_END=0.0
PRIMER_MAX_END_STABILITY=100.0
PRIMER_WT_END_STABILITY=0.0
PRIMER_MAX_NS_ACCEPTED=0
PRIMER_INTERNAL_MAX_NS_ACCEPTED=0
PRIMER_WT_NUM_NS=0.0
PRIMER_INTERNAL_WT_NUM_NS=0.0
PRIMER_MAX_POLY_X=5
PRIMER_INTERNAL_MAX_POLY_X=5
PRIMER_MIN_THREE_PRIME_DISTANCE=-1
PRIMER_PICK_ANYWAY=0
PRIMER_LOWERCASE_MASKING=0
PRIMER_EXPLAIN_FLAG=0
PRIMER_LIBERAL_BASE=0
PRIMER_FIRST_BASE_INDEX=0
PRIMER_MAX_TEMPLATE_MISPRIMING=-1.00
PRIMER_PAIR_MAX_TEMPLATE_MISPRIMING=-1.00
PRIMER_WT_TEMPLATE_MISPRIMING=0.0
PRIMER_PAIR_WT_TEMPLATE_MISPRIMING=0.0
PRIMER_LIB_AMBIGUITY_CODES_CONSENSUS=1
PRIMER_MAX_LIBRARY_MISPRIMING=12.00
PRIMER_INTERNAL_MAX_LIBRARY_MISHYB=12.00
PRIMER_PAIR_MAX_LIBRARY_MISPRIMING=24.00
PRIMER_WT_LIBRARY_MISPRIMING=0.0
PRIMER_INTERNAL_WT_LIBRARY_MISHYB=0.0
PRIMER_PAIR_WT_LIBRARY_MISPRIMING=0.0
PRIMER_MIN_QUALITY=0
PRIMER_INTERNAL_MIN_QUALITY=0
PRIMER_MIN_END_QUALITY=0
PRIMER_QUALITY_RANGE_MIN=0
PRIMER_QUALITY_RANGE_MAX=100
PRIMER_WT_SEQ_QUAL=0.0
PRIMER_INTERNAL_WT_SEQ_QUAL=0.0
PRIMER_PAIR_WT_PR_PENALTY=1.0
PRIMER_PAIR_WT_IO_PENALTY=0.0
PRIMER_INSIDE_PENALTY=-1.0
PRIMER_OUTSIDE_PENALTY=0.0
PRIMER_WT_POS_PENALTY=1.0
PRIMER_SEQUENCING_LEAD=50
PRIMER_SEQUENCING_SPACING=500
PRIMER_SEQUENCING_INTERVAL=250
PRIMER_SEQUENCING_ACCURACY=20
PRIMER_WT_END_QUAL=0.0
PRIMER_INTERNAL_WT_END_QUAL=0.0
P3_SETTINGS_FILE_END=
SEQUENCE_ID=test_settings
SEQUENCE_TEMPLATE=atggatttgatggacatggatgccatcaatgacctccacttctctggacacagctccctcaccaacacccctacttccgacgaggattatggttgcacctggaaccactggtctcccatcgtcaactgggacacctttacaggtgccccagatgactttcaccacctcatggacaccatcatcgaggacagaacaactgtcctcgaacagctcagtccatctatcaccacaaccaccaccaccaccacaaccacggatgaggaagaagaagaaatggaaacaacaaccacaacaacaacaacggcaataaaaacgcatgaagttggtgatgattcaaaagggctaaaactagtgcacctattgatggctggcgcggaagccttaaccggttcaaccaaaaaccgtgacttagctcgagtgatattgatccggctcaaggaattagtctcacaacatgctaacggctccaacatggagagacttgccgctcatttcaccgaagcccttcatggactactagaaggtgctgggggtgcgcataataaccaccatcaccacaacaacaacaaacattacctcaccacaaatggtccccacgacaaccaaaacgacacacttgctgctttccaactacttcaagacatgtcaccttacgtcaaattcggccacttcacagccaatcaagccatcatcgaagccgtggcccacgaacgccgcgtccatgtcatcgactacgatatcatggaaggggtccaatgggcctcattaatccaatcacttgcttccaacaacaacggtccacatcttcggataaccgcattatcgcggacaggaaccggccggaggtcaatcgccaccgtacaagaaaccggcaggcgattaacctcctttgccgcttccctcggacaaccattttcttttcatcactgcagattagactccgatgaaactttccgtccttctgcattaaagcttgtacgtggagaggctttggttttcaactgcatgctgaatttacctcaccttagttaccgtgcaccggaatcagttgcttcgtttttaaacggagcaaaaacgttgaatccaaagcttgtgacgttggttgaagaagaagttggttctgttattggtgggtttgtggaaaggttcatggactcacttcatcattattcagcggtttttgattcattggaggctggttttccgatgcagaaccgggcccggactttggtggagagggtattttttgggcctagaattgcaggctcgttgggccggatatatagaacgggtggtgaagaggagagaaggtcatggggggagtggttaggtgaggtagggtttaggggagttccggtgagctttgcaaatcattgtcaagcaaagctgttgttagggctttttaatgatgggtatagggttgaagaggtgggtgtgggtagtaataagttggtgttggattggaaatcaagacgtttgctttctgcttccctttggacttgttcttcttcagattctgatttatag
PRIMER_LEFT_NUM_RETURNED=5
PRIMER_RIGHT_NUM_RETURNED=5
PRIMER_INTERNAL_NUM_RETURNED=0
PRIMER_PAIR_NUM_RETURNED=5
PRIMER_PAIR_0_PENALTY=0.013026
PRIMER_LEFT_0_PENALTY=0.006937
PRIMER_RIGHT_0_PENALTY=0.006089
PRIMER_LEFT_0_SEQUENCE=gtcctcgaacagctcagtcc
PRIMER_RIGHT_0_SEQUENCE=gcgtttttattgccgttgtt
PRIMER_LEFT_0=198,20
PRIMER_RIGHT_0=315,20
PRIMER_LEFT_0_TM=59.993
PRIMER_RIGHT_0_TM=60.006
PRIMER_LEFT_0_GC_PERCENT=60.000
PRIMER_RIGHT_0_GC_PERCENT=40.000
PRIMER_LEFT_0_SELF_ANY_TH=0.00
PRIMER_RIGHT_0_SELF_ANY_TH=0.00
PRIMER_LEFT_0_SELF_END_TH=0.00
PRIMER_RIGHT_0_SELF_END_TH=0.00
PRIMER_LEFT_0_HAIRPIN_TH=0.00
PRIMER_RIGHT_0_HAIRPIN_TH=0.00
PRIMER_LEFT_0_END_STABILITY=7.6000
PRIMER_RIGHT_0_END_STABILITY=7.0000
PRIMER_PAIR_0_COMPL_ANY_TH=0.00
PRIMER_PAIR_0_COMPL_END_TH=0.00
PRIMER_PAIR_0_PRODUCT_SIZE=118
PRIMER_PAIR_0_PRODUCT_TM=74.3
PRIMER_PAIR_1_PENALTY=0.020508
PRIMER_LEFT_1_PENALTY=0.014419
PRIMER_RIGHT_1_PENALTY=0.006089
PRIMER_LEFT_1_SEQUENCE=ttctctggacacagctccct
PRIMER_RIGHT_1_SEQUENCE=gcgtttttattgccgttgtt
PRIMER_LEFT_1=39,20
PRIMER_RIGHT_1=315,20
PRIMER_LEFT_1_TM=59.986
PRIMER_RIGHT_1_TM=60.006
PRIMER_LEFT_1_GC_PERCENT=55.000
PRIMER_RIGHT_1_GC_PERCENT=40.000
PRIMER_LEFT_1_SELF_ANY_TH=0.00
PRIMER_RIGHT_1_SELF_ANY_TH=0.00
PRIMER_LEFT_1_SELF_END_TH=0.00
PRIMER_RIGHT_1_SELF_END_TH=0.00
PRIMER_LEFT_1_HAIRPIN_TH=41.16
PRIMER_RIGHT_1_HAIRPIN_TH=0.00
PRIMER_LEFT_1_END_STABILITY=9.4000
PRIMER_RIGHT_1_END_STABILITY=7.0000
PRIMER_PAIR_1_COMPL_ANY_TH=0.00
PRIMER_PAIR_1_COMPL_END_TH=0.00
PRIMER_PAIR_1_PRODUCT_SIZE=277
PRIMER_PAIR_1_PRODUCT_TM=78.6
PRIMER_PAIR_2_PENALTY=0.020508
PRIMER_LEFT_2_PENALTY=0.014419
PRIMER_RIGHT_2_PENALTY=0.006089
PRIMER_LEFT_2_SEQUENCE=cttctctggacacagctccc
PRIMER_RIGHT_2_SEQUENCE=gcgtttttattgccgttgtt
PRIMER_LEFT_2=38,20
PRIMER_RIGHT_2=315,20
PRIMER_LEFT_2_TM=59.986
PRIMER_RIGHT_2_TM=60.006
PRIMER_LEFT_2_GC_PERCENT=60.000
PRIMER_RIGHT_2_GC_PERCENT=40.000
PRIMER_LEFT_2_SELF_ANY_TH=0.00
PRIMER_RIGHT_2_SELF_ANY_TH=0.00
PRIMER_LEFT_2_SELF_END_TH=0.00
PRIMER_RIGHT_2_SELF_END_TH=0.00
PRIMER_LEFT_2_HAIRPIN_TH=41.16
PRIMER_RIGHT_2_HAIRPIN_TH=0.00
PRIMER_LEFT_2_END_STABILITY=9.4000
PRIMER_RIGHT_2_END_STABILITY=7.0000
PRIMER_PAIR_2_COMPL_ANY_TH=0.00
PRIMER_PAIR_2_COMPL_END_TH=0.00
PRIMER_PAIR_2_PRODUCT_SIZE=278
PRIMER_PAIR_2_PRODUCT_TM=78.7
PRIMER_PAIR_3_PENALTY=0.021356
PRIMER_LEFT_3_PENALTY=0.014419
PRIMER_RIGHT_3_PENALTY=0.006937
PRIMER_LEFT_3_SEQUENCE=ttctctggacacagctccct
PRIMER_RIGHT_3_SEQUENCE=ggactgagctgttcgaggac
PRIMER_LEFT_3=39,20
PRIMER_RIGHT_3=217,20
PRIMER_LEFT_3_TM=59.986
PRIMER_RIGHT_3_TM=59.993
PRIMER_LEFT_3_GC_PERCENT=55.000
PRIMER_RIGHT_3_GC_PERCENT=60.000
PRIMER_LEFT_3_SELF_ANY_TH=0.00
PRIMER_RIGHT_3_SELF_ANY_TH=0.00
PRIMER_LEFT_3_SELF_END_TH=0.00
PRIMER_RIGHT_3_SELF_END_TH=0.00
PRIMER_LEFT_3_HAIRPIN_TH=41.16
PRIMER_RIGHT_3_HAIRPIN_TH=0.00
PRIMER_LEFT_3_END_STABILITY=9.4000
PRIMER_RIGHT_3_END_STABILITY=7.6000
PRIMER_PAIR_3_COMPL_ANY_TH=17.27
PRIMER_PAIR_3_COMPL_END_TH=5.56
PRIMER_PAIR_3_PRODUCT_SIZE=179
PRIMER_PAIR_3_PRODUCT_TM=78.8
PRIMER_PAIR_4_PENALTY=0.021356
PRIMER_LEFT_4_PENALTY=0.014419
PRIMER_RIGHT_4_PENALTY=0.006937
PRIMER_LEFT_4_SEQUENCE=cttctctggacacagctccc
PRIMER_RIGHT_4_SEQUENCE=ggactgagctgttcgaggac
PRIMER_LEFT_4=38,20
PRIMER_RIGHT_4=217,20
PRIMER_LEFT_4_TM=59.986
PRIMER_RIGHT_4_TM=59.993
PRIMER_LEFT_4_GC_PERCENT=60.000
PRIMER_RIGHT_4_GC_PERCENT=60.000
PRIMER_LEFT_4_SELF_ANY_TH=0.00
PRIMER_RIGHT_4_SELF_ANY_TH=0.00
PRIMER_LEFT_4_SELF_END_TH=0.00
PRIMER_RIGHT_4_SELF_END_TH=0.00
PRIMER_LEFT_4_HAIRPIN_TH=41.16
PRIMER_RIGHT_4_HAIRPIN_TH=0.00
PRIMER_LEFT_4_END_STABILITY=9.4000
PRIMER_RIGHT_4_END_STABILITY=7.6000
PRIMER_PAIR_4_COMPL_ANY_TH=17.27
PRIMER_PAIR_4_COMPL_END_TH=9.22
PRIMER_PAIR_4_PRODUCT_SIZE=180
PRIMER_PAIR_4_PRODUCT_TM=78.9
=
