PRIMER_SEQUENCE_ID=template_mis_1
PRIMER_NUM_RETURN=1
PRIMER_MAX_TEMPLATE_MISPRIMING=100
PRIMER_PAIR_MAX_TEMPLATE_MISPRIMING=100
SEQUENCE=TCCTACAGCTGTGGGAAAATGatgcgtacgatccatgctagctagctactatcgattagctatcatctactatcatctactatctactacacatctactatcatctacacacacacacacactaggccgctatatcatctagcGCCGCCATGTACACACTG
=
PRIMER_SEQUENCE_ID=template_mis_2
PRIMER_NUM_RETURN=1
PRIMER_EXPLAIN_FLAG=1
PRIMER_PICK_ANYWAY=1
PRIMER_MAX_TEMPLATE_MISPRIMING=100
PRIMER_LEFT_INPUT=TCCTACAGCTGTGGGAAAATGat
PRIMER_PAIR_MAX_TEMPLATE_MISPRIMING=100
PRIMER_PAIR_WT_TEMPLATE_MISPRIMING=1
PRIMER_WT_SIZE_GT=0
PRIMER_WT_SIZE_LT=0
PRIMER_WT_TM_GT=.05
PRIMER_WT_TM_LT=.05
SEQUENCE=TCCTACAGCTGTGGGAAAATGatgcgtacgatTCCTACAGCTGTGGGAAAATGatgcgtacgatccatgctagctagctactatcgattagctatcatctactatcatctactatctactacacatctactatcatctacacacacacacacactaggccgctatatcatctagcGCCGCCATGTACACACTGatatcatctagcGCCGCCATGTACACACTG
=
PRIMER_SEQUENCE_ID=template_mis_3
PRIMER_NUM_RETURN=1
PRIMER_EXPLAIN_FLAG=1
PRIMER_PICK_ANYWAY=1
PRIMER_MAX_TEMPLATE_MISPRIMING=100
PRIMER_LEFT_INPUT=TCCTACAGCTGTGGGAAAATGat
PRIMER_RIGHT_INPUT=GGGGGGGGGGGGGGGGGG
PRIMER_PAIR_MAX_TEMPLATE_MISPRIMING=100
PRIMER_PAIR_WT_TEMPLATE_MISPRIMING=1
PRIMER_WT_SIZE_GT=0
PRIMER_WT_SIZE_LT=0
PRIMER_WT_TM_GT=.05
PRIMER_WT_TM_LT=.05
SEQUENCE=TCCTACAGCTGTGGGAAAATGatgcgtacgatTCCTACAGCTGTGGGAAAATGatgcgtacgatccatgctagctagctactatcgattagctatcatctactatcatctactatctactacacatctactatcatctacacacacacacacactaggccgctatatcatctagcGCCGCCATGTACACACTGatatcatctagcGCCGCCATGTACACACTGCCCCCCCCCCCCCCCCCC
=
PRIMER_SEQUENCE_ID=template_mis_4
PRIMER_NUM_RETURN=1
PRIMER_EXPLAIN_FLAG=1
PRIMER_PICK_ANYWAY=1
PRIMER_MAX_TEMPLATE_MISPRIMING=100
PRIMER_LEFT_INPUT=TCCTACAGCTGTGGGAAAATGat
PRIMER_RIGHT_INPUT=GGGGGGGGGGGGGGGGGG
PRIMER_PAIR_MAX_TEMPLATE_MISPRIMING=100
PRIMER_PAIR_WT_TEMPLATE_MISPRIMING=1
PRIMER_WT_SIZE_GT=0
PRIMER_WT_SIZE_LT=0
PRIMER_WT_TM_GT=.05
PRIMER_WT_TM_LT=.05
PRIMER_LIBERAL_BASE=1
SEQUENCE=TCCTACAGCTGTGGGAAAATGatTCCTACAGCTGTGGGAAAATGatgcgtacgatccatgctagctagctactatcgattagctatcatctactatcatctactatctactacacatctactatcatctacacacacacacacactaggccgctatatcatctagcGCCGCCATGTACACACTGatatcatctagcGCCGCCATGTACACACTGCCCCCCCCCCCCCCCCCCACSCCCCCCCCCCCCCCCCA
=
PRIMER_SEQUENCE_ID=template_mis_5
PRIMER_NUM_RETURN=1
PRIMER_EXPLAIN_FLAG=1
PRIMER_PICK_ANYWAY=1
PRIMER_MAX_TEMPLATE_MISPRIMING=100
PRIMER_LEFT_INPUT=TCCTACAGCTGTGGGAAAATGat
PRIMER_RIGHT_INPUT=GGGGGGGGGGGGGGGGGG
PRIMER_PAIR_MAX_TEMPLATE_MISPRIMING=100
PRIMER_PAIR_WT_TEMPLATE_MISPRIMING=1
PRIMER_WT_SIZE_GT=0
PRIMER_WT_SIZE_LT=0
PRIMER_WT_TM_GT=.05
PRIMER_WT_TM_LT=.05
PRIMER_LIBERAL_BASE=1
SEQUENCE=TCCTACAGCTGTGGGAAAATGatTCCTACAGCTGTGGGAAAATGatgcgtacgatccatgctagctagctactatcgattagctatcatctactatcatctactatctactacacatctactatcatctacacacacacacacactaggccgctatatcatctagcGCCGCCATGTACACACTGatatcatctagcGCCGCCATGTACACACTGCCCCCCCCCCCCCCCCCCACTCCCCCCCCCCCCCCCCA
=
PRIMER_SEQUENCE_ID=template_mis_6
PRIMER_NUM_RETURN=1
PRIMER_EXPLAIN_FLAG=1
PRIMER_PICK_ANYWAY=1
PRIMER_MAX_TEMPLATE_MISPRIMING=100
PRIMER_LEFT_INPUT=TCCTACAGCTGTGGGAAAATGat
PRIMER_RIGHT_INPUT=GGGGGGGGGGGGGGGGGG
PRIMER_PAIR_MAX_TEMPLATE_MISPRIMING=100
PRIMER_PAIR_WT_TEMPLATE_MISPRIMING=1
PRIMER_WT_SIZE_GT=0
PRIMER_WT_SIZE_LT=0
PRIMER_WT_TM_GT=.05
PRIMER_WT_TM_LT=.05
PRIMER_LIBERAL_BASE=1
PRIMER_PRODUCT_SIZE_RANGE=36-300
SEQUENCE=TCCTACAGCTGTGGGAAAATGatNgcgtacNCCCCCCCCCACCCCCCCCACCCCCCCCCCCCCCCCCC
=
PRIMER_SEQUENCE_ID=template_mis_7
PRIMER_EXPLAIN_FLAG=1
PRIMER_PICK_ANYWAY=1
PRIMER_MAX_TEMPLATE_MISPRIMING=100
PRIMER_LEFT_INPUT=TCCTACAGCTGTGGGAAAATGat
PRIMER_RIGHT_INPUT=GGGGGGGGGGGGGGGGGG
PRIMER_PAIR_MAX_TEMPLATE_MISPRIMING=100
PRIMER_PAIR_WT_TEMPLATE_MISPRIMING=1
PRIMER_WT_SIZE_GT=0
PRIMER_WT_SIZE_LT=0
PRIMER_WT_TM_GT=.05
PRIMER_WT_TM_LT=.05
PRIMER_LIBERAL_BASE=1
PRIMER_PRODUCT_SIZE_RANGE=36-300
SEQUENCE=TCCTACAGCTGTGGGAAAATGatNgcgtacNCCCCCCCCCAAAAAAAAAACCCCCCCCCCCCCCCCCC
=
PRIMER_SEQUENCE_ID=template_mis_8
PRIMER_NUM_RETURN=1
PRIMER_EXPLAIN_FLAG=1
PRIMER_PICK_ANYWAY=1
PRIMER_MAX_TEMPLATE_MISPRIMING=11
PRIMER_MAX_POLY_X=40
PRIMER_PAIR_MAX_TEMPLATE_MISPRIMING=100
PRIMER_PAIR_WT_TEMPLATE_MISPRIMING=1
PRIMER_WT_SIZE_GT=0
PRIMER_WT_SIZE_LT=0
PRIMER_WT_TM_GT=.05
PRIMER_WT_TM_LT=.05
PRIMER_LIBERAL_BASE=1
PRIMER_PRODUCT_SIZE_RANGE=36-300
PRIMER_MAX_GC=100
PRIMER_MAX_TM=100
PRIMER_RIGHT_INPUT=GGGGGGGGGGGGGGGGGG
SEQUENCE=TCCTACAGCTGTGGGAAAATGatNgcgtacNCCCCCCCCCAAAAAAAAAACCCCCCCCCCCCCCCCCC
COMMENT=Should succeed
=
PRIMER_SEQUENCE_ID=template_mis_9
PRIMER_NUM_RETURN=1
PRIMER_EXPLAIN_FLAG=1
PRIMER_PICK_ANYWAY=1
PRIMER_MAX_TEMPLATE_MISPRIMING=9
PRIMER_MAX_POLY_X=40
PRIMER_SELF_END=100
PRIMER_PAIR_MAX_TEMPLATE_MISPRIMING=100
PRIMER_PAIR_WT_TEMPLATE_MISPRIMING=1
PRIMER_WT_SIZE_GT=0
PRIMER_WT_SIZE_LT=0
PRIMER_WT_TM_GT=.05
PRIMER_WT_TM_LT=.05
PRIMER_LIBERAL_BASE=1
PRIMER_PRODUCT_SIZE_RANGE=36-300
PRIMER_MAX_GC=100
SEQUENCE=TCCTACAGCTGTGGGAAAATGatNgcgtacNCCCCCCCCCAAAAAAAAAACCCCCCCCCCCCCCCCCC
COMMENT=Should succeed
=
PRIMER_SEQUENCE_ID=template_mis_10
PRIMER_NUM_RETURN=1
PRIMER_EXPLAIN_FLAG=1
PRIMER_PICK_ANYWAY=1
PRIMER_MAX_TEMPLATE_MISPRIMING=6.7
PRIMER_MAX_POLY_X=40
PRIMER_SELF_END=100
PRIMER_PAIR_MAX_TEMPLATE_MISPRIMING=100
PRIMER_PAIR_WT_TEMPLATE_MISPRIMING=1
PRIMER_WT_SIZE_GT=0
PRIMER_WT_SIZE_LT=0
PRIMER_WT_TM_GT=.05
PRIMER_WT_TM_LT=.05
PRIMER_LIBERAL_BASE=1
PRIMER_PRODUCT_SIZE_RANGE=36-300
PRIMER_MAX_GC=100
SEQUENCE=TCCTACAGCTGTGGGAAAATGatNgcgtacNCCCCCCCCCAAAAAAAAAACCCCCCCCCCCCCCCCCC
COMMENT=Should fail
=
PRIMER_SEQUENCE_ID=template_mis_11
PRIMER_NUM_RETURN=1
PRIMER_EXPLAIN_FLAG=1
PRIMER_PICK_ANYWAY=1
PRIMER_MAX_POLY_X=40
PRIMER_SELF_END=100
PRIMER_WT_SIZE_GT=0
PRIMER_WT_SIZE_LT=0
PRIMER_WT_TM_GT=.05
PRIMER_WT_TM_LT=.05
PRIMER_MAX_GC=100
PRIMER_MAX_TM=100
PRIMER_TASK=pick_left_only
PRIMER_MAX_TEMPLATE_MISPRIMING=100
PRIMER_LEFT_INPUT=cTTGATGGAGAATTGCGCAGAGGGGc
SEQUENCE=aTTGATGGAGAATTGCGCAGAGGGGcTTGATGGAGAATTGCGCAGAGGGGc
COMMENT=Test off-by-one error in checking for mispriming on the same strand as the oligo
=
PRIMER_SEQUENCE_ID=template_mis_12
PRIMER_NUM_RETURN=1
PRIMER_EXPLAIN_FLAG=1
PRIMER_PICK_ANYWAY=1
PRIMER_MAX_POLY_X=40
PRIMER_SELF_END=100
PRIMER_WT_SIZE_GT=0
PRIMER_WT_SIZE_LT=0
PRIMER_WT_TM_GT=.05
PRIMER_WT_TM_LT=.05
PRIMER_MAX_GC=100
PRIMER_MAX_TM=100
PRIMER_TASK=pick_left_only
PRIMER_MAX_TEMPLATE_MISPRIMING=100
PRIMER_LEFT_INPUT=cTTGATGGAGAATTGCGCAGAGGGGc
INCLUDED_REGION=25,26
SEQUENCE=aTTGATGGAGAATTGCGCAGAGGGGcTTGATGGAGAATTGCGCAGAGGGGc
COMMENT=Test off-by-one error in checking for mispriming on the same strand as the oligo plus former error in ignoring included_region offset
=
PRIMER_SEQUENCE_ID=template_mis_13
PRIMER_NUM_RETURN=1
PRIMER_EXPLAIN_FLAG=1
PRIMER_PICK_ANYWAY=1
PRIMER_MAX_POLY_X=40
PRIMER_SELF_END=100
PRIMER_WT_SIZE_GT=0
PRIMER_WT_SIZE_LT=0
PRIMER_WT_TM_GT=.05
PRIMER_WT_TM_LT=.05
PRIMER_MAX_GC=100
PRIMER_MAX_TM=100
PRIMER_TASK=pick_left_only
PRIMER_MAX_TEMPLATE_MISPRIMING=100
PRIMER_LEFT_INPUT=cTTGATGGAGAATTGCGCAGAGGGGc
SEQUENCE=cTTGATGGAGAATTGCGCAGAGGGGcTTGATGGAGAATTGCGCAGAGGGc
COMMENT=Test off-by-one error in checking for mispriming on the same strand as the oligo
=
PRIMER_SEQUENCE_ID=template_mis_14
PRIMER_NUM_RETURN=1
PRIMER_EXPLAIN_FLAG=1
PRIMER_PICK_ANYWAY=1
PRIMER_MAX_POLY_X=40
PRIMER_SELF_END=100
PRIMER_WT_SIZE_GT=0
PRIMER_WT_SIZE_LT=0
PRIMER_WT_TM_GT=.05
PRIMER_WT_TM_LT=.05
PRIMER_MAX_GC=100
PRIMER_MAX_TM=100
PRIMER_TASK=pick_right_only
PRIMER_MAX_TEMPLATE_MISPRIMING=100
PRIMER_RIGHT_INPUT=cTTGATGGAGAATTGCGCAGAGGGGc
SEQUENCE=GCCCCTCTGCGCAATTCTCCATCAAGCCCCTCTGCGCAATTCTCCATCAAT
COMMENT=Test off-by-one error in checking for mispriming on the same strand as the oligo; SEQUENCE is complements of template_mis_11
=
PRIMER_SEQUENCE_ID=template_mis_15
PRIMER_NUM_RETURN=1
PRIMER_EXPLAIN_FLAG=1
PRIMER_PICK_ANYWAY=1
PRIMER_MAX_POLY_X=40
PRIMER_SELF_END=100
PRIMER_WT_SIZE_GT=0
PRIMER_WT_SIZE_LT=0
PRIMER_WT_TM_GT=.05
PRIMER_WT_TM_LT=.05
PRIMER_MAX_GC=100
PRIMER_MAX_TM=100
PRIMER_TASK=pick_right_only
PRIMER_MAX_TEMPLATE_MISPRIMING=100
PRIMER_RIGHT_INPUT=cTTGATGGAGAATTGCGCAGAGGGGc
SEQUENCE=GCCCTCTGCGCAATTCTCCATCAAGCCCCTCTGCGCAATTCTCCATCAAG
COMMENT=Test off-by-one error in checking for mispriming on the same strand as the oligo; SEQUENCE is complements of template_mis_13
=
PRIMER_SEQUENCE_ID=template_mis_16
PRIMER_NUM_RETURN=1
PRIMER_EXPLAIN_FLAG=1
PRIMER_PICK_ANYWAY=1
PRIMER_MAX_POLY_X=40
PRIMER_SELF_END=100
PRIMER_WT_SIZE_GT=0
PRIMER_WT_SIZE_LT=0
PRIMER_WT_TM_GT=.05
PRIMER_WT_TM_LT=.05
PRIMER_MAX_GC=100
PRIMER_MAX_TM=100
PRIMER_TASK=pick_right_only
PRIMER_MAX_TEMPLATE_MISPRIMING=100
PRIMER_RIGHT_INPUT=cTTGATGGAGAATTGCGCAGAGGGGc
INCLUDED_REGION=24,26
SEQUENCE=GCCCTCTGCGCAATTCTCCATCAAGCCCCTCTGCGCAATTCTCCATCAAG
COMMENT=Test off-by-one error in checking for mispriming on the same strand as the oligo; SEQUENCE is complements of template_mis_13
=
