PRIMER_FIRST_BASE_INDEX=1
MARKER_NAME=boundary_test_00
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
PRIMER_EXPLAIN_FLAG=1
PRIMER_MAX_POLY_X=0
PRIMER_INTERNAL_OLIGO_MAX_POLY_X=0
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_OPT_SIZE=25
PRIMER_MAX_GC=100
PRIMER_MIN_GC=0
PRIMER_SELF_END=100
PRIMER_SELF_ANY=100
=
MARKER_NAME=boundary_test_01
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
PRIMER_PRODUCT_SIZE_RANGE=55-100
=
MARKER_NAME=boundary_test_02
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
PRIMER_PRODUCT_SIZE_RANGE=55-55
=
MARKER_NAME=boundary_test_03
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
PRIMER_PRODUCT_SIZE_RANGE="56-100"
COMMENT=should fail
=
MARKER_NAME=boundary_test_04
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
PRIMER_PRODUCT_SIZE_RANGE="50-54"
COMMENT=should fail
=
MARKER_NAME=boundary_test_05
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
PRIMER_PRODUCT_SIZE_RANGE="55-55"
PRIMER_MIN_SIZE=24
PRIMER_MAX_SIZE=24
PRIMER_OPT_SIZE=24
=
MARKER_NAME=boundary_test_06
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
PRIMER_PRODUCT_SIZE_RANGE="55-55"
PRIMER_MIN_SIZE=26
PRIMER_MAX_SIZE=26
PRIMER_OPT_SIZE=26
COMMENT=should fail
=
MARKER_NAME=boundary_test_07
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
PRIMER_PRODUCT_SIZE_RANGE="55-55"
PRIMER_MIN_SIZE=25
PRIMER_MAX_SIZE=25
PRIMER_OPT_SIZE=25
INCLUDED_REGION=3,55
=
MARKER_NAME=boundary_test_08
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
PRIMER_PRODUCT_SIZE_RANGE="50-100"
PRIMER_MIN_SIZE=25
PRIMER_MAX_SIZE=25
PRIMER_OPT_SIZE=25
INCLUDED_REGION=4,55
COMMENT=should fail
=
MARKER_NAME=boundary_test_09
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
PRIMER_PRODUCT_SIZE_RANGE="50-100"
INCLUDED_REGION=3,54
COMMENT=should fail
=
MARKER_NAME=boundary_test_10
SEQUENCE=NNCACGTCATCTNATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
PRIMER_PRODUCT_SIZE_RANGE="55-55"
PRIMER_MIN_TM=0.0
PRIMER_MAX_TM=100.0
PRIMER_MIN_SIZE=25
PRIMER_MAX_SIZE=25
PRIMER_OPT_SIZE=25
PRIMER_MAX_GC=100
PRIMER_MIN_GC=0
PRIMER_SELF_END=100
PRIMER_SELF_ANY=100
COMMENT=should fail
=
MARKER_NAME=boundary_test_11
PRIMER_NUM_NS_ACCEPTED=1
SEQUENCE=NNCACGTCATCTNATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
=
MARKER_NAME=boundary_test_11
PRIMER_NUM_NS_ACCEPTED=1
SEQUENCE=NNCACGTCATCNNATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
=
MARKER_NAME=boundary_test_12
PRIMER_NUM_NS_ACCEPTED=2
SEQUENCE=NNCACGTCATCNNATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
=
MARKER_NAME=boundary_test_13
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
SEQUENCE=NNAAAAAAAAAAAAAAAAAAAAAAAAANNNNNACTCACTGTCATTTCCAAACAATTCNN
=
MARKER_NAME=boundary_test_14
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=.0001
SEQUENCE=NNAAAAAAAAAAAAAAAAAAAAAAAAANNNNNACTCACTGTCATTTCCAAACAATTCNN
=
MARKER_NAME=boundary_test_15
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=20
PRIMER_MAX_GC=100
SEQUENCE=NNGGGGGGGGGGGGGGGGGGGGGGGGGNNNNNACTCACTGTCATTTCCAAACAATTCNN
=
MARKER_NAME=boundary_test_16
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=.0001
SEQUENCE=NNGGGGGGGGGGGGGGGGGGGGGGGGGNNNNNACTCACTGTCATTTCCAAACAATTCNN
=
MARKER_NAME=boundary_test_17
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
INCLUDED_REGION=3,55
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
=
MARKER_NAME=boundary_test_18
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
INCLUDED_REGION=4,55
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
=
MARKER_NAME=boundary_test_19
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
INCLUDED_REGION=3,54
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
=
MARKER_NAME=boundary_test_20
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
PRIMER_PRODUCT_SIZE_RANGE="54-55"
INCLUDED_REGION=3,54
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
=
MARKER_NAME=boundary_test_21
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
TARGET=28,5,X
PRIMER_PRODUCT_SIZE_RANGE="55-55"
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
=
PRIMER_SELF_END=100
PRIMER_SELF_ANY=100
PRIMER_MIN_SIZE=25
PRIMER_MAX_SIZE=25
PRIMER_OPT_SIZE=25
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
MARKER_NAME=boundary_test_22
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
TARGET=27,6,X
PRIMER_PRODUCT_SIZE_RANGE="55-55"
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
COMMENT=should fail
=
MARKER_NAME=boundary_test_23
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
TARGET=28,6,X
PRIMER_PRODUCT_SIZE_RANGE="55-55"
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
COMMENT=should fail
=
MARKER_NAME=boundary_test_24
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
TARGET=29,5,X
PRIMER_PRODUCT_SIZE_RANGE="55-55"
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
COMMENT=should fail
=
MARKER_NAME=boundary_test_25
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
TARGET=28,1,X
TARGET=29,4,X
PRIMER_PRODUCT_SIZE_RANGE="55-55"
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
=
MARKER_NAME=boundary_test_26
PRIMER_SELF_END=100
PRIMER_SELF_ANY=100
PRIMER_MIN_SIZE=25
PRIMER_MAX_SIZE=25
PRIMER_OPT_SIZE=25
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
TARGET=27,1,X
TARGET=28,5,X
PRIMER_PRODUCT_SIZE_RANGE="55-55"
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
COMMENT=should fail
=
MARKER_NAME=boundary_test_27
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
TARGET=28,1,X
TARGET=29,5,X
PRIMER_PRODUCT_SIZE_RANGE="55-55"
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
COMMENT=should fail
=
MARKER_NAME=boundary_test_28
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
TARGET=29,1,X
TARGET=30,4,X
PRIMER_PRODUCT_SIZE_RANGE="55-55"
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
COMMENT=should fail
=
MARKER_NAME=boundary_test_29
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
TARGET=29,1,X
PRIMER_PRODUCT_SIZE_RANGE="55-55"
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
=
MARKER_NAME=boundary_test_30
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
TARGET=29,0,X
PRIMER_PRODUCT_SIZE_RANGE="55-55"
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
=
MARKER_NAME=boundary_test_31
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
TARGET=1,1,X
PRIMER_PRODUCT_SIZE_RANGE="55-55"
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
COMMENT=should fail
=
MARKER_NAME=boundary_test_32
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
EXCLUDED_REGION=28,5
PRIMER_PRODUCT_SIZE_RANGE="55-55"
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
=
MARKER_NAME=boundary_test_33
PRIMER_SELF_END=100
PRIMER_SELF_ANY=100
PRIMER_MIN_SIZE=25
PRIMER_MAX_SIZE=25
PRIMER_OPT_SIZE=25
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
EXCLUDED_REGION=27,6
PRIMER_PRODUCT_SIZE_RANGE="55-55"
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
COMMENT=should fail
=
MARKER_NAME=boundary_test_34
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
EXCLUDED_REGION=28,6
PRIMER_PRODUCT_SIZE_RANGE="55-55"
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
COMMENT=should fail
=
MARKER_NAME=boundary_test_35
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
EXCLUDED_REGION=29,5
PRIMER_PRODUCT_SIZE_RANGE="55-55"
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
COMMENT=should fail
=
MARKER_NAME=boundary_test_36
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
EXCLUDED_REGION=28,1
EXCLUDED_REGION=29,4
PRIMER_PRODUCT_SIZE_RANGE="55-55"
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
=
MARKER_NAME=boundary_test_37
PRIMER_SELF_END=100
PRIMER_SELF_ANY=100
PRIMER_MIN_SIZE=25
PRIMER_MAX_SIZE=25
PRIMER_OPT_SIZE=25
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
EXCLUDED_REGION=27,1
EXCLUDED_REGION=28,5
PRIMER_PRODUCT_SIZE_RANGE="55-55"
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
COMMENT=should fail
=
MARKER_NAME=boundary_test_37
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
EXCLUDED_REGION=28,1
EXCLUDED_REGION=29,5
PRIMER_PRODUCT_SIZE_RANGE="55-55"
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
COMMENT=should fail
=
MARKER_NAME=boundary_test_38
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
EXCLUDED_REGION=29,1
EXCLUDED_REGION=30,4
PRIMER_PRODUCT_SIZE_RANGE="55-55"
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
COMMENT=should fail
=
MARKER_NAME=boundary_test_39
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
EXCLUDED_REGION=29,1
PRIMER_PRODUCT_SIZE_RANGE="55-55"
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
=
MARKER_NAME=boundary_test_40
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
EXCLUDED_REGION=29,0
PRIMER_PRODUCT_SIZE_RANGE="55-55"
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
=
MARKER_NAME=boundary_test_41
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
EXCLUDED_REGION=11,0
PRIMER_PRODUCT_SIZE_RANGE="55-55"
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
=
MARKER_NAME=boundary_test_42
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
EXCLUDED_REGION=29,1
PRIMER_PRODUCT_SIZE_RANGE="55-55"
PRIMER_MAX_SIZE=25
PRIMER_MIN_SIZE=25
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
COMMENT="should succeed"
=
MARKER_NAME=boundary_test_43
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
EXCLUDED_REGION=29,1
PRIMER_PRODUCT_SIZE_RANGE="55-55"
PRIMER_MAX_SIZE=25
PRIMER_MIN_SIZE=25
PRIMER_SELF_END=9.99
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
COMMENT="should fail (because one primer has end compl == 10.00)"
=
MARKER_NAME=boundary_test_44
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
EXCLUDED_REGION=29,1
PRIMER_PRODUCT_SIZE_RANGE="55-55"
PRIMER_MAX_SIZE=25
PRIMER_MIN_SIZE=25
PRIMER_SELF_END=10.01
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
COMMENT=should succeed
=
MARKER_NAME=boundary_test_45
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
EXCLUDED_REGION=29,1
PRIMER_PRODUCT_SIZE_RANGE="55-55"
PRIMER_MAX_SIZE=25
PRIMER_MIN_SIZE=25
PRIMER_SELF_END=100
PRIMER_SELF_ANY=12.01
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
COMMENT=should succeed
=
MARKER_NAME=boundary_test_46
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
EXCLUDED_REGION=29,1
PRIMER_PRODUCT_SIZE_RANGE="55-55"
PRIMER_MAX_SIZE=25
PRIMER_MIN_SIZE=25
PRIMER_SELF_END=100
PRIMER_SELF_ANY=11.99
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
COMMENT="should fail (because self any for one primer is 12.00"
=
MARKER_NAME=boundary_test_47
PRIMER_GC_CLAMP=0
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
EXCLUDED_REGION=29,1
PRIMER_PRODUCT_SIZE_RANGE="55-55"
PRIMER_MAX_SIZE=25
PRIMER_MIN_SIZE=25
PRIMER_SELF_END=100
PRIMER_SELF_ANY=100
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
COMMENT="should succeed"
=
MARKER_NAME=boundary_test_48
PRIMER_GC_CLAMP=1
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
EXCLUDED_REGION=29,1
PRIMER_PRODUCT_SIZE_RANGE="55-55"
PRIMER_MAX_SIZE=25
PRIMER_MIN_SIZE=25
PRIMER_SELF_END=100
PRIMER_SELF_ANY=100
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
COMMENT="should fail (because of GC clamp)"
=
MARKER_NAME=boundary_test_49
PRIMER_GC_CLAMP=1
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
EXCLUDED_REGION=29,1
PRIMER_PRODUCT_SIZE_RANGE="55-55"
PRIMER_MAX_SIZE=25
PRIMER_MIN_SIZE=25
PRIMER_SELF_END=100
PRIMER_SELF_ANY=100
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNCCTCACTGTCATTTCCAAACAATTCNN
COMMENT="should succeed"
=
MARKER_NAME=boundary_test_50
PRIMER_GC_CLAMP=2
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
EXCLUDED_REGION=29,1
PRIMER_PRODUCT_SIZE_RANGE="55-55"
PRIMER_MAX_SIZE=25
PRIMER_MIN_SIZE=25
PRIMER_SELF_END=100
PRIMER_SELF_ANY=100
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNCCTCACTGTCATTTCCAAACAATTCNN
COMMENT="should fail (because of GC clamp)"
=
MARKER_NAME=boundary_test_51
PRIMER_MAX_DIFF_TM=100
PRIMER_GC_CLAMP=0
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
EXCLUDED_REGION=29,1
PRIMER_PRODUCT_SIZE_RANGE="55-55"
PRIMER_MAX_SIZE=25
PRIMER_MIN_SIZE=25
PRIMER_SELF_END=100
PRIMER_SELF_ANY=100
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNCCTCACTGTCATTTCCAAACAATTCNN
COMMENT="should succeed"
=
MARKER_NAME=boundary_test_52
PRIMER_MAX_DIFF_TM=0.29
PRIMER_GC_CLAMP=0
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
EXCLUDED_REGION=29,1
PRIMER_PRODUCT_SIZE_RANGE="55-55"
PRIMER_MAX_SIZE=25
PRIMER_MIN_SIZE=25
PRIMER_SELF_END=100
PRIMER_SELF_ANY=100
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNCCTCACTGTCATTTCCAAACAATTCNN
COMMENT="should succeed"
=
MARKER_NAME=boundary_test_53
PRIMER_MAX_DIFF_TM=0.28
PRIMER_GC_CLAMP=0
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
EXCLUDED_REGION=29,1
PRIMER_PRODUCT_SIZE_RANGE="55-55"
PRIMER_MAX_SIZE=25
PRIMER_MIN_SIZE=25
PRIMER_SELF_END=100
PRIMER_SELF_ANY=100
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNCCTCACTGTCATTTCCAAACAATTCNN
COMMENT="should fail (due to max diff tm)"
=
MARKER_NAME=boundary_test_54
PRIMER_LIBERAL_BASE=1
PRIMER_MAX_DIFF_TM=0.29
PRIMER_GC_CLAMP=0
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
EXCLUDED_REGION=29,1
PRIMER_PRODUCT_SIZE_RANGE="55-55"
PRIMER_MAX_SIZE=25
PRIMER_MIN_SIZE=25
PRIMER_SELF_END=100
PRIMER_SELF_ANY=100
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNKNNCCTCACTGTCATTTCCAAACAATTCNN
COMMENT="should succeed"
=
MARKER_NAME=boundary_test_55
PRIMER_LIBERAL_BASE=0
PRIMER_MAX_DIFF_TM=0.29
PRIMER_GC_CLAMP=0
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
EXCLUDED_REGION=29,1
PRIMER_PRODUCT_SIZE_RANGE="55-55"
PRIMER_MAX_SIZE=25
PRIMER_MIN_SIZE=25
PRIMER_SELF_END=100
PRIMER_SELF_ANY=100
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNKNNCCTCACTGTCATTTCCAAACAATTCNN
COMMENT="should generate error"
=
PRIMER_SEQUENCE_ID=poly_x_1
SEQUENCE=AAAAAATTTTTTGGGGGGCCCCCCAAAAAAGGGGGGTTTTTTCCCCCCAAAAAAGGGGGGTTTTTTCCCCCCAAAAAAGGGGGGCCCCCCTTTTTTGGGGGGAAAAAACCCCCCTTTTTTGGGGGGAAAAAACCCCCCTTTTTTAAAAAAGGGGGGCCCCCCAAAAAAGGGGGGTTTTTTTCCCCCC
PRIMER_MAX_POLY_X=5
PRIMER_INTERNAL_OLIGO_MAX_POLY_X=6
PRIMER_PRODUCT_SIZE_RANGE=50-300
PRIMER_PICK_INTERNAL_OLIGO=1
PRIMER_MAX_DIFF_TM=100
PRIMER_SELF_ANY=100
PRIMER_SELF_END=100
=
PRIMER_SEQUENCE_ID=poly_x_2
PRIMER_INTERNAL_OLIGO_MIN_TM=0
PRIMER_INTERNAL_OLIGO_MAX_TM=100
SEQUENCE=AAAAATTTTTCCCCCGGGGGAAAAACCCCCTTTTTGGGGGAAAAATTTTTCCCCCGGGGGAAAAACCCCCTTTTTGGGGGAAAAACCCCCTTTTTGGGGGAAAAACCCCCTTTTTGGGGGAAAAATTTTTCCCCCGGGGGAAAAACCCCCTTTTTGGGGGAAAAACCCCCTTTTTGGGGG
=
PRIMER_SEQUENCE_ID=poly_x_3
SEQUENCE=AAAAAACCCCCCTTTTTTGGGGGGAAAAAACCCCCCTTTTTTGGGGGGAAAAAACCCCCCTTTTTTGGGGGGAAAAAAACCCCCCTTTTTTGGGGGGAAAAAACCCCCCCTTTTTTGGGGGGAAAAAACCCCCCTTTTTTGGGGGGAAAAAAACCCCCCTTTTTTGGGGGGAAAAAACCCCCCTTTTTTTGGGGGGGGGGGGGG
PRIMER_MAX_POLY_X=6
PRIMER_INTERNAL_OLIGO_MAX_POLY_X=5
=
MARKER_NAME=boundary_test_59
PRIMER_PICK_INTERNAL_OLIGO=0
PRIMER_MIN_SIZE=25
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
EXCLUDED_REGION=28,0
PRIMER_PRODUCT_SIZE_RANGE="55-55"
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
COMMENT=ok (excluded region is between G and N and end of left primer).
=
MARKER_NAME=boundary_test_60
PRIMER_PICK_INTERNAL_OLIGO=0
PRIMER_MIN_SIZE=25
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
EXCLUDED_REGION=27,0
PRIMER_PRODUCT_SIZE_RANGE="55-55"
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
COMMENT=should fail (excluded region is between T and G at end of left primer).
=
MARKER_NAME=boundary_test_61
PRIMER_PICK_INTERNAL_OLIGO=0
PRIMER_MIN_SIZE=25
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
EXCLUDED_REGION=27,-1
PRIMER_PRODUCT_SIZE_RANGE="55-55"
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
COMMENT=should fail (negative excluded region size).
=
MARKER_NAME=boundary_test_62
PRIMER_PICK_INTERNAL_OLIGO=0
PRIMER_MIN_SIZE=25
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
INCLUDED_REGION=3,55
EXCLUDED_REGION=2,1
PRIMER_PRODUCT_SIZE_RANGE=55-55
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
COMMENT=should succeed with PRIMER_WARNING EXCLUDED_REGION outside of INCLUDED REGION
=
MARKER_NAME=boundary_test_63
PRIMER_PICK_INTERNAL_OLIGO=0
PRIMER_MIN_SIZE=25
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
INCLUDED_REGION=3,55
EXCLUDED_REGION=3,1
PRIMER_PRODUCT_SIZE_RANGE=55-55
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
COMMENT=should fail with no legal primers
=
MARKER_NAME=boundary_test_64
PRIMER_PICK_INTERNAL_OLIGO=0
PRIMER_MIN_SIZE=25
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
INCLUDED_REGION=3,55
EXCLUDED_REGION=60,1
PRIMER_PRODUCT_SIZE_RANGE=55-55
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
COMMENT=should fail with EXCLUDED_REGION outside of sequence
=
MARKER_NAME=boundary_test_65
PRIMER_PICK_INTERNAL_OLIGO=0
PRIMER_MIN_SIZE=25
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
INCLUDED_REGION=3,55
EXCLUDED_REGION=59,1
PRIMER_PRODUCT_SIZE_RANGE=55-55
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
COMMENT=should succeed with PRIMER_WARNING EXCLUDED_REGION outside of INCLUDED_REGION
=
MARKER_NAME=boundary_test_66
PRIMER_PICK_INTERNAL_OLIGO=0
PRIMER_MIN_SIZE=25
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
INCLUDED_REGION=3,55
EXCLUDED_REGION=57,1
PRIMER_PRODUCT_SIZE_RANGE=55-55
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
COMMENT=should fail with no legal primers
=
MARKER_NAME=boundary_test_67
PRIMER_PICK_INTERNAL_OLIGO=0
PRIMER_MIN_SIZE=25
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
INCLUDED_REGION=3,55
EXCLUDED_REGION=57,2
PRIMER_PRODUCT_SIZE_RANGE=50-55
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
COMMENT=should fail to pick primers and warn EXCLUDED_REGION outside of INCLUDED_REGION
=
MARKER_NAME=boundary_test_68
PRIMER_PICK_INTERNAL_OLIGO=0
PRIMER_MIN_SIZE=25
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
TARGET=28,0
PRIMER_PRODUCT_SIZE_RANGE=55-55
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
COMMENT=ok (TARGET is between G and N and end of left primer).
=
MARKER_NAME=boundary_test_69
PRIMER_PICK_INTERNAL_OLIGO=0
PRIMER_MIN_SIZE=25
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
TARGET=27,0
PRIMER_PRODUCT_SIZE_RANGE="55-55"
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
COMMENT=should fail (TARGET is between T and G at end of left primer).
=
MARKER_NAME=boundary_test_70
PRIMER_PICK_INTERNAL_OLIGO=0
PRIMER_MIN_SIZE=25
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
TARGET=27,-1
PRIMER_PRODUCT_SIZE_RANGE="55-55"
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
COMMENT=should fail (negative TARGET size).
=
MARKER_NAME=boundary_test_71
PRIMER_PICK_INTERNAL_OLIGO=0
PRIMER_MIN_SIZE=25
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
INCLUDED_REGION=3,55
TARGET=2,1
PRIMER_PRODUCT_SIZE_RANGE=55-55
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
COMMENT=should fail to find legal primers, and warn TARGET outside of INCLUDED REGION
=
MARKER_NAME=boundary_test_72
PRIMER_PICK_INTERNAL_OLIGO=0
PRIMER_MIN_SIZE=25
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
INCLUDED_REGION=3,55
TARGET=3,1
PRIMER_PRODUCT_SIZE_RANGE=55-55
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
COMMENT=should fail with no legal primers
=
MARKER_NAME=boundary_test_73
PRIMER_PICK_INTERNAL_OLIGO=0
PRIMER_MIN_SIZE=25
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
INCLUDED_REGION=3,55
TARGET=60,1
PRIMER_PRODUCT_SIZE_RANGE=55-55
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
COMMENT=should fail with TARGET outside of sequence
=
MARKER_NAME=boundary_test_74
PRIMER_PICK_INTERNAL_OLIGO=0
PRIMER_MIN_SIZE=25
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
INCLUDED_REGION=3,55
TARGET=59,1
PRIMER_PRODUCT_SIZE_RANGE=55-55
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
COMMENT=should fail to find primers (none spans target), and warn TARGET outside of INCLUDED_REGION
=
MARKER_NAME=boundary_test_75
PRIMER_PICK_INTERNAL_OLIGO=0
PRIMER_MIN_SIZE=25
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
INCLUDED_REGION=3,55
TARGET=57,1
PRIMER_PRODUCT_SIZE_RANGE=55-55
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
COMMENT=should fail with no legal primers
=
MARKER_NAME=boundary_test_76
PRIMER_PICK_INTERNAL_OLIGO=0
PRIMER_MIN_SIZE=25
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
INCLUDED_REGION=3,55
TARGET=57,2
PRIMER_PRODUCT_SIZE_RANGE=50-55
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
COMMENT=should fail to pick primers, and warn TARGET outside of INCLUDED_REGION
=
MARKER_NAME=boundary_test_77
PRIMER_PICK_INTERNAL_OLIGO=0
PRIMER_MIN_SIZE=25
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
INCLUDED_REGION=3,55
TARGET=28,1
PRIMER_PRODUCT_SIZE_RANGE=50-55
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
COMMENT=should succeed (target is at TTG^NNN)
=
MARKER_NAME=boundary_test_78
PRIMER_PICK_INTERNAL_OLIGO=0
PRIMER_MIN_SIZE=25
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
INCLUDED_REGION=3,55
TARGET=28,5
PRIMER_PRODUCT_SIZE_RANGE=50-55
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
COMMENT=should succeed (target is the middle run of N)
=
MARKER_NAME=boundary_test_79
PRIMER_PICK_INTERNAL_OLIGO=0
PRIMER_MIN_SIZE=25
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
INCLUDED_REGION=3,55
TARGET=28,0
PRIMER_PRODUCT_SIZE_RANGE=50-55
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
COMMENT=should succeed
=
MARKER_NAME=boundary_test_80
PRIMER_PICK_INTERNAL_OLIGO=0
PRIMER_MIN_SIZE=25
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
INCLUDED_REGION=3,55
TARGET=32,1
PRIMER_PRODUCT_SIZE_RANGE=50-55
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
COMMENT=should succeed
=
MARKER_NAME=boundary_test_81
PRIMER_PICK_INTERNAL_OLIGO=0
PRIMER_MIN_SIZE=25
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
INCLUDED_REGION=3,55
TARGET=33,0
PRIMER_PRODUCT_SIZE_RANGE=50-55
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
COMMENT=should succeed
=
MARKER_NAME=boundary_test_82
PRIMER_PICK_INTERNAL_OLIGO=0
PRIMER_MIN_SIZE=25
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
INCLUDED_REGION=1,59
TARGET=33,0 1,1 59,1
PRIMER_PRODUCT_SIZE_RANGE=50-55
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
COMMENT=should succeed
=
MARKER_NAME=boundary_test_83
PRIMER_PICK_INTERNAL_OLIGO=0
PRIMER_MIN_SIZE=25
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
INCLUDED_REGION=1,59
TARGET=1,1 59,1
PRIMER_PRODUCT_SIZE_RANGE=50-55
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
COMMENT=should fail (no target)
=
MARKER_NAME=boundary_test_84
PRIMER_PICK_INTERNAL_OLIGO=0
PRIMER_MIN_SIZE=25
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
INCLUDED_REGION=1,59
TARGET=1,1 33,0
PRIMER_PRODUCT_SIZE_RANGE=50-55
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
COMMENT=should succeed
=
MARKER_NAME=boundary_test_85
PRIMER_PICK_INTERNAL_OLIGO=0
PRIMER_MIN_SIZE=25
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
INCLUDED_REGION=1,59
TARGET=33,0 59,1
PRIMER_PRODUCT_SIZE_RANGE=50-55
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
COMMENT=should succeed
=
MARKER_NAME=boundary_test_86
PRIMER_PICK_INTERNAL_OLIGO=0
PRIMER_MIN_SIZE=35
PRIMER_MAX_SIZE=35
PRIMER_OPT_SIZE=35
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
PRIMER_PRODUCT_SIZE_RANGE=75-75
SEQUENCE=NNCACGTCATCTATATATATATCATCAAATTTGATTGNNNNNACTCATATATATATACTGTCATTTCCAAACAATTCNN
COMMENT=should succeed (testing hard limit MAX_PRIMER_LENGTH)
=
MARKER_NAME=boundary_test_71
PRIMER_PICK_INTERNAL_OLIGO=0
PRIMER_MIN_SIZE=25
PRIMER_MAX_SIZE=25
PRIMER_OPT_SIZE=25
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
INCLUDED_REGION=3,55
TARGET=2,1 28,1
PRIMER_PRODUCT_SIZE_RANGE=55-55
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
COMMENT=should warn TARGET outside of INCLUDED REGION
=
MARKER_NAME=boundary_test_72
PRIMER_PICK_INTERNAL_OLIGO=0
PRIMER_MIN_SIZE=25
PRIMER_MAX_SIZE=25
PRIMER_OPT_SIZE=25
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
INCLUDED_REGION=3,56
PRIMER_PRODUCT_SIZE_RANGE=54-54 55-55 56-56
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
COMMENT=should succed with exactly one pair
=
MARKER_NAME=boundary_test_73
PRIMER_PICK_INTERNAL_OLIGO=0
PRIMER_MIN_SIZE=25
PRIMER_MAX_SIZE=25
PRIMER_OPT_SIZE=25
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
INCLUDED_REGION=3,56
PRIMER_PRODUCT_SIZE_RANGE=54-54 56-56
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
COMMENT=should fail (no primers with acceptable product size)
=
MARKER_NAME=boundary_test_74
PRIMER_PICK_INTERNAL_OLIGO=0
PRIMER_MIN_SIZE=25
PRIMER_MAX_SIZE=25
PRIMER_OPT_SIZE=25
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
INCLUDED_REGION=3,56
PRIMER_PRODUCT_SIZE_RANGE=54-55 55-56
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
COMMENT=should succeed with exactly one primer pair
=
MARKER_NAME=boundary_test_75
PRIMER_PICK_INTERNAL_OLIGO=0
PRIMER_MIN_SIZE=25
PRIMER_MAX_SIZE=25
PRIMER_OPT_SIZE=25
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
INCLUDED_REGION=3,55
PRIMER_PRODUCT_SIZE_RANGE=54-54 55-55
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
COMMENT=should succeed with exactly one primer pair
=
MARKER_NAME=boundary_test_76
PRIMER_PICK_INTERNAL_OLIGO=0
PRIMER_MIN_SIZE=25
PRIMER_MAX_SIZE=25
PRIMER_OPT_SIZE=25
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
INCLUDED_REGION=3,56
PRIMER_PRODUCT_SIZE_RANGE=55-55 56-56
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
COMMENT=should succeed with exactly one primer pair
=
MARKER_NAME=boundary_test_77
PRIMER_PICK_INTERNAL_OLIGO=0
PRIMER_MIN_SIZE=25
PRIMER_MAX_SIZE=25
PRIMER_OPT_SIZE=25
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
INCLUDED_REGION=3,82
PRIMER_PRODUCT_SIZE_RANGE=55-55 82-82
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNNACTCACTGTCATTTCCAAACAATTCNN
COMMENT=should succeed with exactly 2 primer pairs, biggest product second
=
MARKER_NAME=boundary_test_78
PRIMER_PICK_INTERNAL_OLIGO=0
PRIMER_MIN_SIZE=25
PRIMER_MAX_SIZE=25
PRIMER_OPT_SIZE=25
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
INCLUDED_REGION=3,82
PRIMER_PRODUCT_SIZE_RANGE=82-82 55-55
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNNACTCACTGTCATTTCCAAACAATTCNN
COMMENT=should succeed with exactly 2 primer pairs, biggest product first
=
MARKER_NAME=boundary_test_79
PRIMER_PICK_INTERNAL_OLIGO=0
PRIMER_MIN_SIZE=25
PRIMER_MAX_SIZE=25
PRIMER_OPT_SIZE=25
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
INCLUDED_REGION=3,82
PRIMER_PRODUCT_SIZE_RANGE=55-55 55-82
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNNACTCACTGTCATTTCCAAACAATTCNN
COMMENT=should succeed with exactly 2 primer pairs, biggest product second
=
MARKER_NAME=boundary_test_80
PRIMER_PICK_INTERNAL_OLIGO=0
PRIMER_MIN_SIZE=25
PRIMER_MAX_SIZE=25
PRIMER_OPT_SIZE=25
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
INCLUDED_REGION=3,82
PRIMER_PRODUCT_SIZE_RANGE=82-82 55-82
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNNACTCACTGTCATTTCCAAACAATTCNN
COMMENT=should succeed with exactly 2 primer pairs, biggest product first
=
MARKER_NAME=boundary_test_81
PRIMER_PICK_INTERNAL_OLIGO=0
PRIMER_MIN_SIZE=25
PRIMER_MAX_SIZE=25
PRIMER_OPT_SIZE=25
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
INCLUDED_REGION=3,55
PRIMER_PRODUCT_SIZE_RANGE=55-55
PRIMER_SELF_ANY=11
SEQUENCE=NNAATGTGATTGCATCAAATGTGATTGNNNNNAATGTGATTGTCATTTCCACAATTCNN
COMMENT=should succeed (testing pairwise complementarity checking)
=
MARKER_NAME=boundary_test_82
PRIMER_PICK_INTERNAL_OLIGO=0
PRIMER_MIN_SIZE=25
PRIMER_MAX_SIZE=25
PRIMER_OPT_SIZE=25
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
INCLUDED_REGION=3,55
PRIMER_PRODUCT_SIZE_RANGE=55-55
PRIMER_SELF_ANY=10.99
SEQUENCE=NNAATGTGATTGCATCAAATGTGATTGNNNNNAATGTGATTGTCATTTCCACAATTCNN
COMMENT=should fail (self any for pairs)
=
MARKER_NAME=boundary_test_83
PRIMER_PICK_INTERNAL_OLIGO=0
PRIMER_MIN_SIZE=25
PRIMER_MAX_SIZE=25
PRIMER_OPT_SIZE=25
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
INCLUDED_REGION=3,55
PRIMER_PRODUCT_SIZE_RANGE=55-55
PRIMER_SELF_ANY=11
PRIMER_SELF_END=10
SEQUENCE=NNAATGTGATTGCATCAAATGTGATTGNNNNNAATGTGATTGTCATTTCCACAATTCNN
COMMENT=should succeed (testing pairwise complementarity checking)
=
MARKER_NAME=boundary_test_84
PRIMER_PICK_INTERNAL_OLIGO=0
PRIMER_MIN_SIZE=25
PRIMER_MAX_SIZE=25
PRIMER_OPT_SIZE=25
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
INCLUDED_REGION=3,55
PRIMER_PRODUCT_SIZE_RANGE=55-55
PRIMER_SELF_ANY=11
PRIMER_SELF_END=9.99
SEQUENCE=NNAATGTGATTGCATCAAATGTGATTGNNNNNAATGTGATTGTCATTTCCACAATTCNN
COMMENT=should fail (self end for pairs)
=
MARKER_NAME=boundary_test_85
PRIMER_PICK_INTERNAL_OLIGO=0
PRIMER_MIN_SIZE=25
PRIMER_MAX_SIZE=25
PRIMER_OPT_SIZE=25
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
INCLUDED_REGION=3,55
PRIMER_PRODUCT_SIZE_RANGE=55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 
PRIMER_SELF_ANY=11
PRIMER_SELF_END=10
SEQUENCE=NNAATGTGATTGCATCAAATGTGATTGNNNNNAATGTGATTGTCATTTCCACAATTCNN
COMMENT=should succeed (testing number of product size ranges)
=
MARKER_NAME=boundary_test_86
PRIMER_PICK_INTERNAL_OLIGO=0
PRIMER_MIN_SIZE=25
PRIMER_MAX_SIZE=25
PRIMER_OPT_SIZE=25
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
INCLUDED_REGION=3,55
PRIMER_PRODUCT_SIZE_RANGE=55-55
TARGET=28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1
PRIMER_SELF_ANY=11
PRIMER_SELF_END=10
SEQUENCE=NNAATGTGATTGCATCAAATGTGATTGNNNNNAATGTGATTGTCATTTCCACAATTCNN
COMMENT=should succeed (testing number of targets)
=
MARKER_NAME=boundary_test_87
PRIMER_PICK_INTERNAL_OLIGO=0
PRIMER_MIN_SIZE=25
PRIMER_MAX_SIZE=25
PRIMER_OPT_SIZE=25
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
INCLUDED_REGION=3,55
PRIMER_PRODUCT_SIZE_RANGE=55-55
TARGET=28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1
PRIMER_SELF_ANY=11
PRIMER_SELF_END=10
SEQUENCE=NNAATGTGATTGCATCAAATGTGATTGNNNNNAATGTGATTGTCATTTCCACAATTCNN
COMMENT=should fail (testing number of targets)
=
MARKER_NAME=boundary_test_88
PRIMER_PICK_INTERNAL_OLIGO=0
PRIMER_MIN_SIZE=25
PRIMER_MAX_SIZE=25
PRIMER_OPT_SIZE=25
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
INCLUDED_REGION=3,55
PRIMER_PRODUCT_SIZE_RANGE=55-55
EXCLUDED_REGION=28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1
PRIMER_SELF_ANY=11
PRIMER_SELF_END=10
SEQUENCE=NNAATGTGATTGCATCAAATGTGATTGNNNNNAATGTGATTGTCATTTCCACAATTCNN
COMMENT=should succeed (testing number of excluded regions)
=
MARKER_NAME=boundary_test_89
PRIMER_PICK_INTERNAL_OLIGO=0
PRIMER_MIN_SIZE=25
PRIMER_MAX_SIZE=25
PRIMER_OPT_SIZE=25
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
INCLUDED_REGION=3,55
PRIMER_PRODUCT_SIZE_RANGE=55-55
EXCLUDED_REGION=28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1 28,1
PRIMER_SELF_ANY=11
PRIMER_SELF_END=10
SEQUENCE=NNAATGTGATTGCATCAAATGTGATTGNNNNNAATGTGATTGTCATTTCCACAATTCNN
COMMENT=should fail (testing number of excluded regions)
=
