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SEQUENCE_ID=io_compl
PRIMER_PRODUCT_SIZE_RANGE=50-500
PRIMER_TASK=pick_pcr_primers_and_hyb_probe
PRIMER_INTERNAL_MIN_TM=50
PRIMER_INTERNAL_MAX_TM=70
PRIMER_EXPLAIN_FLAG=1
PRIMER_PAIR_WT_IO_PENALTY=1
PRIMER_PAIR_WT_PR_PENALTY=0
PRIMER_WT_TM_GT=0
PRIMER_WT_TM_LT=0
PRIMER_WT_SIZE_LT=0
PRIMER_WT_SIZE_GT=0
PRIMER_PICK_INTERNAL_OLIGO=1
PRIMER_INTERNAL_WT_TM_GT=0
PRIMER_INTERNAL_WT_TM_LT=0
PRIMER_INTERNAL_WT_SIZE_LT=0
PRIMER_INTERNAL_WT_SIZE_GT=0
PRIMER_INTERNAL_WT_SELF_ANY=1
PRIMER_INTERNAL_WT_SELF_END=2
SEQUENCE_TEMPLATE=AAGCCGAGGATGACTTCACTTTCCGACCCTGCAGAGCCGAGTTTCACCCACGAGTGAAGACTCCGCCAGCCTTGCCCCTCGGGCCTCTCCCTCAACTCACCATGATGACCGTCAGGCTGAGGAGGCAGGCGGACTGAGGCGTGGTCCGCGGGGCTCAGGGAGGTGGCTCCTGCGCCGG
=
SEQUENCE_ID=diff_tm
PRIMER_PAIR_WT_IO_PENALTY=0
PRIMER_PAIR_WT_PR_PENALTY=1
PRIMER_PAIR_WT_DIFF_TM=1
PRIMER_PICK_INTERNAL_OLIGO=0
PRIMER_TASK=pick_pcr_primers
SEQUENCE_TEMPLATE=AAGCCGAGGATGACTTCACTTTCCGACCCTGCAGAGCCGAGTTTCACCCACGAGTGAAGACTCCGCCAGCCTTGCCCCTCGGGCCTCTCCCTCAACTCACCATGATGACCGTCAGGCTGAGGAGGCAGGCGGACTGAGGCGTGGTCCGCGGGGCTCAGGGAGGTGGCTCCTGCGCCGG
=
SEQUENCE_ID=num_NS
PRIMER_PAIR_WT_DIFF_TM=0
PRIMER_WT_NUM_NS=1
PRIMER_MAX_NS_ACCEPTED=15
SEQUENCE_TEMPLATE=AAGCCGNGGATGANTTCACTTTCNGACCNTGCAGAGCCGANTTTCACNCACGAGNGAAGACTNCGCCAGCCTTGCCCCTNGGGCCTCTNCCTCAACTCNCCATGATGNCCGTCAGGNNNNNNNNNCAGGCGNACTGAGGCGTGGTNCGCGGGGCTCAGGNNNNNNNNNCCTGCGCCGG
=
SEQUENCE_ID=product_size
PRIMER_WT_NUM_NS=0
PRIMER_PRODUCT_OPT_SIZE=60
PRIMER_PAIR_WT_PRODUCT_SIZE_LT=1
PRIMER_PAIR_WT_PRODUCT_SIZE_GT=1
PRIMER_PICK_INTERNAL_OLIGO=0
PRIMER_PAIR_WT_DIFF_TM=0
PRIMER_INTERNAL_MIN_TM=50
PRIMER_INTERNAL_MAX_TM=70
PRIMER_EXPLAIN_FLAG=1
PRIMER_WT_TM_GT=0
PRIMER_WT_TM_LT=0
PRIMER_WT_SIZE_LT=0
PRIMER_WT_SIZE_GT=0
PRIMER_WT_LIBRARY_MISPRIMING=0
SEQUENCE_TEMPLATE=AAGCCGAGGATGACTTCACTTTCCGACCCTGCAGAGCCGAGTTTCACCCACGAGTGAAGACTCCGCCAGCCTTGCCCCTC
PRIMER_MAX_TM=70
PRIMER_OPT_TM=55
PRIMER_MAX_SELF_ANY=12
PRIMER_MAX_SELF_END=12
PRIMER_PAIR_MAX_COMPL_ANY=12
PRIMER_PAIR_MAX_COMPL_END=12
PRIMER_MIN_TM=50
PRIMER_PAIR_MAX_DIFF_TM=3
PRIMER_MISPRIMING_LIBRARY=
=
SEQUENCE_ID=rep_sim
PRIMER_PAIR_WT_PRODUCT_SIZE_LT=0
PRIMER_PAIR_WT_PRODUCT_SIZE_GT=0
PRIMER_MAX_LIBRARY_MISPRIMING=20
PRIMER_WT_LIBRARY_MISPRIMING=1
PRIMER_MISPRIMING_LIBRARY=not_for_production.lib
SEQUENCE_TEMPLATE=AAGCCGAGGATGACTTCACTTTCCGACCCTGCAGAGCCGAGTTTCACCCACGAGTGAAGACTCCGCCAGCCTTGCCCCTC
=
SEQUENCE_ID=pair_rep_sim
PRIMER_WT_LIBRARY_MISPRIMING=0
PRIMER_PAIR_WT_LIBRARY_MISPRIMING=1
SEQUENCE_TEMPLATE=AAGCCGAGGATGACTTCACTTTCCGACCCTGCAGAGCCGAGTTTCACCCACGAGTGAAGACTCCGCCAGCCTTGCCCCTC
=
SEQUENCE_ID=product_tm
PRIMER_PAIR_WT_PRODUCT_TM_LT=1
PRIMER_PAIR_WT_PRODUCT_TM_GT=1
PRIMER_PAIR_WT_LIBRARY_MISPRIMING=0
PRIMER_PRODUCT_OPT_TM=80
PRIMER_MISPRIMING_LIBRARY=
SEQUENCE_TEMPLATE=AAGCCGAGGATGACTTCACTTTCCGACCCTGCAGAGCCGAGTTTCACCCACGAGTGAAGACTCCGCCAGCCTTGCCCCTCGGGCCT
=
SEQUENCE_ID=primer_compl
PRIMER_MIN_GC=1.0
PRIMER_MAX_GC=99.0
PRIMER_PAIR_WT_PRODUCT_TM_LT=0
PRIMER_PAIR_WT_PRODUCT_TM_GT=0
PRIMER_PRODUCT_OPT_SIZE=200
PRIMER_PAIR_WT_PRODUCT_SIZE_LT=0
PRIMER_PAIR_WT_PRODUCT_SIZE_GT=0
PRIMER_PRODUCT_OPT_TM=0
PRIMER_WT_LIBRARY_MISPRIMING=0
PRIMER_WT_SELF_ANY=1
PRIMER_WT_SELF_END=2
SEQUENCE_TEMPLATE=CTCCATGAAGTACAAAAAAACCTTAAGTTTGTAACAGGGCCCAAATCCCATTATTCATAATGCATTTCAAGGTAAAAATGAGGTATGAATACAATACCCTAACATCAATTCCTCCAACAAATAGACATCATAATTAGATACAC
=
PRIMER_MISPRIMING_LIBRARY=
PRIMER_INTERNAL_MISHYB_LIBRARY=not_for_production.lib
PRIMER_PICK_INTERNAL_OLIGO=1
PRIMER_WT_SELF_ANY=0
PRIMER_WT_SELF_END=0
PRIMER_INTERNAL_WT_TM_GT=0
PRIMER_INTERNAL_WT_TM_LT=0
PRIMER_INTERNAL_WT_SIZE_LT=0
PRIMER_INTERNAL_WT_SIZE_GT=0
PRIMER_INTERNAL_WT_SELF_ANY=0
PRIMER_INTERNAL_WT_SELF_END=0
PRIMER_INTERNAL_WT_LIBRARY_MISHYB=1
PRIMER_PAIR_WT_COMPL_ANY=0
PRIMER_PAIR_WT_COMPL_END=0
PRIMER_INTERNAL_MAX_LIBRARY_MISHYB=20
PRIMER_PAIR_WT_PR_PENALTY=0
PRIMER_PAIR_WT_IO_PENALTY=1
SEQUENCE_ID=io_rep_sim
SEQUENCE_TEMPLATE=CTCCATGAAGTACAAAAAAACCTTAAGTTTGTAACAGGGCCCAAATCCCATTATTCATAATGCATTTCAAGGTAAAAATGAGGTATGAATAACCTATACATAATGTGAAATATAATTTTT
=
SEQUENCE_ID=end_stability
PRIMER_INTERNAL_MIN_TM=50
PRIMER_INTERNAL_MAX_TM=70
PRIMER_INTERNAL_MISHYB_LIBRARY=
PRIMER_PICK_INTERNAL_OLIGO=0
PRIMER_PAIR_WT_PR_PENALTY=1
PRIMER_PAIR_WT_IO_PENALTY=0
PRIMER_INTERNAL_WT_LIBRARY_MISHYB=0
PRIMER_WT_END_STABILITY=1
PRIMER_EXPLAIN_FLAG=1
SEQUENCE_TEMPLATE=AAGCCGAGGATGACTTCACTTTCCGACCCTGCAGAGCCGAGTTTCACCCACGAGTGAAGACTCCGCCAGCCTTGCCCCTCGGGCCTCTCCCTCAACTCACCATGATGGCGGCAGGCAGCAGTTCCCGACCGGCTCGAGGAGGAGCAGAGGCTGTGCTTGGCG
PRIMER_MAX_TM=70
PRIMER_OPT_TM=55
PRIMER_MAX_SELF_ANY=12
PRIMER_MAX_SELF_END=12
PRIMER_PAIR_MAX_COMPL_ANY=12
PRIMER_PAIR_MAX_COMPL_END=12
PRIMER_MIN_TM=50
=
SEQUENCE_ID=position_penalty
SEQUENCE_TARGET=298,45
PRIMER_OUTSIDE_PENALTY=20.0
PRIMER_INSIDE_PENALTY=1000.0
PRIMER_EXPLAIN_FLAG=1
PRIMER_PRODUCT_SIZE_RANGE=36-2000
PRIMER_WT_POS_PENALTY=1
PRIMER_WT_END_STABILITY=0
SEQUENCE_TEMPLATE=TTCTATAAAGCTGAGGAGAAGAGTGAGGGAGTGTGGGCAAGAGAGGTGGCTCAGGCTTTCCCTGGGCCTGATTGAACTTTAAAACTTCTCTACTAATTAAACAACACTGGGCTCTACACTTTGCTTAACCCTGGGAACTGGTCATCAGCCTTTGACCTCAGTTCCCCCTCCTGACCAGCTCTCTGCCCCACCCTGTCCTCTGGAACCTCTGCGAGATTTAGAGGAAAGAACCAGTTTTCAGGCGGATTGCCTCAGATCACACTATCTCCACTTGCCCAGCCCTGTGGAAGATTAGCGGCCATGTATTCCAATGTGATAGGAACTGTAACCTCTGGAAAAAGGTAAGAGGGGTGAGCTTTCCCCTTGCCTGCCCCTACTGGGTTTTGTGACCTCCAAA
=
SEQUENCE_ID=sequence_quality
PRIMER_WT_POS_PENALTY=0
PRIMER_WT_SEQ_QUAL=1
SEQUENCE_TEMPLATE=ATCGTAGCTGATCGTAGCTGATCGTAGCTAGTCAGTCTACTACTGATCTAGCTGATCATCGTAGCTAGCTAGTCATCATCGTACTACGTAGCTACTAGTCATCTAGCTAGCTAGTCGATGC
PRIMER_PRODUCT_SIZE_RANGE=50-500
PRIMER_QUALITY_RANGE_MAX=70
SEQUENCE_QUALITY=10 20 30 40 50 50 50 50 50 50 50 60 50 50 60 50 50 50 50 50 50 55 50 50 55 50 60 50 50 50 50 60 60 60 60 60 60 60 20 20 20 30 30 30 50 50 30 53 30 50 60 60 60 60 60 60 60 50 70 70 70 70 70 70 70 70 70 70 70 70 70 70 70 70 70 70 50 50 50 50 50 50 50 50 50 50 50 60 60 60 60 60 60 60 60 60 60 50 50 50 50 50 20 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10
=
SEQUENCE_ID=sequence_quality_io
PRIMER_PICK_INTERNAL_OLIGO=1
PRIMER_INTERNAL_WT_SEQ_QUAL=1
PRIMER_PAIR_MAX_DIFF_TM=20
PRIMER_MIN_TM=20
PRIMER_MAX_TM=100
PRIMER_INTERNAL_WT_SELF_ANY=0
PRIMER_INTERNAL_WT_SELF_END=0
PRIMER_INTERNAL_MAX_SELF_ANY=20
PRIMER_INTERNAL_MAX_SELF_END=20
PRIMER_INTERNAL_MIN_TM=20
PRIMER_INTERNAL_MAX_TM=100
PRIMER_MAX_SELF_ANY=20
PRIMER_MAX_SELF_END=20
PRIMER_MAX_SELF_ANY=20
PRIMER_MAX_SELF_END=20
PRIMER_PAIR_MAX_COMPL_ANY=20
PRIMER_PAIR_MAX_COMPL_END=20
PRIMER_INTERNAL_WT_END_QUAL=2
PRIMER_PAIR_WT_PR_PENALTY=0
PRIMER_PAIR_WT_IO_PENALTY=1
PRIMER_WT_SEQ_QUAL=0
PRIMER_WT_END_QUAL=0
SEQUENCE_TEMPLATE=ATCGTAGCTGATCGTAGCTGATCGTAGCTAGTCAGTCTACTACTGATCTAGCTGATCATCGTAGCTAGCTAGTCATCATC
SEQUENCE_QUALITY=10 20 30 40 50 50 50 50 50 50 50 60 50 50 60 50 50 50 50 50 50 55 50 50 55 50 60 50 50 50 50 60 60 60 60 60 60 60 20 20 20 30 30 30 50 50 30 53 30 50 60 60 60 60 60 60 60 50 50 50 50 50 50 50 50 50 70 70 70 70 70 70 70 70 70 70 70 70 70 70
=
SEQUENCE_ID=io_gc_content
PRIMER_WT_SEQ_QUAL=0
PRIMER_INTERNAL_WT_SEQ_QUAL=0
PRIMER_PRODUCT_SIZE_RANGE=50-500
PRIMER_TASK=pick_pcr_primers_and_hyb_probe
PRIMER_INTERNAL_MIN_TM=0
PRIMER_INTERNAL_MAX_TM=100
PRIMER_INTERNAL_MIN_GC=40
PRIMER_INTERNAL_OPT_GC_PERCENT=50
PRIMER_INTERNAL_MAX_GC=60
PRIMER_INTERNAL_WT_GC_PERCENT_GT=1
PRIMER_INTERNAL_WT_GC_PERCENT_LT=1
PRIMER_EXPLAIN_FLAG=1
PRIMER_PAIR_WT_IO_PENALTY=1
PRIMER_PAIR_WT_PR_PENALTY=0
PRIMER_WT_TM_GT=0
PRIMER_WT_TM_LT=0
PRIMER_WT_SIZE_LT=0
PRIMER_WT_SIZE_GT=0
PRIMER_PICK_INTERNAL_OLIGO=1
PRIMER_INTERNAL_WT_TM_GT=0
PRIMER_INTERNAL_WT_TM_LT=0
PRIMER_INTERNAL_WT_SIZE_LT=0
PRIMER_INTERNAL_WT_SIZE_GT=0
PRIMER_INTERNAL_WT_SELF_ANY=0
PRIMER_INTERNAL_WT_SELF_END=0
SEQUENCE_TEMPLATE=AAGCCGAGGATGACTTCACTTTCCGACCCTGCAGAGCCGAGTTTCACCCACGAGTGAAGACTCCGCCAGCCTTGCCCCTCGGGCCTCTCCCTCAACTCACCATGATGACCGTCAGGCTGAGGAGGCAGGCGGACTGAGGCGTGGTCCGCGGGGCTCAGGGAGGTGGCTCCTGCGCCGG
=
SEQUENCE_ID=primer_gc_content
PRIMER_WT_SEQ_QUAL=0
PRIMER_INTERNAL_WT_SEQ_QUAL=0
PRIMER_PRODUCT_SIZE_RANGE=50-500
PRIMER_TASK=pick_pcr_primers_and_hyb_probe
PRIMER_INTERNAL_MIN_TM=0
PRIMER_INTERNAL_MAX_TM=100
PRIMER_MIN_GC=40
PRIMER_OPT_GC_PERCENT=50
PRIMER_MAX_GC=60
PRIMER_WT_GC_PERCENT_GT=1
PRIMER_WT_GC_PERCENT_LT=1
PRIMER_EXPLAIN_FLAG=1
PRIMER_PAIR_WT_PR_PENALTY=1
PRIMER_WT_TM_GT=0
PRIMER_WT_TM_LT=0
PRIMER_WT_SIZE_LT=0
PRIMER_WT_SIZE_GT=0
PRIMER_PICK_INTERNAL_OLIGO=1
PRIMER_INTERNAL_WT_TM_GT=0
PRIMER_INTERNAL_WT_TM_LT=0
PRIMER_INTERNAL_WT_SIZE_LT=0
PRIMER_INTERNAL_WT_SIZE_GT=0
PRIMER_INTERNAL_WT_SELF_ANY=0
PRIMER_INTERNAL_WT_SELF_END=0
SEQUENCE_TEMPLATE=AAGCCGAGGATGACTTCACTTTCCGACCCTGCAGAGCCGAGTTTCACCCACGAGTGAAGACTCCGCCAGCCTTGCCCCTCGGGCCTCTCCCTCAACTCACCATGATGACCGTCAGGCTGAGGAGGCAGGCGGACTGAGGCGTGGTCCGCGGGGCTCAGGGAGGTGGCTCCTGCGCCGG
=
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