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
PRIMER_LEFT_EXPLAIN=considered 10, too many Ns 9, ok 1
PRIMER_RIGHT_EXPLAIN=considered 10, too many Ns 9, ok 1
PRIMER_PAIR_EXPLAIN=considered 1, ok 1
PRIMER_PAIR_PENALTY=3.3813
PRIMER_LEFT_PENALTY=2.731673
PRIMER_RIGHT_PENALTY=0.649600
PRIMER_LEFT_SEQUENCE=CACGTCATCTCATCAAATTTGATTG
PRIMER_RIGHT_SEQUENCE=GAATTGTTTGGAAATGACAGTGAGT
PRIMER_LEFT=3,25
PRIMER_RIGHT=57,25
PRIMER_LEFT_TM=62.732
PRIMER_RIGHT_TM=60.650
PRIMER_LEFT_GC_PERCENT=36.000
PRIMER_RIGHT_GC_PERCENT=36.000
PRIMER_LEFT_SELF_ANY=12.00
PRIMER_RIGHT_SELF_ANY=4.00
PRIMER_LEFT_SELF_END=10.00
PRIMER_RIGHT_SELF_END=3.00
PRIMER_LEFT_END_STABILITY=6.9000
PRIMER_RIGHT_END_STABILITY=6.4000
PRIMER_PAIR_COMPL_ANY=7.00
PRIMER_PAIR_COMPL_END=1.00
PRIMER_PRODUCT_SIZE=55
=
MARKER_NAME=boundary_test_01
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
PRIMER_PRODUCT_SIZE_RANGE=55-100
PRIMER_LEFT_EXPLAIN=considered 5, too many Ns 4, ok 1
PRIMER_RIGHT_EXPLAIN=considered 5, too many Ns 4, ok 1
PRIMER_PAIR_EXPLAIN=considered 1, ok 1
PRIMER_PAIR_PENALTY=3.3813
PRIMER_LEFT_PENALTY=2.731673
PRIMER_RIGHT_PENALTY=0.649600
PRIMER_LEFT_SEQUENCE=CACGTCATCTCATCAAATTTGATTG
PRIMER_RIGHT_SEQUENCE=GAATTGTTTGGAAATGACAGTGAGT
PRIMER_LEFT=3,25
PRIMER_RIGHT=57,25
PRIMER_LEFT_TM=62.732
PRIMER_RIGHT_TM=60.650
PRIMER_LEFT_GC_PERCENT=36.000
PRIMER_RIGHT_GC_PERCENT=36.000
PRIMER_LEFT_SELF_ANY=12.00
PRIMER_RIGHT_SELF_ANY=4.00
PRIMER_LEFT_SELF_END=10.00
PRIMER_RIGHT_SELF_END=3.00
PRIMER_LEFT_END_STABILITY=6.9000
PRIMER_RIGHT_END_STABILITY=6.4000
PRIMER_PAIR_COMPL_ANY=7.00
PRIMER_PAIR_COMPL_END=1.00
PRIMER_PRODUCT_SIZE=55
=
MARKER_NAME=boundary_test_02
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
PRIMER_PRODUCT_SIZE_RANGE=55-55
PRIMER_LEFT_EXPLAIN=considered 5, too many Ns 4, ok 1
PRIMER_RIGHT_EXPLAIN=considered 5, too many Ns 4, ok 1
PRIMER_PAIR_EXPLAIN=considered 1, ok 1
PRIMER_PAIR_PENALTY=3.3813
PRIMER_LEFT_PENALTY=2.731673
PRIMER_RIGHT_PENALTY=0.649600
PRIMER_LEFT_SEQUENCE=CACGTCATCTCATCAAATTTGATTG
PRIMER_RIGHT_SEQUENCE=GAATTGTTTGGAAATGACAGTGAGT
PRIMER_LEFT=3,25
PRIMER_RIGHT=57,25
PRIMER_LEFT_TM=62.732
PRIMER_RIGHT_TM=60.650
PRIMER_LEFT_GC_PERCENT=36.000
PRIMER_RIGHT_GC_PERCENT=36.000
PRIMER_LEFT_SELF_ANY=12.00
PRIMER_RIGHT_SELF_ANY=4.00
PRIMER_LEFT_SELF_END=10.00
PRIMER_RIGHT_SELF_END=3.00
PRIMER_LEFT_END_STABILITY=6.9000
PRIMER_RIGHT_END_STABILITY=6.4000
PRIMER_PAIR_COMPL_ANY=7.00
PRIMER_PAIR_COMPL_END=1.00
PRIMER_PRODUCT_SIZE=55
=
MARKER_NAME=boundary_test_03
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
PRIMER_PRODUCT_SIZE_RANGE="56-100"
COMMENT=should fail
PRIMER_LEFT_EXPLAIN=considered 4, too many Ns 3, ok 1
PRIMER_RIGHT_EXPLAIN=considered 4, too many Ns 3, ok 1
PRIMER_PAIR_EXPLAIN=considered 1, unacceptable product size 1, ok 0
=
MARKER_NAME=boundary_test_04
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
PRIMER_PRODUCT_SIZE_RANGE="50-54"
COMMENT=should fail
PRIMER_LEFT_EXPLAIN=considered 10, too many Ns 9, ok 1
PRIMER_RIGHT_EXPLAIN=considered 10, too many Ns 9, ok 1
PRIMER_PAIR_EXPLAIN=considered 1, unacceptable product size 1, ok 0
=
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
PRIMER_LEFT_EXPLAIN=considered 5, too many Ns 3, ok 2
PRIMER_RIGHT_EXPLAIN=considered 5, too many Ns 3, ok 2
PRIMER_PAIR_EXPLAIN=considered 4, unacceptable product size 3, ok 1
PRIMER_PAIR_PENALTY=0.3310
PRIMER_LEFT_PENALTY=0.243965
PRIMER_RIGHT_PENALTY=0.087031
PRIMER_LEFT_SEQUENCE=CACGTCATCTCATCAAATTTGATT
PRIMER_RIGHT_SEQUENCE=GAATTGTTTGGAAATGACAGTGAG
PRIMER_LEFT=3,24
PRIMER_RIGHT=57,24
PRIMER_LEFT_TM=60.244
PRIMER_RIGHT_TM=59.913
PRIMER_LEFT_GC_PERCENT=33.333
PRIMER_RIGHT_GC_PERCENT=37.500
PRIMER_LEFT_SELF_ANY=12.00
PRIMER_RIGHT_SELF_ANY=4.00
PRIMER_LEFT_SELF_END=10.00
PRIMER_RIGHT_SELF_END=1.00
PRIMER_LEFT_END_STABILITY=6.9000
PRIMER_RIGHT_END_STABILITY=6.4000
PRIMER_PAIR_COMPL_ANY=7.00
PRIMER_PAIR_COMPL_END=2.00
PRIMER_PRODUCT_SIZE=55
=
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
PRIMER_LEFT_EXPLAIN=considered 5, too many Ns 5, ok 0
PRIMER_RIGHT_EXPLAIN=considered 5, too many Ns 5, ok 0
PRIMER_PAIR_EXPLAIN=considered 0, ok 0
=
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
PRIMER_LEFT_EXPLAIN=considered 1, ok 1
PRIMER_RIGHT_EXPLAIN=considered 1, ok 1
PRIMER_PAIR_EXPLAIN=considered 1, ok 1
PRIMER_PAIR_PENALTY=3.3813
PRIMER_LEFT_PENALTY=2.731673
PRIMER_RIGHT_PENALTY=0.649600
PRIMER_LEFT_SEQUENCE=CACGTCATCTCATCAAATTTGATTG
PRIMER_RIGHT_SEQUENCE=GAATTGTTTGGAAATGACAGTGAGT
PRIMER_LEFT=3,25
PRIMER_RIGHT=57,25
PRIMER_LEFT_TM=62.732
PRIMER_RIGHT_TM=60.650
PRIMER_LEFT_GC_PERCENT=36.000
PRIMER_RIGHT_GC_PERCENT=36.000
PRIMER_LEFT_SELF_ANY=12.00
PRIMER_RIGHT_SELF_ANY=4.00
PRIMER_LEFT_SELF_END=10.00
PRIMER_RIGHT_SELF_END=3.00
PRIMER_LEFT_END_STABILITY=6.9000
PRIMER_RIGHT_END_STABILITY=6.4000
PRIMER_PAIR_COMPL_ANY=7.00
PRIMER_PAIR_COMPL_END=1.00
PRIMER_PRODUCT_SIZE=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
PRIMER_LEFT_EXPLAIN=considered 6, too many Ns 6, ok 0
PRIMER_RIGHT_EXPLAIN=considered 6, too many Ns 5, ok 1
PRIMER_PAIR_EXPLAIN=considered 0, ok 0
=
MARKER_NAME=boundary_test_09
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
PRIMER_PRODUCT_SIZE_RANGE="50-100"
INCLUDED_REGION=3,54
COMMENT=should fail
PRIMER_LEFT_EXPLAIN=considered 5, too many Ns 4, ok 1
PRIMER_RIGHT_EXPLAIN=considered 5, too many Ns 5, ok 0
PRIMER_PAIR_EXPLAIN=considered 0, ok 0
=
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
PRIMER_LEFT_EXPLAIN=considered 5, too many Ns 5, ok 0
PRIMER_RIGHT_EXPLAIN=considered 5, too many Ns 4, ok 1
PRIMER_PAIR_EXPLAIN=considered 0, ok 0
=
MARKER_NAME=boundary_test_11
PRIMER_NUM_NS_ACCEPTED=1
SEQUENCE=NNCACGTCATCTNATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
PRIMER_LEFT_EXPLAIN=considered 5, too many Ns 4, ok 1
PRIMER_RIGHT_EXPLAIN=considered 5, too many Ns 2, ok 3
PRIMER_PAIR_EXPLAIN=considered 3, unacceptable product size 2, ok 1
PRIMER_PAIR_PENALTY=1.8269
PRIMER_LEFT_PENALTY=1.177322
PRIMER_RIGHT_PENALTY=0.649600
PRIMER_LEFT_SEQUENCE=CACGTCATCTNATCAAATTTGATTG
PRIMER_RIGHT_SEQUENCE=GAATTGTTTGGAAATGACAGTGAGT
PRIMER_LEFT=3,25
PRIMER_RIGHT=57,25
PRIMER_LEFT_TM=61.177
PRIMER_RIGHT_TM=60.650
PRIMER_LEFT_GC_PERCENT=33.333
PRIMER_RIGHT_GC_PERCENT=36.000
PRIMER_LEFT_SELF_ANY=12.00
PRIMER_RIGHT_SELF_ANY=4.00
PRIMER_LEFT_SELF_END=9.50
PRIMER_RIGHT_SELF_END=3.00
PRIMER_LEFT_END_STABILITY=6.9000
PRIMER_RIGHT_END_STABILITY=6.4000
PRIMER_PAIR_COMPL_ANY=6.00
PRIMER_PAIR_COMPL_END=1.75
PRIMER_PRODUCT_SIZE=55
=
MARKER_NAME=boundary_test_11
PRIMER_NUM_NS_ACCEPTED=1
SEQUENCE=NNCACGTCATCNNATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
PRIMER_LEFT_EXPLAIN=considered 5, too many Ns 5, ok 0
PRIMER_RIGHT_EXPLAIN=considered 5, too many Ns 2, ok 3
PRIMER_PAIR_EXPLAIN=considered 0, ok 0
=
MARKER_NAME=boundary_test_12
PRIMER_NUM_NS_ACCEPTED=2
SEQUENCE=NNCACGTCATCNNATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
PRIMER_LEFT_EXPLAIN=considered 5, too many Ns 4, ok 1
PRIMER_RIGHT_EXPLAIN=considered 5, ok 5
PRIMER_PAIR_EXPLAIN=considered 5, unacceptable product size 4, ok 1
PRIMER_PAIR_PENALTY=3.8708
PRIMER_LEFT_PENALTY=3.221174
PRIMER_RIGHT_PENALTY=0.649600
PRIMER_LEFT_SEQUENCE=CACGTCATCNNATCAAATTTGATTG
PRIMER_RIGHT_SEQUENCE=GAATTGTTTGGAAATGACAGTGAGT
PRIMER_LEFT=3,25
PRIMER_RIGHT=57,25
PRIMER_LEFT_TM=63.221
PRIMER_RIGHT_TM=60.650
PRIMER_LEFT_GC_PERCENT=34.783
PRIMER_RIGHT_GC_PERCENT=36.000
PRIMER_LEFT_SELF_ANY=12.00
PRIMER_RIGHT_SELF_ANY=4.00
PRIMER_LEFT_SELF_END=11.00
PRIMER_RIGHT_SELF_END=3.00
PRIMER_LEFT_END_STABILITY=6.9000
PRIMER_RIGHT_END_STABILITY=6.4000
PRIMER_PAIR_COMPL_ANY=6.00
PRIMER_PAIR_COMPL_END=1.00
PRIMER_PRODUCT_SIZE=55
=
MARKER_NAME=boundary_test_13
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
SEQUENCE=NNAAAAAAAAAAAAAAAAAAAAAAAAANNNNNACTCACTGTCATTTCCAAACAATTCNN
PRIMER_LEFT_EXPLAIN=considered 5, too many Ns 4, ok 1
PRIMER_RIGHT_EXPLAIN=considered 5, too many Ns 4, ok 1
PRIMER_PAIR_EXPLAIN=considered 1, ok 1
PRIMER_PAIR_PENALTY=4.8116
PRIMER_LEFT_PENALTY=4.161950
PRIMER_RIGHT_PENALTY=0.649600
PRIMER_LEFT_SEQUENCE=AAAAAAAAAAAAAAAAAAAAAAAAA
PRIMER_RIGHT_SEQUENCE=GAATTGTTTGGAAATGACAGTGAGT
PRIMER_LEFT=3,25
PRIMER_RIGHT=57,25
PRIMER_LEFT_TM=55.838
PRIMER_RIGHT_TM=60.650
PRIMER_LEFT_GC_PERCENT=0.000
PRIMER_RIGHT_GC_PERCENT=36.000
PRIMER_LEFT_SELF_ANY=0.00
PRIMER_RIGHT_SELF_ANY=4.00
PRIMER_LEFT_SELF_END=0.00
PRIMER_RIGHT_SELF_END=3.00
PRIMER_LEFT_END_STABILITY=7.6000
PRIMER_RIGHT_END_STABILITY=6.4000
PRIMER_PAIR_COMPL_ANY=4.00
PRIMER_PAIR_COMPL_END=1.00
PRIMER_PRODUCT_SIZE=55
=
MARKER_NAME=boundary_test_14
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=.0001
SEQUENCE=NNAAAAAAAAAAAAAAAAAAAAAAAAANNNNNACTCACTGTCATTTCCAAACAATTCNN
PRIMER_LEFT_EXPLAIN=considered 5, too many Ns 4, GC content failed 1, ok 0
PRIMER_RIGHT_EXPLAIN=considered 5, too many Ns 4, ok 1
PRIMER_PAIR_EXPLAIN=considered 0, ok 0
=
MARKER_NAME=boundary_test_15
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=20
PRIMER_MAX_GC=100
SEQUENCE=NNGGGGGGGGGGGGGGGGGGGGGGGGGNNNNNACTCACTGTCATTTCCAAACAATTCNN
PRIMER_LEFT_EXPLAIN=considered 5, too many Ns 4, ok 1
PRIMER_RIGHT_EXPLAIN=considered 5, too many Ns 4, ok 1
PRIMER_PAIR_EXPLAIN=considered 1, ok 1
PRIMER_PAIR_PENALTY=31.1024
PRIMER_LEFT_PENALTY=30.452761
PRIMER_RIGHT_PENALTY=0.649600
PRIMER_LEFT_SEQUENCE=GGGGGGGGGGGGGGGGGGGGGGGGG
PRIMER_RIGHT_SEQUENCE=GAATTGTTTGGAAATGACAGTGAGT
PRIMER_LEFT=3,25
PRIMER_RIGHT=57,25
PRIMER_LEFT_TM=90.453
PRIMER_RIGHT_TM=60.650
PRIMER_LEFT_GC_PERCENT=100.000
PRIMER_RIGHT_GC_PERCENT=36.000
PRIMER_LEFT_SELF_ANY=0.00
PRIMER_RIGHT_SELF_ANY=4.00
PRIMER_LEFT_SELF_END=0.00
PRIMER_RIGHT_SELF_END=3.00
PRIMER_LEFT_END_STABILITY=12.4000
PRIMER_RIGHT_END_STABILITY=6.4000
PRIMER_PAIR_COMPL_ANY=1.00
PRIMER_PAIR_COMPL_END=0.00
PRIMER_PRODUCT_SIZE=55
=
MARKER_NAME=boundary_test_16
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=.0001
SEQUENCE=NNGGGGGGGGGGGGGGGGGGGGGGGGGNNNNNACTCACTGTCATTTCCAAACAATTCNN
PRIMER_LEFT_EXPLAIN=considered 5, too many Ns 4, GC content failed 1, ok 0
PRIMER_RIGHT_EXPLAIN=considered 5, too many Ns 4, GC content failed 1, ok 0
PRIMER_PAIR_EXPLAIN=considered 0, ok 0
=
MARKER_NAME=boundary_test_17
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
INCLUDED_REGION=3,55
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
PRIMER_LEFT_EXPLAIN=considered 1, ok 1
PRIMER_RIGHT_EXPLAIN=considered 1, ok 1
PRIMER_PAIR_EXPLAIN=considered 1, ok 1
PRIMER_PAIR_PENALTY=3.3813
PRIMER_LEFT_PENALTY=2.731673
PRIMER_RIGHT_PENALTY=0.649600
PRIMER_LEFT_SEQUENCE=CACGTCATCTCATCAAATTTGATTG
PRIMER_RIGHT_SEQUENCE=GAATTGTTTGGAAATGACAGTGAGT
PRIMER_LEFT=3,25
PRIMER_RIGHT=57,25
PRIMER_LEFT_TM=62.732
PRIMER_RIGHT_TM=60.650
PRIMER_LEFT_GC_PERCENT=36.000
PRIMER_RIGHT_GC_PERCENT=36.000
PRIMER_LEFT_SELF_ANY=12.00
PRIMER_RIGHT_SELF_ANY=4.00
PRIMER_LEFT_SELF_END=10.00
PRIMER_RIGHT_SELF_END=3.00
PRIMER_LEFT_END_STABILITY=6.9000
PRIMER_RIGHT_END_STABILITY=6.4000
PRIMER_PAIR_COMPL_ANY=7.00
PRIMER_PAIR_COMPL_END=1.00
PRIMER_PRODUCT_SIZE=55
=
MARKER_NAME=boundary_test_18
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
INCLUDED_REGION=4,55
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
PRIMER_LEFT_EXPLAIN=considered 1, too many Ns 1, ok 0
PRIMER_RIGHT_EXPLAIN=considered 1, too many Ns 1, ok 0
PRIMER_PAIR_EXPLAIN=considered 0, ok 0
=
MARKER_NAME=boundary_test_19
PRIMER_NUM_NS_ACCEPTED=0
PRIMER_MIN_GC=0
PRIMER_MAX_GC=100
INCLUDED_REGION=3,54
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
PRIMER_ERROR=INCLUDED_REGION length < min PRIMER_PRODUCT_SIZE_RANGE
=
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
PRIMER_LEFT_EXPLAIN=considered 1, ok 1
PRIMER_RIGHT_EXPLAIN=considered 1, too many Ns 1, ok 0
PRIMER_PAIR_EXPLAIN=considered 0, ok 0
=
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_LEFT_EXPLAIN=considered 3, too many Ns 2, ok 1
PRIMER_RIGHT_EXPLAIN=considered 3, too many Ns 2, ok 1
PRIMER_PAIR_EXPLAIN=considered 1, ok 1
PRIMER_PAIR_PENALTY=3.3813
PRIMER_LEFT_PENALTY=2.731673
PRIMER_RIGHT_PENALTY=0.649600
PRIMER_LEFT_SEQUENCE=CACGTCATCTCATCAAATTTGATTG
PRIMER_RIGHT_SEQUENCE=GAATTGTTTGGAAATGACAGTGAGT
PRIMER_LEFT=3,25
PRIMER_RIGHT=57,25
PRIMER_LEFT_TM=62.732
PRIMER_RIGHT_TM=60.650
PRIMER_LEFT_GC_PERCENT=36.000
PRIMER_RIGHT_GC_PERCENT=36.000
PRIMER_LEFT_SELF_ANY=12.00
PRIMER_RIGHT_SELF_ANY=4.00
PRIMER_LEFT_SELF_END=10.00
PRIMER_RIGHT_SELF_END=3.00
PRIMER_LEFT_END_STABILITY=6.9000
PRIMER_RIGHT_END_STABILITY=6.4000
PRIMER_PAIR_COMPL_ANY=7.00
PRIMER_PAIR_COMPL_END=1.00
PRIMER_PRODUCT_SIZE=55
=
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
PRIMER_LEFT_EXPLAIN=considered 2, too many Ns 2, ok 0
PRIMER_RIGHT_EXPLAIN=considered 3, too many Ns 2, ok 1
PRIMER_PAIR_EXPLAIN=considered 0, ok 0
=
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
PRIMER_LEFT_EXPLAIN=considered 3, too many Ns 2, ok 1
PRIMER_RIGHT_EXPLAIN=considered 2, too many Ns 2, ok 0
PRIMER_PAIR_EXPLAIN=considered 0, ok 0
=
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
PRIMER_LEFT_EXPLAIN=considered 4, too many Ns 3, ok 1
PRIMER_RIGHT_EXPLAIN=considered 2, too many Ns 2, ok 0
PRIMER_PAIR_EXPLAIN=considered 0, ok 0
=
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
PRIMER_LEFT_EXPLAIN=considered 4, too many Ns 3, ok 1
PRIMER_RIGHT_EXPLAIN=considered 5, too many Ns 4, ok 1
PRIMER_PAIR_EXPLAIN=considered 1, ok 1
PRIMER_PAIR_PENALTY=3.3813
PRIMER_LEFT_PENALTY=2.731673
PRIMER_RIGHT_PENALTY=0.649600
PRIMER_LEFT_SEQUENCE=CACGTCATCTCATCAAATTTGATTG
PRIMER_RIGHT_SEQUENCE=GAATTGTTTGGAAATGACAGTGAGT
PRIMER_LEFT=3,25
PRIMER_RIGHT=57,25
PRIMER_LEFT_TM=62.732
PRIMER_RIGHT_TM=60.650
PRIMER_LEFT_GC_PERCENT=36.000
PRIMER_RIGHT_GC_PERCENT=36.000
PRIMER_LEFT_SELF_ANY=12.00
PRIMER_RIGHT_SELF_ANY=4.00
PRIMER_LEFT_SELF_END=10.00
PRIMER_RIGHT_SELF_END=3.00
PRIMER_LEFT_END_STABILITY=6.9000
PRIMER_RIGHT_END_STABILITY=6.4000
PRIMER_PAIR_COMPL_ANY=7.00
PRIMER_PAIR_COMPL_END=1.00
PRIMER_PRODUCT_SIZE=55
=
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
PRIMER_LEFT_EXPLAIN=considered 3, too many Ns 2, overlap target 1, ok 0
PRIMER_RIGHT_EXPLAIN=considered 5, too many Ns 4, ok 1
PRIMER_PAIR_EXPLAIN=considered 0, ok 0
=
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
PRIMER_LEFT_EXPLAIN=considered 4, too many Ns 3, ok 1
PRIMER_RIGHT_EXPLAIN=considered 5, too many Ns 4, overlap target 1, ok 0
PRIMER_PAIR_EXPLAIN=considered 0, ok 0
=
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
PRIMER_LEFT_EXPLAIN=considered 5, too many Ns 4, ok 1
PRIMER_RIGHT_EXPLAIN=considered 5, too many Ns 4, overlap target 1, ok 0
PRIMER_PAIR_EXPLAIN=considered 0, ok 0
=
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
PRIMER_LEFT_EXPLAIN=considered 4, too many Ns 3, ok 1
PRIMER_RIGHT_EXPLAIN=considered 5, too many Ns 4, ok 1
PRIMER_PAIR_EXPLAIN=considered 1, ok 1
PRIMER_PAIR_PENALTY=3.3813
PRIMER_LEFT_PENALTY=2.731673
PRIMER_RIGHT_PENALTY=0.649600
PRIMER_LEFT_SEQUENCE=CACGTCATCTCATCAAATTTGATTG
PRIMER_RIGHT_SEQUENCE=GAATTGTTTGGAAATGACAGTGAGT
PRIMER_LEFT=3,25
PRIMER_RIGHT=57,25
PRIMER_LEFT_TM=62.732
PRIMER_RIGHT_TM=60.650
PRIMER_LEFT_GC_PERCENT=36.000
PRIMER_RIGHT_GC_PERCENT=36.000
PRIMER_LEFT_SELF_ANY=12.00
PRIMER_RIGHT_SELF_ANY=4.00
PRIMER_LEFT_SELF_END=10.00
PRIMER_RIGHT_SELF_END=3.00
PRIMER_LEFT_END_STABILITY=6.9000
PRIMER_RIGHT_END_STABILITY=6.4000
PRIMER_PAIR_COMPL_ANY=7.00
PRIMER_PAIR_COMPL_END=1.00
PRIMER_PRODUCT_SIZE=55
=
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
PRIMER_LEFT_EXPLAIN=considered 4, too many Ns 3, ok 1
PRIMER_RIGHT_EXPLAIN=considered 5, too many Ns 4, ok 1
PRIMER_PAIR_EXPLAIN=considered 1, ok 1
PRIMER_PAIR_PENALTY=3.3813
PRIMER_LEFT_PENALTY=2.731673
PRIMER_RIGHT_PENALTY=0.649600
PRIMER_LEFT_SEQUENCE=CACGTCATCTCATCAAATTTGATTG
PRIMER_RIGHT_SEQUENCE=GAATTGTTTGGAAATGACAGTGAGT
PRIMER_LEFT=3,25
PRIMER_RIGHT=57,25
PRIMER_LEFT_TM=62.732
PRIMER_RIGHT_TM=60.650
PRIMER_LEFT_GC_PERCENT=36.000
PRIMER_RIGHT_GC_PERCENT=36.000
PRIMER_LEFT_SELF_ANY=12.00
PRIMER_RIGHT_SELF_ANY=4.00
PRIMER_LEFT_SELF_END=10.00
PRIMER_RIGHT_SELF_END=3.00
PRIMER_LEFT_END_STABILITY=6.9000
PRIMER_RIGHT_END_STABILITY=6.4000
PRIMER_PAIR_COMPL_ANY=7.00
PRIMER_PAIR_COMPL_END=1.00
PRIMER_PRODUCT_SIZE=55
=
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
PRIMER_LEFT_EXPLAIN=considered 5, too many Ns 4, ok 1
PRIMER_RIGHT_EXPLAIN=considered 5, too many Ns 4, ok 1
PRIMER_PAIR_EXPLAIN=considered 1, no target 1, ok 0
=
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
PRIMER_LEFT_EXPLAIN=considered 5, too many Ns 4, ok 1
PRIMER_RIGHT_EXPLAIN=considered 5, too many Ns 4, ok 1
PRIMER_PAIR_EXPLAIN=considered 1, ok 1
PRIMER_PAIR_PENALTY=3.3813
PRIMER_LEFT_PENALTY=2.731673
PRIMER_RIGHT_PENALTY=0.649600
PRIMER_LEFT_SEQUENCE=CACGTCATCTCATCAAATTTGATTG
PRIMER_RIGHT_SEQUENCE=GAATTGTTTGGAAATGACAGTGAGT
PRIMER_LEFT=3,25
PRIMER_RIGHT=57,25
PRIMER_LEFT_TM=62.732
PRIMER_RIGHT_TM=60.650
PRIMER_LEFT_GC_PERCENT=36.000
PRIMER_RIGHT_GC_PERCENT=36.000
PRIMER_LEFT_SELF_ANY=12.00
PRIMER_RIGHT_SELF_ANY=4.00
PRIMER_LEFT_SELF_END=10.00
PRIMER_RIGHT_SELF_END=3.00
PRIMER_LEFT_END_STABILITY=6.9000
PRIMER_RIGHT_END_STABILITY=6.4000
PRIMER_PAIR_COMPL_ANY=7.00
PRIMER_PAIR_COMPL_END=1.00
PRIMER_PRODUCT_SIZE=55
=
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
PRIMER_LEFT_EXPLAIN=considered 5, too many Ns 4, overlap excluded region 1, ok 0
PRIMER_RIGHT_EXPLAIN=considered 5, too many Ns 4, ok 1
PRIMER_PAIR_EXPLAIN=considered 0, ok 0
=
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
PRIMER_LEFT_EXPLAIN=considered 5, too many Ns 4, ok 1
PRIMER_RIGHT_EXPLAIN=considered 5, too many Ns 4, overlap excluded region 1, ok 0
PRIMER_PAIR_EXPLAIN=considered 0, ok 0
=
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
PRIMER_LEFT_EXPLAIN=considered 5, too many Ns 4, ok 1
PRIMER_RIGHT_EXPLAIN=considered 5, too many Ns 4, overlap excluded region 1, ok 0
PRIMER_PAIR_EXPLAIN=considered 0, ok 0
=
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
PRIMER_LEFT_EXPLAIN=considered 5, too many Ns 4, ok 1
PRIMER_RIGHT_EXPLAIN=considered 5, too many Ns 4, ok 1
PRIMER_PAIR_EXPLAIN=considered 1, ok 1
PRIMER_PAIR_PENALTY=3.3813
PRIMER_LEFT_PENALTY=2.731673
PRIMER_RIGHT_PENALTY=0.649600
PRIMER_LEFT_SEQUENCE=CACGTCATCTCATCAAATTTGATTG
PRIMER_RIGHT_SEQUENCE=GAATTGTTTGGAAATGACAGTGAGT
PRIMER_LEFT=3,25
PRIMER_RIGHT=57,25
PRIMER_LEFT_TM=62.732
PRIMER_RIGHT_TM=60.650
PRIMER_LEFT_GC_PERCENT=36.000
PRIMER_RIGHT_GC_PERCENT=36.000
PRIMER_LEFT_SELF_ANY=12.00
PRIMER_RIGHT_SELF_ANY=4.00
PRIMER_LEFT_SELF_END=10.00
PRIMER_RIGHT_SELF_END=3.00
PRIMER_LEFT_END_STABILITY=6.9000
PRIMER_RIGHT_END_STABILITY=6.4000
PRIMER_PAIR_COMPL_ANY=7.00
PRIMER_PAIR_COMPL_END=1.00
PRIMER_PRODUCT_SIZE=55
=
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
PRIMER_LEFT_EXPLAIN=considered 5, too many Ns 4, overlap excluded region 1, ok 0
PRIMER_RIGHT_EXPLAIN=considered 5, too many Ns 4, ok 1
PRIMER_PAIR_EXPLAIN=considered 0, ok 0
=
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
PRIMER_LEFT_EXPLAIN=considered 5, too many Ns 4, ok 1
PRIMER_RIGHT_EXPLAIN=considered 5, too many Ns 4, overlap excluded region 1, ok 0
PRIMER_PAIR_EXPLAIN=considered 0, ok 0
=
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
PRIMER_LEFT_EXPLAIN=considered 5, too many Ns 4, ok 1
PRIMER_RIGHT_EXPLAIN=considered 5, too many Ns 4, overlap excluded region 1, ok 0
PRIMER_PAIR_EXPLAIN=considered 0, ok 0
=
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
PRIMER_LEFT_EXPLAIN=considered 5, too many Ns 4, ok 1
PRIMER_RIGHT_EXPLAIN=considered 5, too many Ns 4, ok 1
PRIMER_PAIR_EXPLAIN=considered 1, ok 1
PRIMER_PAIR_PENALTY=3.3813
PRIMER_LEFT_PENALTY=2.731673
PRIMER_RIGHT_PENALTY=0.649600
PRIMER_LEFT_SEQUENCE=CACGTCATCTCATCAAATTTGATTG
PRIMER_RIGHT_SEQUENCE=GAATTGTTTGGAAATGACAGTGAGT
PRIMER_LEFT=3,25
PRIMER_RIGHT=57,25
PRIMER_LEFT_TM=62.732
PRIMER_RIGHT_TM=60.650
PRIMER_LEFT_GC_PERCENT=36.000
PRIMER_RIGHT_GC_PERCENT=36.000
PRIMER_LEFT_SELF_ANY=12.00
PRIMER_RIGHT_SELF_ANY=4.00
PRIMER_LEFT_SELF_END=10.00
PRIMER_RIGHT_SELF_END=3.00
PRIMER_LEFT_END_STABILITY=6.9000
PRIMER_RIGHT_END_STABILITY=6.4000
PRIMER_PAIR_COMPL_ANY=7.00
PRIMER_PAIR_COMPL_END=1.00
PRIMER_PRODUCT_SIZE=55
=
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
PRIMER_LEFT_EXPLAIN=considered 5, too many Ns 4, ok 1
PRIMER_RIGHT_EXPLAIN=considered 5, too many Ns 4, ok 1
PRIMER_PAIR_EXPLAIN=considered 1, ok 1
PRIMER_PAIR_PENALTY=3.3813
PRIMER_LEFT_PENALTY=2.731673
PRIMER_RIGHT_PENALTY=0.649600
PRIMER_LEFT_SEQUENCE=CACGTCATCTCATCAAATTTGATTG
PRIMER_RIGHT_SEQUENCE=GAATTGTTTGGAAATGACAGTGAGT
PRIMER_LEFT=3,25
PRIMER_RIGHT=57,25
PRIMER_LEFT_TM=62.732
PRIMER_RIGHT_TM=60.650
PRIMER_LEFT_GC_PERCENT=36.000
PRIMER_RIGHT_GC_PERCENT=36.000
PRIMER_LEFT_SELF_ANY=12.00
PRIMER_RIGHT_SELF_ANY=4.00
PRIMER_LEFT_SELF_END=10.00
PRIMER_RIGHT_SELF_END=3.00
PRIMER_LEFT_END_STABILITY=6.9000
PRIMER_RIGHT_END_STABILITY=6.4000
PRIMER_PAIR_COMPL_ANY=7.00
PRIMER_PAIR_COMPL_END=1.00
PRIMER_PRODUCT_SIZE=55
=
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
PRIMER_LEFT_EXPLAIN=considered 5, too many Ns 4, overlap excluded region 1, ok 0
PRIMER_RIGHT_EXPLAIN=considered 5, too many Ns 4, ok 1
PRIMER_PAIR_EXPLAIN=considered 0, ok 0
=
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"
PRIMER_LEFT_EXPLAIN=considered 5, too many Ns 4, ok 1
PRIMER_RIGHT_EXPLAIN=considered 5, too many Ns 4, ok 1
PRIMER_PAIR_EXPLAIN=considered 1, ok 1
PRIMER_PAIR_PENALTY=3.3813
PRIMER_LEFT_PENALTY=2.731673
PRIMER_RIGHT_PENALTY=0.649600
PRIMER_LEFT_SEQUENCE=CACGTCATCTCATCAAATTTGATTG
PRIMER_RIGHT_SEQUENCE=GAATTGTTTGGAAATGACAGTGAGT
PRIMER_LEFT=3,25
PRIMER_RIGHT=57,25
PRIMER_LEFT_TM=62.732
PRIMER_RIGHT_TM=60.650
PRIMER_LEFT_GC_PERCENT=36.000
PRIMER_RIGHT_GC_PERCENT=36.000
PRIMER_LEFT_SELF_ANY=12.00
PRIMER_RIGHT_SELF_ANY=4.00
PRIMER_LEFT_SELF_END=10.00
PRIMER_RIGHT_SELF_END=3.00
PRIMER_LEFT_END_STABILITY=6.9000
PRIMER_RIGHT_END_STABILITY=6.4000
PRIMER_PAIR_COMPL_ANY=7.00
PRIMER_PAIR_COMPL_END=1.00
PRIMER_PRODUCT_SIZE=55
=
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)"
PRIMER_LEFT_EXPLAIN=considered 5, too many Ns 4, high end compl 1, ok 0
PRIMER_RIGHT_EXPLAIN=considered 5, too many Ns 4, ok 1
PRIMER_PAIR_EXPLAIN=considered 0, ok 0
=
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
PRIMER_LEFT_EXPLAIN=considered 5, too many Ns 4, ok 1
PRIMER_RIGHT_EXPLAIN=considered 5, too many Ns 4, ok 1
PRIMER_PAIR_EXPLAIN=considered 1, ok 1
PRIMER_PAIR_PENALTY=3.3813
PRIMER_LEFT_PENALTY=2.731673
PRIMER_RIGHT_PENALTY=0.649600
PRIMER_LEFT_SEQUENCE=CACGTCATCTCATCAAATTTGATTG
PRIMER_RIGHT_SEQUENCE=GAATTGTTTGGAAATGACAGTGAGT
PRIMER_LEFT=3,25
PRIMER_RIGHT=57,25
PRIMER_LEFT_TM=62.732
PRIMER_RIGHT_TM=60.650
PRIMER_LEFT_GC_PERCENT=36.000
PRIMER_RIGHT_GC_PERCENT=36.000
PRIMER_LEFT_SELF_ANY=12.00
PRIMER_RIGHT_SELF_ANY=4.00
PRIMER_LEFT_SELF_END=10.00
PRIMER_RIGHT_SELF_END=3.00
PRIMER_LEFT_END_STABILITY=6.9000
PRIMER_RIGHT_END_STABILITY=6.4000
PRIMER_PAIR_COMPL_ANY=7.00
PRIMER_PAIR_COMPL_END=1.00
PRIMER_PRODUCT_SIZE=55
=
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
PRIMER_LEFT_EXPLAIN=considered 5, too many Ns 4, ok 1
PRIMER_RIGHT_EXPLAIN=considered 5, too many Ns 4, ok 1
PRIMER_PAIR_EXPLAIN=considered 1, ok 1
PRIMER_PAIR_PENALTY=3.3813
PRIMER_LEFT_PENALTY=2.731673
PRIMER_RIGHT_PENALTY=0.649600
PRIMER_LEFT_SEQUENCE=CACGTCATCTCATCAAATTTGATTG
PRIMER_RIGHT_SEQUENCE=GAATTGTTTGGAAATGACAGTGAGT
PRIMER_LEFT=3,25
PRIMER_RIGHT=57,25
PRIMER_LEFT_TM=62.732
PRIMER_RIGHT_TM=60.650
PRIMER_LEFT_GC_PERCENT=36.000
PRIMER_RIGHT_GC_PERCENT=36.000
PRIMER_LEFT_SELF_ANY=12.00
PRIMER_RIGHT_SELF_ANY=4.00
PRIMER_LEFT_SELF_END=10.00
PRIMER_RIGHT_SELF_END=3.00
PRIMER_LEFT_END_STABILITY=6.9000
PRIMER_RIGHT_END_STABILITY=6.4000
PRIMER_PAIR_COMPL_ANY=7.00
PRIMER_PAIR_COMPL_END=1.00
PRIMER_PRODUCT_SIZE=55
=
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"
PRIMER_LEFT_EXPLAIN=considered 5, too many Ns 4, high any compl 1, ok 0
PRIMER_RIGHT_EXPLAIN=considered 5, too many Ns 4, ok 1
PRIMER_PAIR_EXPLAIN=considered 0, ok 0
=
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"
PRIMER_LEFT_EXPLAIN=considered 5, too many Ns 4, ok 1
PRIMER_RIGHT_EXPLAIN=considered 5, too many Ns 4, ok 1
PRIMER_PAIR_EXPLAIN=considered 1, ok 1
PRIMER_PAIR_PENALTY=3.3813
PRIMER_LEFT_PENALTY=2.731673
PRIMER_RIGHT_PENALTY=0.649600
PRIMER_LEFT_SEQUENCE=CACGTCATCTCATCAAATTTGATTG
PRIMER_RIGHT_SEQUENCE=GAATTGTTTGGAAATGACAGTGAGT
PRIMER_LEFT=3,25
PRIMER_RIGHT=57,25
PRIMER_LEFT_TM=62.732
PRIMER_RIGHT_TM=60.650
PRIMER_LEFT_GC_PERCENT=36.000
PRIMER_RIGHT_GC_PERCENT=36.000
PRIMER_LEFT_SELF_ANY=12.00
PRIMER_RIGHT_SELF_ANY=4.00
PRIMER_LEFT_SELF_END=10.00
PRIMER_RIGHT_SELF_END=3.00
PRIMER_LEFT_END_STABILITY=6.9000
PRIMER_RIGHT_END_STABILITY=6.4000
PRIMER_PAIR_COMPL_ANY=7.00
PRIMER_PAIR_COMPL_END=1.00
PRIMER_PRODUCT_SIZE=55
=
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)"
PRIMER_LEFT_EXPLAIN=considered 5, too many Ns 4, ok 1
PRIMER_RIGHT_EXPLAIN=considered 5, too many Ns 4, GC clamp failed 1, ok 0
PRIMER_PAIR_EXPLAIN=considered 0, ok 0
=
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"
PRIMER_LEFT_EXPLAIN=considered 5, too many Ns 4, ok 1
PRIMER_RIGHT_EXPLAIN=considered 5, too many Ns 4, ok 1
PRIMER_PAIR_EXPLAIN=considered 1, ok 1
PRIMER_PAIR_PENALTY=5.7521
PRIMER_LEFT_PENALTY=2.731673
PRIMER_RIGHT_PENALTY=3.020452
PRIMER_LEFT_SEQUENCE=CACGTCATCTCATCAAATTTGATTG
PRIMER_RIGHT_SEQUENCE=GAATTGTTTGGAAATGACAGTGAGG
PRIMER_LEFT=3,25
PRIMER_RIGHT=57,25
PRIMER_LEFT_TM=62.732
PRIMER_RIGHT_TM=63.020
PRIMER_LEFT_GC_PERCENT=36.000
PRIMER_RIGHT_GC_PERCENT=40.000
PRIMER_LEFT_SELF_ANY=12.00
PRIMER_RIGHT_SELF_ANY=4.00
PRIMER_LEFT_SELF_END=10.00
PRIMER_RIGHT_SELF_END=0.00
PRIMER_LEFT_END_STABILITY=6.9000
PRIMER_RIGHT_END_STABILITY=8.2000
PRIMER_PAIR_COMPL_ANY=7.00
PRIMER_PAIR_COMPL_END=2.00
PRIMER_PRODUCT_SIZE=55
=
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)"
PRIMER_LEFT_EXPLAIN=considered 5, too many Ns 4, GC clamp failed 1, ok 0
PRIMER_RIGHT_EXPLAIN=considered 5, too many Ns 4, ok 1
PRIMER_PAIR_EXPLAIN=considered 0, ok 0
=
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"
PRIMER_LEFT_EXPLAIN=considered 5, too many Ns 4, ok 1
PRIMER_RIGHT_EXPLAIN=considered 5, too many Ns 4, ok 1
PRIMER_PAIR_EXPLAIN=considered 1, ok 1
PRIMER_PAIR_PENALTY=5.7521
PRIMER_LEFT_PENALTY=2.731673
PRIMER_RIGHT_PENALTY=3.020452
PRIMER_LEFT_SEQUENCE=CACGTCATCTCATCAAATTTGATTG
PRIMER_RIGHT_SEQUENCE=GAATTGTTTGGAAATGACAGTGAGG
PRIMER_LEFT=3,25
PRIMER_RIGHT=57,25
PRIMER_LEFT_TM=62.732
PRIMER_RIGHT_TM=63.020
PRIMER_LEFT_GC_PERCENT=36.000
PRIMER_RIGHT_GC_PERCENT=40.000
PRIMER_LEFT_SELF_ANY=12.00
PRIMER_RIGHT_SELF_ANY=4.00
PRIMER_LEFT_SELF_END=10.00
PRIMER_RIGHT_SELF_END=0.00
PRIMER_LEFT_END_STABILITY=6.9000
PRIMER_RIGHT_END_STABILITY=8.2000
PRIMER_PAIR_COMPL_ANY=7.00
PRIMER_PAIR_COMPL_END=2.00
PRIMER_PRODUCT_SIZE=55
=
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"
PRIMER_LEFT_EXPLAIN=considered 5, too many Ns 4, ok 1
PRIMER_RIGHT_EXPLAIN=considered 5, too many Ns 4, ok 1
PRIMER_PAIR_EXPLAIN=considered 1, ok 1
PRIMER_PAIR_PENALTY=5.7521
PRIMER_LEFT_PENALTY=2.731673
PRIMER_RIGHT_PENALTY=3.020452
PRIMER_LEFT_SEQUENCE=CACGTCATCTCATCAAATTTGATTG
PRIMER_RIGHT_SEQUENCE=GAATTGTTTGGAAATGACAGTGAGG
PRIMER_LEFT=3,25
PRIMER_RIGHT=57,25
PRIMER_LEFT_TM=62.732
PRIMER_RIGHT_TM=63.020
PRIMER_LEFT_GC_PERCENT=36.000
PRIMER_RIGHT_GC_PERCENT=40.000
PRIMER_LEFT_SELF_ANY=12.00
PRIMER_RIGHT_SELF_ANY=4.00
PRIMER_LEFT_SELF_END=10.00
PRIMER_RIGHT_SELF_END=0.00
PRIMER_LEFT_END_STABILITY=6.9000
PRIMER_RIGHT_END_STABILITY=8.2000
PRIMER_PAIR_COMPL_ANY=7.00
PRIMER_PAIR_COMPL_END=2.00
PRIMER_PRODUCT_SIZE=55
=
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)"
PRIMER_LEFT_EXPLAIN=considered 5, too many Ns 4, ok 1
PRIMER_RIGHT_EXPLAIN=considered 5, too many Ns 4, ok 1
PRIMER_PAIR_EXPLAIN=considered 1, tm diff too large 1, ok 0
=
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"
PRIMER_WARNING=Unrecognized base in input sequence
PRIMER_LEFT_EXPLAIN=considered 5, too many Ns 4, ok 1
PRIMER_RIGHT_EXPLAIN=considered 5, too many Ns 4, ok 1
PRIMER_PAIR_EXPLAIN=considered 1, ok 1
PRIMER_PAIR_PENALTY=5.7521
PRIMER_LEFT_PENALTY=2.731673
PRIMER_RIGHT_PENALTY=3.020452
PRIMER_LEFT_SEQUENCE=CACGTCATCTCATCAAATTTGATTG
PRIMER_RIGHT_SEQUENCE=GAATTGTTTGGAAATGACAGTGAGG
PRIMER_LEFT=3,25
PRIMER_RIGHT=57,25
PRIMER_LEFT_TM=62.732
PRIMER_RIGHT_TM=63.020
PRIMER_LEFT_GC_PERCENT=36.000
PRIMER_RIGHT_GC_PERCENT=40.000
PRIMER_LEFT_SELF_ANY=12.00
PRIMER_RIGHT_SELF_ANY=4.00
PRIMER_LEFT_SELF_END=10.00
PRIMER_RIGHT_SELF_END=0.00
PRIMER_LEFT_END_STABILITY=6.9000
PRIMER_RIGHT_END_STABILITY=8.2000
PRIMER_PAIR_COMPL_ANY=7.00
PRIMER_PAIR_COMPL_END=2.00
PRIMER_PRODUCT_SIZE=55
=
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_ERROR=Unrecognized base in input sequence
=
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_LEFT_EXPLAIN=considered 138, long poly-x seq 138, ok 0
PRIMER_RIGHT_EXPLAIN=considered 138, long poly-x seq 138, ok 0
PRIMER_INTERNAL_OLIGO_EXPLAIN=considered 0, ok 0
PRIMER_PAIR_EXPLAIN=considered 0, ok 0
=
PRIMER_SEQUENCE_ID=poly_x_2
PRIMER_INTERNAL_OLIGO_MIN_TM=0
PRIMER_INTERNAL_OLIGO_MAX_TM=100
SEQUENCE=AAAAATTTTTCCCCCGGGGGAAAAACCCCCTTTTTGGGGGAAAAATTTTTCCCCCGGGGGAAAAACCCCCTTTTTGGGGGAAAAACCCCCTTTTTGGGGGAAAAACCCCCTTTTTGGGGGAAAAATTTTTCCCCCGGGGGAAAAACCCCCTTTTTGGGGGAAAAACCCCCTTTTTGGGGG
PRIMER_LEFT_EXPLAIN=considered 131, ok 131
PRIMER_RIGHT_EXPLAIN=considered 131, ok 131
PRIMER_INTERNAL_OLIGO_EXPLAIN=considered 1585, ok 1585
PRIMER_PAIR_EXPLAIN=considered 72, unacceptable product size 52, ok 20
PRIMER_PAIR_PENALTY=15.5472
PRIMER_LEFT_PENALTY=7.773606
PRIMER_RIGHT_PENALTY=7.773606
PRIMER_INTERNAL_OLIGO_PENALTY=1.499588
PRIMER_LEFT_SEQUENCE=CTTTTTGGGGGAAAAATTTTTCCCC
PRIMER_RIGHT_SEQUENCE=GAAAAATTTTTCCCCCAAAAAGGGG
PRIMER_INTERNAL_OLIGO_SEQUENCE=CCCTTTTTGGGGGAAAAAC
PRIMER_LEFT=30,25
PRIMER_RIGHT=131,25
PRIMER_INTERNAL_OLIGO=88,19
PRIMER_LEFT_TM=67.774
PRIMER_RIGHT_TM=67.774
PRIMER_INTERNAL_OLIGO_TM=60.500
PRIMER_LEFT_GC_PERCENT=40.000
PRIMER_RIGHT_GC_PERCENT=40.000
PRIMER_INTERNAL_OLIGO_GC_PERCENT=47.368
PRIMER_LEFT_SELF_ANY=18.00
PRIMER_RIGHT_SELF_ANY=12.00
PRIMER_INTERNAL_OLIGO_SELF_ANY=5.00
PRIMER_LEFT_SELF_END=18.00
PRIMER_RIGHT_SELF_END=3.00
PRIMER_INTERNAL_OLIGO_SELF_END=3.00
PRIMER_LEFT_END_STABILITY=10.9000
PRIMER_RIGHT_END_STABILITY=10.9000
PRIMER_PAIR_COMPL_ANY=22.00
PRIMER_PAIR_COMPL_END=14.00
PRIMER_PRODUCT_SIZE=102
PRIMER_PAIR_PENALTY_1=15.5472
PRIMER_LEFT_1_PENALTY=7.773606
PRIMER_RIGHT_1_PENALTY=7.773606
PRIMER_INTERNAL_OLIGO_1_PENALTY=1.499588
PRIMER_LEFT_1_SEQUENCE=CCCCTTTTTGGGGGAAAAATTTTTC
PRIMER_RIGHT_1_SEQUENCE=GGGAAAAATTTTTCCCCCAAAAAGG
PRIMER_INTERNAL_OLIGO_1_SEQUENCE=CTTTTTGGGGGAAAAACCC
PRIMER_LEFT_1=27,25
PRIMER_RIGHT_1=133,25
PRIMER_INTERNAL_OLIGO_1=90,19
PRIMER_LEFT_1_TM=67.774
PRIMER_RIGHT_1_TM=67.774
PRIMER_INTERNAL_OLIGO_1_TM=60.500
PRIMER_LEFT_1_GC_PERCENT=40.000
PRIMER_RIGHT_1_GC_PERCENT=40.000
PRIMER_INTERNAL_OLIGO_1_GC_PERCENT=47.368
PRIMER_LEFT_1_SELF_ANY=12.00
PRIMER_RIGHT_1_SELF_ANY=16.00
PRIMER_INTERNAL_OLIGO_1_SELF_ANY=5.00
PRIMER_LEFT_1_SELF_END=12.00
PRIMER_RIGHT_1_SELF_END=1.00
PRIMER_INTERNAL_OLIGO_1_SELF_END=1.00
PRIMER_LEFT_1_END_STABILITY=7.3000
PRIMER_RIGHT_1_END_STABILITY=8.5000
PRIMER_PAIR_1_COMPL_ANY=23.00
PRIMER_PAIR_1_COMPL_END=23.00
PRIMER_PRODUCT_SIZE_1=107
PRIMER_PAIR_PENALTY_2=15.5472
PRIMER_LEFT_2_PENALTY=7.773606
PRIMER_RIGHT_2_PENALTY=7.773606
PRIMER_INTERNAL_OLIGO_2_PENALTY=1.499588
PRIMER_LEFT_2_SEQUENCE=CCCCTTTTTGGGGGAAAAATTTTTC
PRIMER_RIGHT_2_SEQUENCE=GGAAAAATTTTTCCCCCAAAAAGGG
PRIMER_INTERNAL_OLIGO_2_SEQUENCE=CCTTTTTGGGGGAAAAACC
PRIMER_LEFT_2=27,25
PRIMER_RIGHT_2=132,25
PRIMER_INTERNAL_OLIGO_2=89,19
PRIMER_LEFT_2_TM=67.774
PRIMER_RIGHT_2_TM=67.774
PRIMER_INTERNAL_OLIGO_2_TM=60.500
PRIMER_LEFT_2_GC_PERCENT=40.000
PRIMER_RIGHT_2_GC_PERCENT=40.000
PRIMER_INTERNAL_OLIGO_2_GC_PERCENT=47.368
PRIMER_LEFT_2_SELF_ANY=12.00
PRIMER_RIGHT_2_SELF_ANY=14.00
PRIMER_INTERNAL_OLIGO_2_SELF_ANY=5.00
PRIMER_LEFT_2_SELF_END=12.00
PRIMER_RIGHT_2_SELF_END=1.00
PRIMER_INTERNAL_OLIGO_2_SELF_END=1.00
PRIMER_LEFT_2_END_STABILITY=7.3000
PRIMER_RIGHT_2_END_STABILITY=9.7000
PRIMER_PAIR_2_COMPL_ANY=24.00
PRIMER_PAIR_2_COMPL_END=24.00
PRIMER_PRODUCT_SIZE_2=106
PRIMER_PAIR_PENALTY_3=15.5472
PRIMER_LEFT_3_PENALTY=7.773606
PRIMER_RIGHT_3_PENALTY=7.773606
PRIMER_INTERNAL_OLIGO_3_PENALTY=1.499588
PRIMER_LEFT_3_SEQUENCE=CCCCTTTTTGGGGGAAAAATTTTTC
PRIMER_RIGHT_3_SEQUENCE=GGGGAAAAATTTTTCCCCCAAAAAG
PRIMER_INTERNAL_OLIGO_3_SEQUENCE=CTTTTTGGGGGAAAAACCC
PRIMER_LEFT_3=27,25
PRIMER_RIGHT_3=134,25
PRIMER_INTERNAL_OLIGO_3=90,19
PRIMER_LEFT_3_TM=67.774
PRIMER_RIGHT_3_TM=67.774
PRIMER_INTERNAL_OLIGO_3_TM=60.500
PRIMER_LEFT_3_GC_PERCENT=40.000
PRIMER_RIGHT_3_GC_PERCENT=40.000
PRIMER_INTERNAL_OLIGO_3_GC_PERCENT=47.368
PRIMER_LEFT_3_SELF_ANY=12.00
PRIMER_RIGHT_3_SELF_ANY=18.00
PRIMER_INTERNAL_OLIGO_3_SELF_ANY=5.00
PRIMER_LEFT_3_SELF_END=12.00
PRIMER_RIGHT_3_SELF_END=3.00
PRIMER_INTERNAL_OLIGO_3_SELF_END=1.00
PRIMER_LEFT_3_END_STABILITY=7.3000
PRIMER_RIGHT_3_END_STABILITY=7.3000
PRIMER_PAIR_3_COMPL_ANY=22.00
PRIMER_PAIR_3_COMPL_END=22.00
PRIMER_PRODUCT_SIZE_3=108
PRIMER_PAIR_PENALTY_4=15.5472
PRIMER_LEFT_4_PENALTY=7.773606
PRIMER_RIGHT_4_PENALTY=7.773606
PRIMER_INTERNAL_OLIGO_4_PENALTY=1.499588
PRIMER_LEFT_4_SEQUENCE=CCTTTTTGGGGGAAAAATTTTTCCC
PRIMER_RIGHT_4_SEQUENCE=GAAAAATTTTTCCCCCAAAAAGGGG
PRIMER_INTERNAL_OLIGO_4_SEQUENCE=CCCTTTTTGGGGGAAAAAC
PRIMER_LEFT_4=29,25
PRIMER_RIGHT_4=131,25
PRIMER_INTERNAL_OLIGO_4=88,19
PRIMER_LEFT_4_TM=67.774
PRIMER_RIGHT_4_TM=67.774
PRIMER_INTERNAL_OLIGO_4_TM=60.500
PRIMER_LEFT_4_GC_PERCENT=40.000
PRIMER_RIGHT_4_GC_PERCENT=40.000
PRIMER_INTERNAL_OLIGO_4_GC_PERCENT=47.368
PRIMER_LEFT_4_SELF_ANY=16.00
PRIMER_RIGHT_4_SELF_ANY=12.00
PRIMER_INTERNAL_OLIGO_4_SELF_ANY=5.00
PRIMER_LEFT_4_SELF_END=16.00
PRIMER_RIGHT_4_SELF_END=3.00
PRIMER_INTERNAL_OLIGO_4_SELF_END=3.00
PRIMER_LEFT_4_END_STABILITY=9.7000
PRIMER_RIGHT_4_END_STABILITY=10.9000
PRIMER_PAIR_4_COMPL_ANY=23.00
PRIMER_PAIR_4_COMPL_END=19.00
PRIMER_PRODUCT_SIZE_4=103
=
PRIMER_SEQUENCE_ID=poly_x_3
SEQUENCE=AAAAAACCCCCCTTTTTTGGGGGGAAAAAACCCCCCTTTTTTGGGGGGAAAAAACCCCCCTTTTTTGGGGGGAAAAAAACCCCCCTTTTTTGGGGGGAAAAAACCCCCCCTTTTTTGGGGGGAAAAAACCCCCCTTTTTTGGGGGGAAAAAAACCCCCCTTTTTTGGGGGGAAAAAACCCCCCTTTTTTTGGGGGGGGGGGGGG
PRIMER_MAX_POLY_X=6
PRIMER_INTERNAL_OLIGO_MAX_POLY_X=5
PRIMER_LEFT_EXPLAIN=considered 155, long poly-x seq 57, ok 98
PRIMER_RIGHT_EXPLAIN=considered 155, long poly-x seq 72, ok 83
PRIMER_INTERNAL_OLIGO_EXPLAIN=considered 187, long poly-x seq 187, ok 0
PRIMER_PAIR_EXPLAIN=considered 0, ok 0
=
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).
PRIMER_LEFT_EXPLAIN=considered 5, too many Ns 4, ok 1
PRIMER_RIGHT_EXPLAIN=considered 5, too many Ns 4, ok 1
PRIMER_PAIR_EXPLAIN=considered 1, ok 1
PRIMER_PAIR_PENALTY=3.3813
PRIMER_LEFT_PENALTY=2.731673
PRIMER_RIGHT_PENALTY=0.649600
PRIMER_LEFT_SEQUENCE=CACGTCATCTCATCAAATTTGATTG
PRIMER_RIGHT_SEQUENCE=GAATTGTTTGGAAATGACAGTGAGT
PRIMER_LEFT=3,25
PRIMER_RIGHT=57,25
PRIMER_LEFT_TM=62.732
PRIMER_RIGHT_TM=60.650
PRIMER_LEFT_GC_PERCENT=36.000
PRIMER_RIGHT_GC_PERCENT=36.000
PRIMER_LEFT_SELF_ANY=12.00
PRIMER_RIGHT_SELF_ANY=4.00
PRIMER_LEFT_SELF_END=10.00
PRIMER_RIGHT_SELF_END=3.00
PRIMER_LEFT_END_STABILITY=6.9000
PRIMER_RIGHT_END_STABILITY=6.4000
PRIMER_PAIR_COMPL_ANY=7.00
PRIMER_PAIR_COMPL_END=1.00
PRIMER_PRODUCT_SIZE=55
=
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).
PRIMER_LEFT_EXPLAIN=considered 5, too many Ns 4, overlap excluded region 1, ok 0
PRIMER_RIGHT_EXPLAIN=considered 5, too many Ns 4, ok 1
PRIMER_PAIR_EXPLAIN=considered 0, ok 0
=
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).
PRIMER_ERROR=Negative EXCLUDED_REGION length
=
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
PRIMER_WARNING=EXCLUDED_REGION outside of INCLUDED_REGION
PRIMER_LEFT_EXPLAIN=considered 1, ok 1
PRIMER_RIGHT_EXPLAIN=considered 1, ok 1
PRIMER_PAIR_EXPLAIN=considered 1, ok 1
PRIMER_PAIR_PENALTY=3.3813
PRIMER_LEFT_PENALTY=2.731673
PRIMER_RIGHT_PENALTY=0.649600
PRIMER_LEFT_SEQUENCE=CACGTCATCTCATCAAATTTGATTG
PRIMER_RIGHT_SEQUENCE=GAATTGTTTGGAAATGACAGTGAGT
PRIMER_LEFT=3,25
PRIMER_RIGHT=57,25
PRIMER_LEFT_TM=62.732
PRIMER_RIGHT_TM=60.650
PRIMER_LEFT_GC_PERCENT=36.000
PRIMER_RIGHT_GC_PERCENT=36.000
PRIMER_LEFT_SELF_ANY=12.00
PRIMER_RIGHT_SELF_ANY=4.00
PRIMER_LEFT_SELF_END=10.00
PRIMER_RIGHT_SELF_END=3.00
PRIMER_LEFT_END_STABILITY=6.9000
PRIMER_RIGHT_END_STABILITY=6.4000
PRIMER_PAIR_COMPL_ANY=7.00
PRIMER_PAIR_COMPL_END=1.00
PRIMER_PRODUCT_SIZE=55
=
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
PRIMER_LEFT_EXPLAIN=considered 1, overlap excluded region 1, ok 0
PRIMER_RIGHT_EXPLAIN=considered 1, ok 1
PRIMER_PAIR_EXPLAIN=considered 0, ok 0
=
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
PRIMER_ERROR=EXCLUDED_REGION beyond end 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
PRIMER_WARNING=EXCLUDED_REGION outside of INCLUDED_REGION
PRIMER_LEFT_EXPLAIN=considered 1, ok 1
PRIMER_RIGHT_EXPLAIN=considered 1, ok 1
PRIMER_PAIR_EXPLAIN=considered 1, ok 1
PRIMER_PAIR_PENALTY=3.3813
PRIMER_LEFT_PENALTY=2.731673
PRIMER_RIGHT_PENALTY=0.649600
PRIMER_LEFT_SEQUENCE=CACGTCATCTCATCAAATTTGATTG
PRIMER_RIGHT_SEQUENCE=GAATTGTTTGGAAATGACAGTGAGT
PRIMER_LEFT=3,25
PRIMER_RIGHT=57,25
PRIMER_LEFT_TM=62.732
PRIMER_RIGHT_TM=60.650
PRIMER_LEFT_GC_PERCENT=36.000
PRIMER_RIGHT_GC_PERCENT=36.000
PRIMER_LEFT_SELF_ANY=12.00
PRIMER_RIGHT_SELF_ANY=4.00
PRIMER_LEFT_SELF_END=10.00
PRIMER_RIGHT_SELF_END=3.00
PRIMER_LEFT_END_STABILITY=6.9000
PRIMER_RIGHT_END_STABILITY=6.4000
PRIMER_PAIR_COMPL_ANY=7.00
PRIMER_PAIR_COMPL_END=1.00
PRIMER_PRODUCT_SIZE=55
=
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
PRIMER_LEFT_EXPLAIN=considered 1, ok 1
PRIMER_RIGHT_EXPLAIN=considered 1, overlap excluded region 1, ok 0
PRIMER_PAIR_EXPLAIN=considered 0, ok 0
=
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
PRIMER_WARNING=EXCLUDED_REGION outside of INCLUDED_REGION
PRIMER_LEFT_EXPLAIN=considered 6, too many Ns 5, ok 1
PRIMER_RIGHT_EXPLAIN=considered 6, too many Ns 5, overlap excluded region 1, ok 0
PRIMER_PAIR_EXPLAIN=considered 0, ok 0
=
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).
PRIMER_LEFT_EXPLAIN=considered 3, too many Ns 2, ok 1
PRIMER_RIGHT_EXPLAIN=considered 5, too many Ns 4, ok 1
PRIMER_PAIR_EXPLAIN=considered 1, ok 1
PRIMER_PAIR_PENALTY=3.3813
PRIMER_LEFT_PENALTY=2.731673
PRIMER_RIGHT_PENALTY=0.649600
PRIMER_LEFT_SEQUENCE=CACGTCATCTCATCAAATTTGATTG
PRIMER_RIGHT_SEQUENCE=GAATTGTTTGGAAATGACAGTGAGT
PRIMER_LEFT=3,25
PRIMER_RIGHT=57,25
PRIMER_LEFT_TM=62.732
PRIMER_RIGHT_TM=60.650
PRIMER_LEFT_GC_PERCENT=36.000
PRIMER_RIGHT_GC_PERCENT=36.000
PRIMER_LEFT_SELF_ANY=12.00
PRIMER_RIGHT_SELF_ANY=4.00
PRIMER_LEFT_SELF_END=10.00
PRIMER_RIGHT_SELF_END=3.00
PRIMER_LEFT_END_STABILITY=6.9000
PRIMER_RIGHT_END_STABILITY=6.4000
PRIMER_PAIR_COMPL_ANY=7.00
PRIMER_PAIR_COMPL_END=1.00
PRIMER_PRODUCT_SIZE=55
=
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).
PRIMER_LEFT_EXPLAIN=considered 2, too many Ns 2, ok 0
PRIMER_RIGHT_EXPLAIN=considered 5, too many Ns 4, ok 1
PRIMER_PAIR_EXPLAIN=considered 0, ok 0
=
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).
PRIMER_ERROR=Negative TARGET length
=
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
PRIMER_WARNING=TARGET outside of INCLUDED_REGION
PRIMER_LEFT_EXPLAIN=considered 1, ok 1
PRIMER_RIGHT_EXPLAIN=considered 1, ok 1
PRIMER_PAIR_EXPLAIN=considered 1, no target 1, ok 0
=
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
PRIMER_LEFT_EXPLAIN=considered 1, overlap target 1, ok 0
PRIMER_RIGHT_EXPLAIN=considered 1, ok 1
PRIMER_PAIR_EXPLAIN=considered 0, ok 0
=
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
PRIMER_ERROR=TARGET beyond end 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
PRIMER_WARNING=TARGET outside of INCLUDED_REGION
PRIMER_LEFT_EXPLAIN=considered 1, ok 1
PRIMER_RIGHT_EXPLAIN=considered 1, ok 1
PRIMER_PAIR_EXPLAIN=considered 1, no target 1, ok 0
=
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
PRIMER_LEFT_EXPLAIN=considered 1, ok 1
PRIMER_RIGHT_EXPLAIN=considered 0, ok 0
PRIMER_PAIR_EXPLAIN=considered 0, ok 0
=
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
PRIMER_WARNING=TARGET outside of INCLUDED_REGION
PRIMER_LEFT_EXPLAIN=considered 6, too many Ns 5, ok 1
PRIMER_RIGHT_EXPLAIN=considered 6, too many Ns 5, overlap target 1, ok 0
PRIMER_PAIR_EXPLAIN=considered 0, ok 0
=
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)
PRIMER_LEFT_EXPLAIN=considered 1, ok 1
PRIMER_RIGHT_EXPLAIN=considered 5, too many Ns 4, ok 1
PRIMER_PAIR_EXPLAIN=considered 1, ok 1
PRIMER_PAIR_PENALTY=3.3813
PRIMER_LEFT_PENALTY=2.731673
PRIMER_RIGHT_PENALTY=0.649600
PRIMER_LEFT_SEQUENCE=CACGTCATCTCATCAAATTTGATTG
PRIMER_RIGHT_SEQUENCE=GAATTGTTTGGAAATGACAGTGAGT
PRIMER_LEFT=3,25
PRIMER_RIGHT=57,25
PRIMER_LEFT_TM=62.732
PRIMER_RIGHT_TM=60.650
PRIMER_LEFT_GC_PERCENT=36.000
PRIMER_RIGHT_GC_PERCENT=36.000
PRIMER_LEFT_SELF_ANY=12.00
PRIMER_RIGHT_SELF_ANY=4.00
PRIMER_LEFT_SELF_END=10.00
PRIMER_RIGHT_SELF_END=3.00
PRIMER_LEFT_END_STABILITY=6.9000
PRIMER_RIGHT_END_STABILITY=6.4000
PRIMER_PAIR_COMPL_ANY=7.00
PRIMER_PAIR_COMPL_END=1.00
PRIMER_PRODUCT_SIZE=55
=
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)
PRIMER_LEFT_EXPLAIN=considered 1, ok 1
PRIMER_RIGHT_EXPLAIN=considered 1, ok 1
PRIMER_PAIR_EXPLAIN=considered 1, ok 1
PRIMER_PAIR_PENALTY=3.3813
PRIMER_LEFT_PENALTY=2.731673
PRIMER_RIGHT_PENALTY=0.649600
PRIMER_LEFT_SEQUENCE=CACGTCATCTCATCAAATTTGATTG
PRIMER_RIGHT_SEQUENCE=GAATTGTTTGGAAATGACAGTGAGT
PRIMER_LEFT=3,25
PRIMER_RIGHT=57,25
PRIMER_LEFT_TM=62.732
PRIMER_RIGHT_TM=60.650
PRIMER_LEFT_GC_PERCENT=36.000
PRIMER_RIGHT_GC_PERCENT=36.000
PRIMER_LEFT_SELF_ANY=12.00
PRIMER_RIGHT_SELF_ANY=4.00
PRIMER_LEFT_SELF_END=10.00
PRIMER_RIGHT_SELF_END=3.00
PRIMER_LEFT_END_STABILITY=6.9000
PRIMER_RIGHT_END_STABILITY=6.4000
PRIMER_PAIR_COMPL_ANY=7.00
PRIMER_PAIR_COMPL_END=1.00
PRIMER_PRODUCT_SIZE=55
=
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
PRIMER_LEFT_EXPLAIN=considered 1, ok 1
PRIMER_RIGHT_EXPLAIN=considered 6, too many Ns 5, ok 1
PRIMER_PAIR_EXPLAIN=considered 1, ok 1
PRIMER_PAIR_PENALTY=3.3813
PRIMER_LEFT_PENALTY=2.731673
PRIMER_RIGHT_PENALTY=0.649600
PRIMER_LEFT_SEQUENCE=CACGTCATCTCATCAAATTTGATTG
PRIMER_RIGHT_SEQUENCE=GAATTGTTTGGAAATGACAGTGAGT
PRIMER_LEFT=3,25
PRIMER_RIGHT=57,25
PRIMER_LEFT_TM=62.732
PRIMER_RIGHT_TM=60.650
PRIMER_LEFT_GC_PERCENT=36.000
PRIMER_RIGHT_GC_PERCENT=36.000
PRIMER_LEFT_SELF_ANY=12.00
PRIMER_RIGHT_SELF_ANY=4.00
PRIMER_LEFT_SELF_END=10.00
PRIMER_RIGHT_SELF_END=3.00
PRIMER_LEFT_END_STABILITY=6.9000
PRIMER_RIGHT_END_STABILITY=6.4000
PRIMER_PAIR_COMPL_ANY=7.00
PRIMER_PAIR_COMPL_END=1.00
PRIMER_PRODUCT_SIZE=55
=
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
PRIMER_LEFT_EXPLAIN=considered 5, too many Ns 4, ok 1
PRIMER_RIGHT_EXPLAIN=considered 1, ok 1
PRIMER_PAIR_EXPLAIN=considered 1, ok 1
PRIMER_PAIR_PENALTY=3.3813
PRIMER_LEFT_PENALTY=2.731673
PRIMER_RIGHT_PENALTY=0.649600
PRIMER_LEFT_SEQUENCE=CACGTCATCTCATCAAATTTGATTG
PRIMER_RIGHT_SEQUENCE=GAATTGTTTGGAAATGACAGTGAGT
PRIMER_LEFT=3,25
PRIMER_RIGHT=57,25
PRIMER_LEFT_TM=62.732
PRIMER_RIGHT_TM=60.650
PRIMER_LEFT_GC_PERCENT=36.000
PRIMER_RIGHT_GC_PERCENT=36.000
PRIMER_LEFT_SELF_ANY=12.00
PRIMER_RIGHT_SELF_ANY=4.00
PRIMER_LEFT_SELF_END=10.00
PRIMER_RIGHT_SELF_END=3.00
PRIMER_LEFT_END_STABILITY=6.9000
PRIMER_RIGHT_END_STABILITY=6.4000
PRIMER_PAIR_COMPL_ANY=7.00
PRIMER_PAIR_COMPL_END=1.00
PRIMER_PRODUCT_SIZE=55
=
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
PRIMER_LEFT_EXPLAIN=considered 6, too many Ns 5, ok 1
PRIMER_RIGHT_EXPLAIN=considered 1, ok 1
PRIMER_PAIR_EXPLAIN=considered 1, ok 1
PRIMER_PAIR_PENALTY=3.3813
PRIMER_LEFT_PENALTY=2.731673
PRIMER_RIGHT_PENALTY=0.649600
PRIMER_LEFT_SEQUENCE=CACGTCATCTCATCAAATTTGATTG
PRIMER_RIGHT_SEQUENCE=GAATTGTTTGGAAATGACAGTGAGT
PRIMER_LEFT=3,25
PRIMER_RIGHT=57,25
PRIMER_LEFT_TM=62.732
PRIMER_RIGHT_TM=60.650
PRIMER_LEFT_GC_PERCENT=36.000
PRIMER_RIGHT_GC_PERCENT=36.000
PRIMER_LEFT_SELF_ANY=12.00
PRIMER_RIGHT_SELF_ANY=4.00
PRIMER_LEFT_SELF_END=10.00
PRIMER_RIGHT_SELF_END=3.00
PRIMER_LEFT_END_STABILITY=6.9000
PRIMER_RIGHT_END_STABILITY=6.4000
PRIMER_PAIR_COMPL_ANY=7.00
PRIMER_PAIR_COMPL_END=1.00
PRIMER_PRODUCT_SIZE=55
=
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
PRIMER_LEFT_EXPLAIN=considered 10, too many Ns 9, ok 1
PRIMER_RIGHT_EXPLAIN=considered 10, too many Ns 9, ok 1
PRIMER_PAIR_EXPLAIN=considered 1, ok 1
PRIMER_PAIR_PENALTY=3.3813
PRIMER_LEFT_PENALTY=2.731673
PRIMER_RIGHT_PENALTY=0.649600
PRIMER_LEFT_SEQUENCE=CACGTCATCTCATCAAATTTGATTG
PRIMER_RIGHT_SEQUENCE=GAATTGTTTGGAAATGACAGTGAGT
PRIMER_LEFT=3,25
PRIMER_RIGHT=57,25
PRIMER_LEFT_TM=62.732
PRIMER_RIGHT_TM=60.650
PRIMER_LEFT_GC_PERCENT=36.000
PRIMER_RIGHT_GC_PERCENT=36.000
PRIMER_LEFT_SELF_ANY=12.00
PRIMER_RIGHT_SELF_ANY=4.00
PRIMER_LEFT_SELF_END=10.00
PRIMER_RIGHT_SELF_END=3.00
PRIMER_LEFT_END_STABILITY=6.9000
PRIMER_RIGHT_END_STABILITY=6.4000
PRIMER_PAIR_COMPL_ANY=7.00
PRIMER_PAIR_COMPL_END=1.00
PRIMER_PRODUCT_SIZE=55
=
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)
PRIMER_LEFT_EXPLAIN=considered 10, too many Ns 9, ok 1
PRIMER_RIGHT_EXPLAIN=considered 10, too many Ns 9, ok 1
PRIMER_PAIR_EXPLAIN=considered 1, no target 1, ok 0
=
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
PRIMER_LEFT_EXPLAIN=considered 8, too many Ns 7, ok 1
PRIMER_RIGHT_EXPLAIN=considered 10, too many Ns 9, ok 1
PRIMER_PAIR_EXPLAIN=considered 1, ok 1
PRIMER_PAIR_PENALTY=3.3813
PRIMER_LEFT_PENALTY=2.731673
PRIMER_RIGHT_PENALTY=0.649600
PRIMER_LEFT_SEQUENCE=CACGTCATCTCATCAAATTTGATTG
PRIMER_RIGHT_SEQUENCE=GAATTGTTTGGAAATGACAGTGAGT
PRIMER_LEFT=3,25
PRIMER_RIGHT=57,25
PRIMER_LEFT_TM=62.732
PRIMER_RIGHT_TM=60.650
PRIMER_LEFT_GC_PERCENT=36.000
PRIMER_RIGHT_GC_PERCENT=36.000
PRIMER_LEFT_SELF_ANY=12.00
PRIMER_RIGHT_SELF_ANY=4.00
PRIMER_LEFT_SELF_END=10.00
PRIMER_RIGHT_SELF_END=3.00
PRIMER_LEFT_END_STABILITY=6.9000
PRIMER_RIGHT_END_STABILITY=6.4000
PRIMER_PAIR_COMPL_ANY=7.00
PRIMER_PAIR_COMPL_END=1.00
PRIMER_PRODUCT_SIZE=55
=
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
PRIMER_LEFT_EXPLAIN=considered 10, too many Ns 9, ok 1
PRIMER_RIGHT_EXPLAIN=considered 3, too many Ns 2, ok 1
PRIMER_PAIR_EXPLAIN=considered 1, ok 1
PRIMER_PAIR_PENALTY=3.3813
PRIMER_LEFT_PENALTY=2.731673
PRIMER_RIGHT_PENALTY=0.649600
PRIMER_LEFT_SEQUENCE=CACGTCATCTCATCAAATTTGATTG
PRIMER_RIGHT_SEQUENCE=GAATTGTTTGGAAATGACAGTGAGT
PRIMER_LEFT=3,25
PRIMER_RIGHT=57,25
PRIMER_LEFT_TM=62.732
PRIMER_RIGHT_TM=60.650
PRIMER_LEFT_GC_PERCENT=36.000
PRIMER_RIGHT_GC_PERCENT=36.000
PRIMER_LEFT_SELF_ANY=12.00
PRIMER_RIGHT_SELF_ANY=4.00
PRIMER_LEFT_SELF_END=10.00
PRIMER_RIGHT_SELF_END=3.00
PRIMER_LEFT_END_STABILITY=6.9000
PRIMER_RIGHT_END_STABILITY=6.4000
PRIMER_PAIR_COMPL_ANY=7.00
PRIMER_PAIR_COMPL_END=1.00
PRIMER_PRODUCT_SIZE=55
=
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)
PRIMER_LEFT_EXPLAIN=considered 5, too many Ns 4, ok 1
PRIMER_RIGHT_EXPLAIN=considered 5, too many Ns 4, ok 1
PRIMER_PAIR_EXPLAIN=considered 1, ok 1
PRIMER_PAIR_PENALTY=4.2026
PRIMER_LEFT_PENALTY=2.838677
PRIMER_RIGHT_PENALTY=1.363932
PRIMER_LEFT_SEQUENCE=CACGTCATCTATATATATATCATCAAATTTGATTG
PRIMER_RIGHT_SEQUENCE=GAATTGTTTGGAAATGACAGTATATATATATGAGT
PRIMER_LEFT=3,35
PRIMER_RIGHT=77,35
PRIMER_LEFT_TM=62.839
PRIMER_RIGHT_TM=61.364
PRIMER_LEFT_GC_PERCENT=25.714
PRIMER_RIGHT_GC_PERCENT=25.714
PRIMER_LEFT_SELF_ANY=12.00
PRIMER_RIGHT_SELF_ANY=10.00
PRIMER_LEFT_SELF_END=10.00
PRIMER_RIGHT_SELF_END=8.00
PRIMER_LEFT_END_STABILITY=6.9000
PRIMER_RIGHT_END_STABILITY=6.4000
PRIMER_PAIR_COMPL_ANY=13.00
PRIMER_PAIR_COMPL_END=8.00
PRIMER_PRODUCT_SIZE=75
=
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
PRIMER_WARNING=TARGET outside of INCLUDED_REGION
PRIMER_LEFT_EXPLAIN=considered 1, ok 1
PRIMER_RIGHT_EXPLAIN=considered 1, ok 1
PRIMER_PAIR_EXPLAIN=considered 1, ok 1
PRIMER_PAIR_PENALTY=3.3813
PRIMER_LEFT_PENALTY=2.731673
PRIMER_RIGHT_PENALTY=0.649600
PRIMER_LEFT_SEQUENCE=CACGTCATCTCATCAAATTTGATTG
PRIMER_RIGHT_SEQUENCE=GAATTGTTTGGAAATGACAGTGAGT
PRIMER_LEFT=3,25
PRIMER_RIGHT=57,25
PRIMER_LEFT_TM=62.732
PRIMER_RIGHT_TM=60.650
PRIMER_LEFT_GC_PERCENT=36.000
PRIMER_RIGHT_GC_PERCENT=36.000
PRIMER_LEFT_SELF_ANY=12.00
PRIMER_RIGHT_SELF_ANY=4.00
PRIMER_LEFT_SELF_END=10.00
PRIMER_RIGHT_SELF_END=3.00
PRIMER_LEFT_END_STABILITY=6.9000
PRIMER_RIGHT_END_STABILITY=6.4000
PRIMER_PAIR_COMPL_ANY=7.00
PRIMER_PAIR_COMPL_END=1.00
PRIMER_PRODUCT_SIZE=55
=
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
PRIMER_LEFT_EXPLAIN=considered 3, too many Ns 2, ok 1
PRIMER_RIGHT_EXPLAIN=considered 3, too many Ns 2, ok 1
PRIMER_PAIR_EXPLAIN=considered 3, unacceptable product size 2, ok 1
PRIMER_PAIR_PENALTY=3.3813
PRIMER_LEFT_PENALTY=2.731673
PRIMER_RIGHT_PENALTY=0.649600
PRIMER_LEFT_SEQUENCE=CACGTCATCTCATCAAATTTGATTG
PRIMER_RIGHT_SEQUENCE=GAATTGTTTGGAAATGACAGTGAGT
PRIMER_LEFT=3,25
PRIMER_RIGHT=57,25
PRIMER_LEFT_TM=62.732
PRIMER_RIGHT_TM=60.650
PRIMER_LEFT_GC_PERCENT=36.000
PRIMER_RIGHT_GC_PERCENT=36.000
PRIMER_LEFT_SELF_ANY=12.00
PRIMER_RIGHT_SELF_ANY=4.00
PRIMER_LEFT_SELF_END=10.00
PRIMER_RIGHT_SELF_END=3.00
PRIMER_LEFT_END_STABILITY=6.9000
PRIMER_RIGHT_END_STABILITY=6.4000
PRIMER_PAIR_COMPL_ANY=7.00
PRIMER_PAIR_COMPL_END=1.00
PRIMER_PRODUCT_SIZE=55
=
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)
PRIMER_LEFT_EXPLAIN=considered 3, too many Ns 2, ok 1
PRIMER_RIGHT_EXPLAIN=considered 3, too many Ns 2, ok 1
PRIMER_PAIR_EXPLAIN=considered 2, unacceptable product size 2, ok 0
=
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
PRIMER_LEFT_EXPLAIN=considered 3, too many Ns 2, ok 1
PRIMER_RIGHT_EXPLAIN=considered 3, too many Ns 2, ok 1
PRIMER_PAIR_EXPLAIN=considered 2, ok 2
PRIMER_PAIR_PENALTY=3.3813
PRIMER_LEFT_PENALTY=2.731673
PRIMER_RIGHT_PENALTY=0.649600
PRIMER_LEFT_SEQUENCE=CACGTCATCTCATCAAATTTGATTG
PRIMER_RIGHT_SEQUENCE=GAATTGTTTGGAAATGACAGTGAGT
PRIMER_LEFT=3,25
PRIMER_RIGHT=57,25
PRIMER_LEFT_TM=62.732
PRIMER_RIGHT_TM=60.650
PRIMER_LEFT_GC_PERCENT=36.000
PRIMER_RIGHT_GC_PERCENT=36.000
PRIMER_LEFT_SELF_ANY=12.00
PRIMER_RIGHT_SELF_ANY=4.00
PRIMER_LEFT_SELF_END=10.00
PRIMER_RIGHT_SELF_END=3.00
PRIMER_LEFT_END_STABILITY=6.9000
PRIMER_RIGHT_END_STABILITY=6.4000
PRIMER_PAIR_COMPL_ANY=7.00
PRIMER_PAIR_COMPL_END=1.00
PRIMER_PRODUCT_SIZE=55
=
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
PRIMER_LEFT_EXPLAIN=considered 2, too many Ns 1, ok 1
PRIMER_RIGHT_EXPLAIN=considered 2, too many Ns 1, ok 1
PRIMER_PAIR_EXPLAIN=considered 2, unacceptable product size 1, ok 1
PRIMER_PAIR_PENALTY=3.3813
PRIMER_LEFT_PENALTY=2.731673
PRIMER_RIGHT_PENALTY=0.649600
PRIMER_LEFT_SEQUENCE=CACGTCATCTCATCAAATTTGATTG
PRIMER_RIGHT_SEQUENCE=GAATTGTTTGGAAATGACAGTGAGT
PRIMER_LEFT=3,25
PRIMER_RIGHT=57,25
PRIMER_LEFT_TM=62.732
PRIMER_RIGHT_TM=60.650
PRIMER_LEFT_GC_PERCENT=36.000
PRIMER_RIGHT_GC_PERCENT=36.000
PRIMER_LEFT_SELF_ANY=12.00
PRIMER_RIGHT_SELF_ANY=4.00
PRIMER_LEFT_SELF_END=10.00
PRIMER_RIGHT_SELF_END=3.00
PRIMER_LEFT_END_STABILITY=6.9000
PRIMER_RIGHT_END_STABILITY=6.4000
PRIMER_PAIR_COMPL_ANY=7.00
PRIMER_PAIR_COMPL_END=1.00
PRIMER_PRODUCT_SIZE=55
=
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
PRIMER_LEFT_EXPLAIN=considered 2, too many Ns 1, ok 1
PRIMER_RIGHT_EXPLAIN=considered 2, too many Ns 1, ok 1
PRIMER_PAIR_EXPLAIN=considered 2, unacceptable product size 1, ok 1
PRIMER_PAIR_PENALTY=3.3813
PRIMER_LEFT_PENALTY=2.731673
PRIMER_RIGHT_PENALTY=0.649600
PRIMER_LEFT_SEQUENCE=CACGTCATCTCATCAAATTTGATTG
PRIMER_RIGHT_SEQUENCE=GAATTGTTTGGAAATGACAGTGAGT
PRIMER_LEFT=3,25
PRIMER_RIGHT=57,25
PRIMER_LEFT_TM=62.732
PRIMER_RIGHT_TM=60.650
PRIMER_LEFT_GC_PERCENT=36.000
PRIMER_RIGHT_GC_PERCENT=36.000
PRIMER_LEFT_SELF_ANY=12.00
PRIMER_RIGHT_SELF_ANY=4.00
PRIMER_LEFT_SELF_END=10.00
PRIMER_RIGHT_SELF_END=3.00
PRIMER_LEFT_END_STABILITY=6.9000
PRIMER_RIGHT_END_STABILITY=6.4000
PRIMER_PAIR_COMPL_ANY=7.00
PRIMER_PAIR_COMPL_END=1.00
PRIMER_PRODUCT_SIZE=55
=
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
PRIMER_LEFT_EXPLAIN=considered 28, too many Ns 27, ok 1
PRIMER_RIGHT_EXPLAIN=considered 28, too many Ns 26, ok 2
PRIMER_PAIR_EXPLAIN=considered 4, unacceptable product size 2, ok 2
PRIMER_PAIR_PENALTY=3.3813
PRIMER_LEFT_PENALTY=2.731673
PRIMER_RIGHT_PENALTY=0.649600
PRIMER_LEFT_SEQUENCE=CACGTCATCTCATCAAATTTGATTG
PRIMER_RIGHT_SEQUENCE=GAATTGTTTGGAAATGACAGTGAGT
PRIMER_LEFT=3,25
PRIMER_RIGHT=57,25
PRIMER_LEFT_TM=62.732
PRIMER_RIGHT_TM=60.650
PRIMER_LEFT_GC_PERCENT=36.000
PRIMER_RIGHT_GC_PERCENT=36.000
PRIMER_LEFT_SELF_ANY=12.00
PRIMER_RIGHT_SELF_ANY=4.00
PRIMER_LEFT_SELF_END=10.00
PRIMER_RIGHT_SELF_END=3.00
PRIMER_LEFT_END_STABILITY=6.9000
PRIMER_RIGHT_END_STABILITY=6.4000
PRIMER_PAIR_COMPL_ANY=7.00
PRIMER_PAIR_COMPL_END=1.00
PRIMER_PRODUCT_SIZE=55
PRIMER_PAIR_PENALTY_1=3.3813
PRIMER_LEFT_1_PENALTY=2.731673
PRIMER_RIGHT_1_PENALTY=0.649600
PRIMER_LEFT_1_SEQUENCE=CACGTCATCTCATCAAATTTGATTG
PRIMER_RIGHT_1_SEQUENCE=GAATTGTTTGGAAATGACAGTGAGT
PRIMER_LEFT_1=3,25
PRIMER_RIGHT_1=84,25
PRIMER_LEFT_1_TM=62.732
PRIMER_RIGHT_1_TM=60.650
PRIMER_LEFT_1_GC_PERCENT=36.000
PRIMER_RIGHT_1_GC_PERCENT=36.000
PRIMER_LEFT_1_SELF_ANY=12.00
PRIMER_RIGHT_1_SELF_ANY=4.00
PRIMER_LEFT_1_SELF_END=10.00
PRIMER_RIGHT_1_SELF_END=3.00
PRIMER_LEFT_1_END_STABILITY=6.9000
PRIMER_RIGHT_1_END_STABILITY=6.4000
PRIMER_PAIR_1_COMPL_ANY=7.00
PRIMER_PAIR_1_COMPL_END=1.00
PRIMER_PRODUCT_SIZE_1=82
=
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
PRIMER_LEFT_EXPLAIN=considered 28, too many Ns 27, ok 1
PRIMER_RIGHT_EXPLAIN=considered 28, too many Ns 26, ok 2
PRIMER_PAIR_EXPLAIN=considered 4, unacceptable product size 2, ok 2
PRIMER_PAIR_PENALTY=3.3813
PRIMER_LEFT_PENALTY=2.731673
PRIMER_RIGHT_PENALTY=0.649600
PRIMER_LEFT_SEQUENCE=CACGTCATCTCATCAAATTTGATTG
PRIMER_RIGHT_SEQUENCE=GAATTGTTTGGAAATGACAGTGAGT
PRIMER_LEFT=3,25
PRIMER_RIGHT=84,25
PRIMER_LEFT_TM=62.732
PRIMER_RIGHT_TM=60.650
PRIMER_LEFT_GC_PERCENT=36.000
PRIMER_RIGHT_GC_PERCENT=36.000
PRIMER_LEFT_SELF_ANY=12.00
PRIMER_RIGHT_SELF_ANY=4.00
PRIMER_LEFT_SELF_END=10.00
PRIMER_RIGHT_SELF_END=3.00
PRIMER_LEFT_END_STABILITY=6.9000
PRIMER_RIGHT_END_STABILITY=6.4000
PRIMER_PAIR_COMPL_ANY=7.00
PRIMER_PAIR_COMPL_END=1.00
PRIMER_PRODUCT_SIZE=82
PRIMER_PAIR_PENALTY_1=3.3813
PRIMER_LEFT_1_PENALTY=2.731673
PRIMER_RIGHT_1_PENALTY=0.649600
PRIMER_LEFT_1_SEQUENCE=CACGTCATCTCATCAAATTTGATTG
PRIMER_RIGHT_1_SEQUENCE=GAATTGTTTGGAAATGACAGTGAGT
PRIMER_LEFT_1=3,25
PRIMER_RIGHT_1=57,25
PRIMER_LEFT_1_TM=62.732
PRIMER_RIGHT_1_TM=60.650
PRIMER_LEFT_1_GC_PERCENT=36.000
PRIMER_RIGHT_1_GC_PERCENT=36.000
PRIMER_LEFT_1_SELF_ANY=12.00
PRIMER_RIGHT_1_SELF_ANY=4.00
PRIMER_LEFT_1_SELF_END=10.00
PRIMER_RIGHT_1_SELF_END=3.00
PRIMER_LEFT_1_END_STABILITY=6.9000
PRIMER_RIGHT_1_END_STABILITY=6.4000
PRIMER_PAIR_1_COMPL_ANY=7.00
PRIMER_PAIR_1_COMPL_END=1.00
PRIMER_PRODUCT_SIZE_1=55
=
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
PRIMER_LEFT_EXPLAIN=considered 28, too many Ns 27, ok 1
PRIMER_RIGHT_EXPLAIN=considered 28, too many Ns 26, ok 2
PRIMER_PAIR_EXPLAIN=considered 4, unacceptable product size 1, ok 3
PRIMER_PAIR_PENALTY=3.3813
PRIMER_LEFT_PENALTY=2.731673
PRIMER_RIGHT_PENALTY=0.649600
PRIMER_LEFT_SEQUENCE=CACGTCATCTCATCAAATTTGATTG
PRIMER_RIGHT_SEQUENCE=GAATTGTTTGGAAATGACAGTGAGT
PRIMER_LEFT=3,25
PRIMER_RIGHT=57,25
PRIMER_LEFT_TM=62.732
PRIMER_RIGHT_TM=60.650
PRIMER_LEFT_GC_PERCENT=36.000
PRIMER_RIGHT_GC_PERCENT=36.000
PRIMER_LEFT_SELF_ANY=12.00
PRIMER_RIGHT_SELF_ANY=4.00
PRIMER_LEFT_SELF_END=10.00
PRIMER_RIGHT_SELF_END=3.00
PRIMER_LEFT_END_STABILITY=6.9000
PRIMER_RIGHT_END_STABILITY=6.4000
PRIMER_PAIR_COMPL_ANY=7.00
PRIMER_PAIR_COMPL_END=1.00
PRIMER_PRODUCT_SIZE=55
PRIMER_PAIR_PENALTY_1=3.3813
PRIMER_LEFT_1_PENALTY=2.731673
PRIMER_RIGHT_1_PENALTY=0.649600
PRIMER_LEFT_1_SEQUENCE=CACGTCATCTCATCAAATTTGATTG
PRIMER_RIGHT_1_SEQUENCE=GAATTGTTTGGAAATGACAGTGAGT
PRIMER_LEFT_1=3,25
PRIMER_RIGHT_1=84,25
PRIMER_LEFT_1_TM=62.732
PRIMER_RIGHT_1_TM=60.650
PRIMER_LEFT_1_GC_PERCENT=36.000
PRIMER_RIGHT_1_GC_PERCENT=36.000
PRIMER_LEFT_1_SELF_ANY=12.00
PRIMER_RIGHT_1_SELF_ANY=4.00
PRIMER_LEFT_1_SELF_END=10.00
PRIMER_RIGHT_1_SELF_END=3.00
PRIMER_LEFT_1_END_STABILITY=6.9000
PRIMER_RIGHT_1_END_STABILITY=6.4000
PRIMER_PAIR_1_COMPL_ANY=7.00
PRIMER_PAIR_1_COMPL_END=1.00
PRIMER_PRODUCT_SIZE_1=82
=
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
PRIMER_LEFT_EXPLAIN=considered 28, too many Ns 27, ok 1
PRIMER_RIGHT_EXPLAIN=considered 28, too many Ns 26, ok 2
PRIMER_PAIR_EXPLAIN=considered 4, unacceptable product size 1, ok 3
PRIMER_PAIR_PENALTY=3.3813
PRIMER_LEFT_PENALTY=2.731673
PRIMER_RIGHT_PENALTY=0.649600
PRIMER_LEFT_SEQUENCE=CACGTCATCTCATCAAATTTGATTG
PRIMER_RIGHT_SEQUENCE=GAATTGTTTGGAAATGACAGTGAGT
PRIMER_LEFT=3,25
PRIMER_RIGHT=84,25
PRIMER_LEFT_TM=62.732
PRIMER_RIGHT_TM=60.650
PRIMER_LEFT_GC_PERCENT=36.000
PRIMER_RIGHT_GC_PERCENT=36.000
PRIMER_LEFT_SELF_ANY=12.00
PRIMER_RIGHT_SELF_ANY=4.00
PRIMER_LEFT_SELF_END=10.00
PRIMER_RIGHT_SELF_END=3.00
PRIMER_LEFT_END_STABILITY=6.9000
PRIMER_RIGHT_END_STABILITY=6.4000
PRIMER_PAIR_COMPL_ANY=7.00
PRIMER_PAIR_COMPL_END=1.00
PRIMER_PRODUCT_SIZE=82
PRIMER_PAIR_PENALTY_1=3.3813
PRIMER_LEFT_1_PENALTY=2.731673
PRIMER_RIGHT_1_PENALTY=0.649600
PRIMER_LEFT_1_SEQUENCE=CACGTCATCTCATCAAATTTGATTG
PRIMER_RIGHT_1_SEQUENCE=GAATTGTTTGGAAATGACAGTGAGT
PRIMER_LEFT_1=3,25
PRIMER_RIGHT_1=57,25
PRIMER_LEFT_1_TM=62.732
PRIMER_RIGHT_1_TM=60.650
PRIMER_LEFT_1_GC_PERCENT=36.000
PRIMER_RIGHT_1_GC_PERCENT=36.000
PRIMER_LEFT_1_SELF_ANY=12.00
PRIMER_RIGHT_1_SELF_ANY=4.00
PRIMER_LEFT_1_SELF_END=10.00
PRIMER_RIGHT_1_SELF_END=3.00
PRIMER_LEFT_1_END_STABILITY=6.9000
PRIMER_RIGHT_1_END_STABILITY=6.4000
PRIMER_PAIR_1_COMPL_ANY=7.00
PRIMER_PAIR_1_COMPL_END=1.00
PRIMER_PRODUCT_SIZE_1=55
=
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)
PRIMER_LEFT_EXPLAIN=considered 1, ok 1
PRIMER_RIGHT_EXPLAIN=considered 1, ok 1
PRIMER_PAIR_EXPLAIN=considered 1, ok 1
PRIMER_PAIR_PENALTY=4.1376
PRIMER_LEFT_PENALTY=2.963671
PRIMER_RIGHT_PENALTY=1.173886
PRIMER_LEFT_SEQUENCE=AATGTGATTGCATCAAATGTGATTG
PRIMER_RIGHT_SEQUENCE=GAATTGTGGAAATGACAATCACATT
PRIMER_LEFT=3,25
PRIMER_RIGHT=57,25
PRIMER_LEFT_TM=62.964
PRIMER_RIGHT_TM=61.174
PRIMER_LEFT_GC_PERCENT=32.000
PRIMER_RIGHT_GC_PERCENT=32.000
PRIMER_LEFT_SELF_ANY=8.00
PRIMER_RIGHT_SELF_ANY=5.00
PRIMER_LEFT_SELF_END=6.00
PRIMER_RIGHT_SELF_END=5.00
PRIMER_LEFT_END_STABILITY=6.9000
PRIMER_RIGHT_END_STABILITY=6.6000
PRIMER_PAIR_COMPL_ANY=11.00
PRIMER_PAIR_COMPL_END=10.00
PRIMER_PRODUCT_SIZE=55
=
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)
PRIMER_LEFT_EXPLAIN=considered 1, ok 1
PRIMER_RIGHT_EXPLAIN=considered 1, ok 1
PRIMER_PAIR_EXPLAIN=considered 1, high any compl 1, ok 0
=
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)
PRIMER_LEFT_EXPLAIN=considered 1, ok 1
PRIMER_RIGHT_EXPLAIN=considered 1, ok 1
PRIMER_PAIR_EXPLAIN=considered 1, ok 1
PRIMER_PAIR_PENALTY=4.1376
PRIMER_LEFT_PENALTY=2.963671
PRIMER_RIGHT_PENALTY=1.173886
PRIMER_LEFT_SEQUENCE=AATGTGATTGCATCAAATGTGATTG
PRIMER_RIGHT_SEQUENCE=GAATTGTGGAAATGACAATCACATT
PRIMER_LEFT=3,25
PRIMER_RIGHT=57,25
PRIMER_LEFT_TM=62.964
PRIMER_RIGHT_TM=61.174
PRIMER_LEFT_GC_PERCENT=32.000
PRIMER_RIGHT_GC_PERCENT=32.000
PRIMER_LEFT_SELF_ANY=8.00
PRIMER_RIGHT_SELF_ANY=5.00
PRIMER_LEFT_SELF_END=6.00
PRIMER_RIGHT_SELF_END=5.00
PRIMER_LEFT_END_STABILITY=6.9000
PRIMER_RIGHT_END_STABILITY=6.6000
PRIMER_PAIR_COMPL_ANY=11.00
PRIMER_PAIR_COMPL_END=10.00
PRIMER_PRODUCT_SIZE=55
=
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)
PRIMER_LEFT_EXPLAIN=considered 1, ok 1
PRIMER_RIGHT_EXPLAIN=considered 1, ok 1
PRIMER_PAIR_EXPLAIN=considered 1, high end compl 1, ok 0
=
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)
PRIMER_LEFT_EXPLAIN=considered 1, ok 1
PRIMER_RIGHT_EXPLAIN=considered 1, ok 1
PRIMER_PAIR_EXPLAIN=considered 200, ok 200
PRIMER_PAIR_PENALTY=4.1376
PRIMER_LEFT_PENALTY=2.963671
PRIMER_RIGHT_PENALTY=1.173886
PRIMER_LEFT_SEQUENCE=AATGTGATTGCATCAAATGTGATTG
PRIMER_RIGHT_SEQUENCE=GAATTGTGGAAATGACAATCACATT
PRIMER_LEFT=3,25
PRIMER_RIGHT=57,25
PRIMER_LEFT_TM=62.964
PRIMER_RIGHT_TM=61.174
PRIMER_LEFT_GC_PERCENT=32.000
PRIMER_RIGHT_GC_PERCENT=32.000
PRIMER_LEFT_SELF_ANY=8.00
PRIMER_RIGHT_SELF_ANY=5.00
PRIMER_LEFT_SELF_END=6.00
PRIMER_RIGHT_SELF_END=5.00
PRIMER_LEFT_END_STABILITY=6.9000
PRIMER_RIGHT_END_STABILITY=6.6000
PRIMER_PAIR_COMPL_ANY=11.00
PRIMER_PAIR_COMPL_END=10.00
PRIMER_PRODUCT_SIZE=55
=
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)
PRIMER_LEFT_EXPLAIN=considered 1, ok 1
PRIMER_RIGHT_EXPLAIN=considered 1, ok 1
PRIMER_PAIR_EXPLAIN=considered 1, ok 1
PRIMER_PAIR_PENALTY=4.1376
PRIMER_LEFT_PENALTY=2.963671
PRIMER_RIGHT_PENALTY=1.173886
PRIMER_LEFT_SEQUENCE=AATGTGATTGCATCAAATGTGATTG
PRIMER_RIGHT_SEQUENCE=GAATTGTGGAAATGACAATCACATT
PRIMER_LEFT=3,25
PRIMER_RIGHT=57,25
PRIMER_LEFT_TM=62.964
PRIMER_RIGHT_TM=61.174
PRIMER_LEFT_GC_PERCENT=32.000
PRIMER_RIGHT_GC_PERCENT=32.000
PRIMER_LEFT_SELF_ANY=8.00
PRIMER_RIGHT_SELF_ANY=5.00
PRIMER_LEFT_SELF_END=6.00
PRIMER_RIGHT_SELF_END=5.00
PRIMER_LEFT_END_STABILITY=6.9000
PRIMER_RIGHT_END_STABILITY=6.6000
PRIMER_PAIR_COMPL_ANY=11.00
PRIMER_PAIR_COMPL_END=10.00
PRIMER_PRODUCT_SIZE=55
=
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)
PRIMER_ERROR=Too many elements for tag TARGET
=
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)
PRIMER_LEFT_EXPLAIN=considered 1, ok 1
PRIMER_RIGHT_EXPLAIN=considered 1, ok 1
PRIMER_PAIR_EXPLAIN=considered 1, ok 1
PRIMER_PAIR_PENALTY=4.1376
PRIMER_LEFT_PENALTY=2.963671
PRIMER_RIGHT_PENALTY=1.173886
PRIMER_LEFT_SEQUENCE=AATGTGATTGCATCAAATGTGATTG
PRIMER_RIGHT_SEQUENCE=GAATTGTGGAAATGACAATCACATT
PRIMER_LEFT=3,25
PRIMER_RIGHT=57,25
PRIMER_LEFT_TM=62.964
PRIMER_RIGHT_TM=61.174
PRIMER_LEFT_GC_PERCENT=32.000
PRIMER_RIGHT_GC_PERCENT=32.000
PRIMER_LEFT_SELF_ANY=8.00
PRIMER_RIGHT_SELF_ANY=5.00
PRIMER_LEFT_SELF_END=6.00
PRIMER_RIGHT_SELF_END=5.00
PRIMER_LEFT_END_STABILITY=6.9000
PRIMER_RIGHT_END_STABILITY=6.6000
PRIMER_PAIR_COMPL_ANY=11.00
PRIMER_PAIR_COMPL_END=10.00
PRIMER_PRODUCT_SIZE=55
=
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)
PRIMER_ERROR=Too many elements for tag EXCLUDED_REGION
=
