File: primer_internal_input

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primer3 2.6.1-6
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file content (227 lines) | stat: -rw-r--r-- 10,416 bytes parent folder | download | duplicates (8) 
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SEQUENCE_ID=boundary_test_00
PRIMER_MAX_POLY_X=0
PRIMER_INTERNAL_MAX_POLY_X=0
PRIMER_EXPLAIN_FLAG=1
SEQUENCE_TEMPLATE=NNCACGTCATCTCATCAAATTTGATTGNNNACGTACGTACGTTGCAGTCGACGCANNACTCACTGTCATTTCCAAACAATTCNN
PRIMER_PRODUCT_SIZE_RANGE=50-100
PRIMER_MIN_TM=0.0
PRIMER_MAX_TM=100.0
PRIMER_MIN_SIZE=25
PRIMER_MAX_SIZE=25
PRIMER_INTERNAL_MIN_SIZE=25
PRIMER_INTERNAL_MAX_SIZE=25
PRIMER_INTERNAL_OPT_SIZE=25
PRIMER_OPT_SIZE=25
PRIMER_MAX_GC=100
PRIMER_MIN_GC=0
PRIMER_MAX_SELF_END=100
PRIMER_MAX_SELF_ANY=100
PRIMER_PAIR_MAX_COMPL_ANY=100
PRIMER_PAIR_MAX_COMPL_END=100
PRIMER_INTERNAL_MAX_SELF_ANY=100
PRIMER_INTERNAL_MAX_SELF_END=100 
PRIMER_INTERNAL_MAX_TM=100
PRIMER_INTERNAL_MIN_TM=30
PRIMER_INTERNAL_MAX_GC=100
PRIMER_INTERNAL_MIN_GC=0
PRIMER_PICK_INTERNAL_OLIGO=1
=
SEQUENCE_ID=boundary_test_01
SEQUENCE_TEMPLATE=NNCACGTCATCTCATCAAATTTGATTGNNCACGTCATCTCATCAAATTTGATTGNNNACTCACTGTCATTTCCAAACAATTCNN
PRIMER_PRODUCT_SIZE_RANGE=55-100
PRIMER_PICK_INTERNAL_OLIGO=1
=
SEQUENCE_ID=boundary_test_02
SEQUENCE_TEMPLATE=NNCACGTCATCTCATCAAATTTGATTGNNCACGTCATCTCATCAAATTTGATTGNNNACTCACTGTCATTTCCAAACAATTCNN
PRIMER_PRODUCT_SIZE_RANGE=80-80
PRIMER_PICK_INTERNAL_OLIGO=1
=
SEQUENCE_ID=boundary_test_05
SEQUENCE_TEMPLATE=NNCACGTCATCTCATCAAATTTGATTGNNCACGTCATCTCATCAAATTTGATTGNNNACTCACTGTCATTTCCAAACAATTCNN
PRIMER_PRODUCT_SIZE_RANGE=80-80
PRIMER_MIN_SIZE=24
PRIMER_MAX_SIZE=24
PRIMER_OPT_SIZE=24
PRIMER_PICK_INTERNAL_OLIGO=1
=
SEQUENCE_ID=boundary_test_11
PRIMER_MAX_NS_ACCEPTED=1
SEQUENCE_TEMPLATE=NNCACGTCATCTNATCAAATTTGATTGNNCACGTCATCTNATCAAATTTGATTGNNNACTCACTGTCATTTCCAAACAATTCNN
PRIMER_PICK_INTERNAL_OLIGO=1
=
SEQUENCE_ID=boundary_test_11_2
PRIMER_MAX_NS_ACCEPTED=2
PRIMER_INTERNAL_MAX_NS_ACCEPTED=2
SEQUENCE_TEMPLATE=NNCACGTCATCNNATCAAATTTGATTGNNCACGTCATCNNATCAAATTTGATTGNNNACTCACTGTCATTTCCAAACAATTCNN
PRIMER_PICK_INTERNAL_OLIGO=1
=
SEQUENCE_ID=boundary_test_12
PRIMER_MAX_NS_ACCEPTED=2
SEQUENCE_TEMPLATE=NNCACGTCATCNNATCAAATTTGATTGNNCACGTCATCNNATCAAATTTGATTGNNNACTCACTGTCATTTCCAAACAATTCNN
PRIMER_PICK_INTERNAL_OLIGO=1
=
SEQUENCE_ID=boundary_test_13
PRIMER_MAX_NS_ACCEPTED=0
PRIMER_MIN_GC=0
SEQUENCE_TEMPLATE=NNAAAAAAAAAAAAAAAAAAAAAAAAANNTTTTTTTTTTTTTTTTTTTTTTTTTNNNACTCACTGTCATTTCCAAACAATTCNN
=
SEQUENCE_ID=boundary_test_14
PRIMER_MAX_NS_ACCEPTED=0
PRIMER_MIN_GC=.0001
SEQUENCE_TEMPLATE=NNAAAAAAAAAAAAAAAAACAAAAAAATTTTTTTTTTTTTTTTTTTTTTTTTNNNNNACTCACTGTCATTTCCAAACAATTCNN
=
SEQUENCE_ID=boundary_test_15
PRIMER_MAX_NS_ACCEPTED=0
PRIMER_MIN_GC=20
PRIMER_MAX_GC=100
SEQUENCE_TEMPLATE=NNGGGGGGGGGGGGGGGGGGGGGGGGGNNNNNTTTTTTTTTTTTTTTTTTTTTTTTTACTCACTGTCATTTCCAAACAATTCNN
=
SEQUENCE_ID=boundary_test_16
PRIMER_MAX_NS_ACCEPTED=0
PRIMER_PRODUCT_SIZE_RANGE=50-200
PRIMER_INTERNAL_MAX_NS_ACCEPTED=5
SEQUENCE_TEMPLATE=NNGGGGGGGGGGGGGGGGGGGGGGGGGNNNNNACTCACTGTCATTTCCAAACAATTCNN
=
SEQUENCE_ID=boundary_test_17
PRIMER_MAX_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
PRIMER_INTERNAL_MIN_GC=20
SEQUENCE_TEMPLATE=NNCACGTCATCTCATCAAATTTGATTGNNTTTTTTTTTTTTTTTTTTTTTTTTGNNNACTCACTGTCATTTCCAAACAATTCNN
=
SEQUENCE_ID=boundary_test_18
PRIMER_MAX_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
SEQUENCE_INTERNAL_EXCLUDED_REGION=10,50
SEQUENCE_TEMPLATE=NNCACGTCATCTCATCAAATTTGATTGNNACCGCTATTGGGCCATTTGCCCATTGCATGNNNNNNNNNNNNNNNNNNNNNNNNNACTCACTGTCATTTCCAAACAATTCNN
=
SEQUENCE_ID=boundary_test_19
PRIMER_NUM_RETURN=7
PRIMER_MAX_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
PRIMER_INTERNAL_MAX_NS_ACCEPTED=0
SEQUENCE_INTERNAL_EXCLUDED_REGION=10,50
SEQUENCE_TEMPLATE=NNCACGTCATCTCATCAAATTTGATTGNNAAGCTAAGCTTGCCCGTATCCCCTGGATNNNCCGTTAGGTGCTAGCCGTGTAGATTNNNACTCACTGTCATTTCCAAACAATTCNN
=
SEQUENCE_ID=boundary_test_20
PRIMER_NUM_RETURN=5
PRIMER_MAX_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
PRIMER_PRODUCT_SIZE_RANGE=100-300
SEQUENCE_INTERNAL_EXCLUDED_REGION=5,50
SEQUENCE_INTERNAL_EXCLUDED_REGION=60,15
SEQUENCE_INCLUDED_REGION=2,250
SEQUENCE_TEMPLATE=NNCACGTCATCTCATCAAATTTGATTGNNAAGCTAAGCTGTCGATGCGGTGGAGACGATACGGTAAGCTAGCTAACTGGTCAAAGCTAGCGGTAGCTTAGCTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNACTCACTGTCATTTCCAAACAATTCATCTCTCTCTCATATATATATATATATATATATATATAT
=
SEQUENCE_ID=boundary_test_21
PRIMER_MAX_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
PRIMER_INTERNAL_MIN_GC=0
PRIMER_INTERNAL_MIN_TM=55.7
PRIMER_INTERNAL_MAX_TM=55.9
PRIMER_INTERNAL_OPT_TM=55.8
SEQUENCE_TEMPLATE=NNCACGTCATCTCATCAAATTTGATTGNNGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGAAAAAAAAAAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGNNNACTCACTGTCATTTCCAAACAATTCNN
=
SEQUENCE_ID=boundary_test_22
PRIMER_EXPLAIN_FLAG=1
SEQUENCE_TEMPLATE=NNCACGTCATCTCATCAAATTTGATTGNNNACGTACGTACGTTGCAGTCGACGCANNACTCACTGTCATTTCCAAACAATTCNN
PRIMER_PRODUCT_SIZE_RANGE=80-80
PRIMER_MIN_TM=0.0
PRIMER_MAX_TM=100.0
PRIMER_MIN_SIZE=25
PRIMER_MAX_SIZE=25
PRIMER_INTERNAL_MIN_SIZE=25
PRIMER_INTERNAL_MAX_SIZE=25
PRIMER_INTERNAL_OPT_SIZE=25
PRIMER_OPT_SIZE=25
PRIMER_MAX_GC=100
PRIMER_MIN_GC=0
PRIMER_MAX_SELF_END=100
PRIMER_MAX_SELF_ANY=100
PRIMER_PAIR_MAX_COMPL_ANY=100
PRIMER_PAIR_MAX_COMPL_END=100
PRIMER_INTERNAL_MAX_SELF_ANY=100
PRIMER_INTERNAL_MAX_SELF_END=100 
PRIMER_INTERNAL_MAX_TM=100
PRIMER_INTERNAL_MIN_TM=30
PRIMER_INTERNAL_MAX_GC=100
PRIMER_INTERNAL_MIN_GC=0
PRIMER_PICK_INTERNAL_OLIGO=1
P3_COMMENT=should succeed
=
SEQUENCE_ID=boundary_test_23
SEQUENCE_TEMPLATE=NNCACGTCATCTCATCAAATTTGATTGNNNACGTACGTACGTTGCAGTCGACGCANNACTCACTGTCATTTCCAAACAATTCNN
SEQUENCE_INCLUDED_REGION=2,80
SEQUENCE_INTERNAL_EXCLUDED_REGION=1,1
P3_COMMENT=should succeed with warning (internal oligo excluded region outside of included region)
=
SEQUENCE_ID=boundary_test_24
SEQUENCE_TEMPLATE=NNCACGTCATCTCATCAAATTTGATTGNNNACGTACGTACGTTGCAGTCGACGCANNACTCACTGTCATTTCCAAACAATTCNN
SEQUENCE_INCLUDED_REGION=2,80
SEQUENCE_INTERNAL_EXCLUDED_REGION=2,1
P3_COMMENT=should succeed
=
SEQUENCE_ID=boundary_test_25
SEQUENCE_TEMPLATE=NNCACGTCATCTCATCAAATTTGATTGNNNACGTACGTACGTTGCAGTCGACGCANNACTCACTGTCATTTCCAAACAATTCNN
SEQUENCE_INCLUDED_REGION=2,80
SEQUENCE_INTERNAL_EXCLUDED_REGION=0,3
P3_COMMENT=should succeed with warning (internal oligo excluded region outside of included region)
=
SEQUENCE_ID=boundary_test_26
SEQUENCE_TEMPLATE=NNCACGTCATCTCATCAAATTTGATTGNNNACGTACGTACGTTGCAGTCGACGCANNACTCACTGTCATTTCCAAACAATTCNN
SEQUENCE_INCLUDED_REGION=2,80
SEQUENCE_INTERNAL_EXCLUDED_REGION=29,1
P3_COMMENT=should succeed
=
SEQUENCE_ID=boundary_test_27
SEQUENCE_TEMPLATE=NNCACGTCATCTCATCAAATTTGATTGNNNACGTACGTACGTTGCAGTCGACGCANNACTCACTGTCATTTCCAAACAATTCNN
SEQUENCE_INCLUDED_REGION=2,80
SEQUENCE_INTERNAL_EXCLUDED_REGION=30,1
P3_COMMENT=should fail w/ no legal internal oligo
=
SEQUENCE_ID=boundary_test_28
SEQUENCE_TEMPLATE=NNCACGTCATCTCATCAAATTTGATTGNNNACGTACGTACGTTGCAGTCGACGCANNACTCACTGTCATTTCCAAACAATTCNN
SEQUENCE_INCLUDED_REGION=2,80
SEQUENCE_INTERNAL_EXCLUDED_REGION=54,1
P3_COMMENT=should fail w/ no legal internal oligo
=
SEQUENCE_ID=boundary_test_29
SEQUENCE_TEMPLATE=NNCACGTCATCTCATCAAATTTGATTGNNNACGTACGTACGTTGCAGTCGACGCANNACTCACTGTCATTTCCAAACAATTCNN
SEQUENCE_INCLUDED_REGION=2,80
SEQUENCE_INTERNAL_EXCLUDED_REGION=55,1
P3_COMMENT=should succeed
=
SEQUENCE_ID=boundary_test_30
SEQUENCE_TEMPLATE=NNCACGTCATCTCATCAAATTTGATTGNNNACGTACGTACGTTGCAGTCGACGCANNACTCACTGTCATTTCCAAACAATTCNN
SEQUENCE_INCLUDED_REGION=2,80
SEQUENCE_INTERNAL_EXCLUDED_REGION=81,1
P3_COMMENT=should succeed
=
SEQUENCE_ID=boundary_test_31
SEQUENCE_TEMPLATE=NNCACGTCATCTCATCAAATTTGATTGNNNACGTACGTACGTTGCAGTCGACGCANNACTCACTGTCATTTCCAAACAATTCNN
SEQUENCE_INCLUDED_REGION=2,80
SEQUENCE_INTERNAL_EXCLUDED_REGION=82,1
P3_COMMENT=should generate warning (external oligo excluded region outside of included region)
=
SEQUENCE_ID=boundary_test_32
SEQUENCE_TEMPLATE=NNCACGTCATCTCATCAAATTTGATTGNNNACGTACGTACGTTGCAGTCGACGCANNACTCACTGTCATTTCCAAACAATTCNN
SEQUENCE_INCLUDED_REGION=2,80
SEQUENCE_INTERNAL_EXCLUDED_REGION=81,2
P3_COMMENT=should generate warning (external oligo excluded region outside of included region)
=
SEQUENCE_ID=boundary_test_33
SEQUENCE_TEMPLATE=NNCACGTCATCTCATCAAATTTGATTGNNNACGTACGTACGTTGCAGTCGACGCANNACTCACTGTCATTTCCAAACAATTCNN
SEQUENCE_INCLUDED_REGION=2,80
SEQUENCE_INTERNAL_EXCLUDED_REGION=81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1
P3_COMMENT=should succeed (testing number of internal oligo excluded regions)
=
SEQUENCE_ID=boundary_test_34
SEQUENCE_TEMPLATE=NNCACGTCATCTCATCAAATTTGATTGNNNACGTACGTACGTTGCAGTCGACGCANNACTCACTGTCATTTCCAAACAATTCNN
SEQUENCE_INCLUDED_REGION=2,80
SEQUENCE_INTERNAL_EXCLUDED_REGION=81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1 81,1
P3_COMMENT=should fail (testing number of internal oligo excluded regions)
=