PRIMER_SEQUENCE_ID=quality_test1
PRIMER_EXPLAIN_FLAG=1
COMMENT=quality scores out of range
PRIMER_MIN_TM=0
PRIMER_INTERNAL_OLIGO_MIN_TM=0
PRIMER_INTERNAL_OLIGO_MAX_TM=100
PRIMER_MAX_TM=100
PRIMER_SELF_ANY=20
PRIMER_SELF_END=20
PRIMER_PRODUCT_SIZE_RANGE=50-70 70-90 90-110 110-500
SEQUENCE=ATCGTAGCTGATCGTAGCTGATCGTAGCTAGTCAGTCTACTACTGATCTAGCTGATCATCGTAGCTAGCTAGTCATCATCGTACTACGTAGCTACTAGTCATCTAGCTAGCTAGTCGATGC
PRIMER_MIN_QUALITY=30
PRIMER_QUALITY_RANGE_MAX=40
PRIMER_SEQUENCE_QUALITY=50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 
PRIMER_ERROR=Sequence quality score out of range
=
PRIMER_SEQUENCE_ID=quality_test2
COMMENT=quality scores out of range
SEQUENCE=ATCGTAGCTGATCGTAGCTGATCGTAGCTAGTCAGTCTACTACTGATCTAGCTGATCATCGTAGCTAGCTAGTCATCATCGTACTACGTAGCTACTAGTCATCTAGCTAGCTAGTCGATGC
PRIMER_SEQUENCE_QUALITY=50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 
PRIMER_MIN_QUALITY=60
PRIMER_QUALITY_RANGE_MIN=60
PRIMER_QUALITY_RANGE_MAX=65
PRIMER_ERROR=Sequence quality score out of range
=
PRIMER_SEQUENCE_ID=quality_test3
COMMENT=quality scores out of range
SEQUENCE=ATCGTAGCTGATCGTAGCTGATCGTAGCTAGTCAGTCTACTACTGATCTAGCTGATCATCGTAGCTAGCTAGTCATCATCGTACTACGTAGCTACTAGTCATCTAGCTAGCTAGTCGATGC
PRIMER_SEQUENCE_QUALITY=50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 
PRIMER_QUALITY_RANGE_MIN=0
PRIMER_MIN_QUALITY=9
PRIMER_QUALITY_RANGE_MAX=49
PRIMER_ERROR=Sequence quality score out of range
=
PRIMER_SEQUENCE_ID=quality_test4
COMMENT=Should return exactly one pair
SEQUENCE=ATCGTAGCTGATCGTAGCTGATCGTAGCTAGTCAGTCTACTACTGATCTAGCTGATCATCGTAGCTAGCTAGTCATCATCGTACTACGTAGCTACTAGTCATCTAGCTAGCTAGTCGATGC
PRIMER_MIN_QUALITY=60
PRIMER_QUALITY_RANGE_MAX=70
PRIMER_MIN_SIZE=10
PRIMER_SEQUENCE_QUALITY=60 60 60 60 60 60 60 60 60 60 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 60 60 60 60 60 60 60 60 60 60 
PRIMER_LEFT_EXPLAIN=considered 89,low sequence quality 88, ok 1
PRIMER_RIGHT_EXPLAIN=considered 89,low sequence quality 88, ok 1
PRIMER_PAIR_EXPLAIN=considered 4, unacceptable product size 3, ok 1
PRIMER_PAIR_PENALTY=104.2328
PRIMER_LEFT_PENALTY=52.299978
PRIMER_RIGHT_PENALTY=51.932846
PRIMER_LEFT_SEQUENCE=ATCGTAGCTG
PRIMER_RIGHT_SEQUENCE=GCATCGACTA
PRIMER_LEFT=0,10
PRIMER_RIGHT=120,10
PRIMER_LEFT_TM=17.700
PRIMER_RIGHT_TM=18.067
PRIMER_LEFT_GC_PERCENT=50.000
PRIMER_RIGHT_GC_PERCENT=50.000
PRIMER_LEFT_SELF_ANY=4.00
PRIMER_RIGHT_SELF_ANY=4.00
PRIMER_LEFT_SELF_END=2.00
PRIMER_RIGHT_SELF_END=2.00
PRIMER_LEFT_MIN_SEQ_QUALITY=60
PRIMER_RIGHT_MIN_SEQ_QUALITY=60
PRIMER_LEFT_END_STABILITY=8.2000
PRIMER_RIGHT_END_STABILITY=5.4000
PRIMER_PAIR_COMPL_ANY=3.00
PRIMER_PAIR_COMPL_END=3.00
PRIMER_PRODUCT_SIZE=121
=
PRIMER_SEQUENCE_ID=quality_test5
COMMENT=Should return exactly one pair
PRIMER_PICK_INTERNAL_OLIGO=1
PRIMER_INTERNAL_OLIGO_MIN_QUALITY=55
PRIMER_INTERNAL_OLIGO_MIN_SIZE=12
SEQUENCE=ATCGTAGCTGATCGTAGCTGATCGTAGCTAGTCAGTCTACTACTGATCTAGCTGATCATCGTAGCTAGCTAGTCATCATCGTACTACGTAGCTACTAGTCATCTAGCTAGCTAGTCGATGC
PRIMER_SEQUENCE_QUALITY=60 60 60 60 60 60 60 60 60 60 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 55 55 55 55 55 55 55 55 55 55 55 55 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 60 60 60 60 60 60 60 60 60 60 
PRIMER_LEFT_EXPLAIN=considered 89,low sequence quality 88, ok 1
PRIMER_RIGHT_EXPLAIN=considered 89,low sequence quality 88, ok 1
PRIMER_INTERNAL_OLIGO_EXPLAIN=considered 111,low sequence quality 110, ok 1
PRIMER_PAIR_EXPLAIN=considered 4, unacceptable product size 3, ok 1
PRIMER_PAIR_PENALTY=104.2328
PRIMER_LEFT_PENALTY=52.299978
PRIMER_RIGHT_PENALTY=51.932846
PRIMER_INTERNAL_OLIGO_PENALTY=44.970813
PRIMER_LEFT_SEQUENCE=ATCGTAGCTG
PRIMER_RIGHT_SEQUENCE=GCATCGACTA
PRIMER_INTERNAL_OLIGO_SEQUENCE=CATCATCGTACT
PRIMER_LEFT=0,10
PRIMER_RIGHT=120,10
PRIMER_INTERNAL_OLIGO=73,12
PRIMER_LEFT_TM=17.700
PRIMER_RIGHT_TM=18.067
PRIMER_INTERNAL_OLIGO_TM=23.029
PRIMER_LEFT_GC_PERCENT=50.000
PRIMER_RIGHT_GC_PERCENT=50.000
PRIMER_INTERNAL_OLIGO_GC_PERCENT=41.667
PRIMER_LEFT_SELF_ANY=4.00
PRIMER_RIGHT_SELF_ANY=4.00
PRIMER_INTERNAL_OLIGO_SELF_ANY=4.00
PRIMER_LEFT_SELF_END=2.00
PRIMER_RIGHT_SELF_END=2.00
PRIMER_INTERNAL_OLIGO_SELF_END=2.00
PRIMER_LEFT_MIN_SEQ_QUALITY=60
PRIMER_RIGHT_MIN_SEQ_QUALITY=60
PRIMER_LEFT_END_STABILITY=8.2000
PRIMER_RIGHT_END_STABILITY=5.4000
PRIMER_INTERNAL_OLIGO_MIN_SEQ_QUALITY=55
PRIMER_PAIR_COMPL_ANY=3.00
PRIMER_PAIR_COMPL_END=3.00
PRIMER_PRODUCT_SIZE=121
=
PRIMER_SEQUENCE_ID=quality_test6
COMMENT=Should fail because of low quality for middle oligo
PRIMER_PICK_INTERNAL_OLIGO=1
PRIMER_INTERNAL_OLIGO_MIN_QUALITY=51
SEQUENCE=ATCGTAGCTGATCGTAGCTGATCGTAGCTAGTCAGTCTACTACTGATCTAGCTGATCATCGTAGCTAGCTAGTCATCATCGTACTACGTAGCTACTAGTCATCTAGCTAGCTAGTCGATGC
PRIMER_SEQUENCE_QUALITY=60 60 60 60 60 60 60 60 60 60 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 53 54 54 54 54 50 54 54 54 54 54 51 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 60 60 60 60 60 60 60 60 60 60 
PRIMER_LEFT_EXPLAIN=considered 89,low sequence quality 88, ok 1
PRIMER_RIGHT_EXPLAIN=considered 89,low sequence quality 88, ok 1
PRIMER_INTERNAL_OLIGO_EXPLAIN=considered 110,low sequence quality 110, ok 0
PRIMER_PAIR_EXPLAIN=considered 0, ok 0
=
PRIMER_SEQUENCE_ID=quality_test7
COMMENT=Should fail as there are too few score values
PRIMER_PICK_INTERNAL_OLIGO=1
PRIMER_INTERNAL_OLIGO_MIN_QUALITY=20
SEQUENCE=ATCGTAGCTGATCGTAGCTGATCGTAGCTAGTCAGTCTACTACTGATCTAGCTGATCATCGTAGCTAGCTAGTCATCATCGTACTACGTAGCTACTAGTCATCTAGCTAGCTAGTCGATGC
PRIMER_SEQUENCE_QUALITY=50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 
PRIMER_ERROR=Error in sequence quality data
=
PRIMER_SEQUENCE_ID=quality_test8
COMMENT=Should fail as there are too many score values
PRIMER_PICK_INTERNAL_OLIGO=1
PRIMER_INTERNAL_OLIGO_MIN_QUALITY=20
SEQUENCE=ATCGTAGCTGATCGTAGCTGATCGTAGCTAGTCAGTCTACTACTGATCTAGCTGATCATCGTAGCTAGCTAGTCATCATCGTACTACGTAGCTACTAGTCATCTAGCTAGCTAGTCGATGC
PRIMER_SEQUENCE_QUALITY= 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 
PRIMER_ERROR=Error in sequence quality data
=
PRIMER_SEQUENCE_ID=quality_test9
COMMENT=Should fail because of low end quality
PRIMER_PICK_INTERNAL_OLIGO=1
PRIMER_INTERNAL_OLIGO_MIN_QUALITY=55
PRIMER_INTERNAL_OLIGO_MIN_SIZE=12
PRIMER_MIN_END_QUALITY=61
SEQUENCE=ATCGTAGCTGATCGTAGCTGATCGTAGCTAGTCAGTCTACTACTGATCTAGCTGATCATCGTAGCTAGCTAGTCATCATCGTACTACGTAGCTACTAGTCATCTAGCTAGCTAGTCGATGC
PRIMER_SEQUENCE_QUALITY=60 60 60 60 60 60 60 60 60 60 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 55 55 55 55 55 55 55 55 55 55 55 55 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 60 60 60 60 60 60 60 60 60 60 
PRIMER_LEFT_EXPLAIN=considered 89,low sequence quality 89, ok 0
PRIMER_RIGHT_EXPLAIN=considered 89,low sequence quality 89, ok 0
PRIMER_INTERNAL_OLIGO_EXPLAIN=considered 0, ok 0
PRIMER_PAIR_EXPLAIN=considered 0, ok 0
=
PRIMER_SEQUENCE_ID=quality_test10
COMMENT=Should return exactly one pair
PRIMER_PICK_INTERNAL_OLIGO=1
PRIMER_INTERNAL_OLIGO_MIN_QUALITY=55
PRIMER_INTERNAL_OLIGO_MIN_SIZE=12
PRIMER_MIN_END_QUALITY=61
SEQUENCE=ATCGTAGCTGATCGTAGCTGATCGTAGCTAGTCAGTCTACTACTGATCTAGCTGATCATCGTAGCTAGCTAGTCATCATCGTACTACGTAGCTACTAGTCATCTAGCTAGCTAGTCGATGC
PRIMER_SEQUENCE_QUALITY=60 60 60 60 60 61 61 61 61 61 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 55 55 55 55 55 55 55 55 55 55 55 55 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 61 61 61 61 61 60 60 60 60 60 
PRIMER_LEFT_EXPLAIN=considered 89,low sequence quality 88, ok 1
PRIMER_RIGHT_EXPLAIN=considered 89,low sequence quality 88, ok 1
PRIMER_INTERNAL_OLIGO_EXPLAIN=considered 111,low sequence quality 110, ok 1
PRIMER_PAIR_EXPLAIN=considered 4, unacceptable product size 3, ok 1
PRIMER_PAIR_PENALTY=104.2328
PRIMER_LEFT_PENALTY=52.299978
PRIMER_RIGHT_PENALTY=51.932846
PRIMER_INTERNAL_OLIGO_PENALTY=44.970813
PRIMER_LEFT_SEQUENCE=ATCGTAGCTG
PRIMER_RIGHT_SEQUENCE=GCATCGACTA
PRIMER_INTERNAL_OLIGO_SEQUENCE=CATCATCGTACT
PRIMER_LEFT=0,10
PRIMER_RIGHT=120,10
PRIMER_INTERNAL_OLIGO=73,12
PRIMER_LEFT_TM=17.700
PRIMER_RIGHT_TM=18.067
PRIMER_INTERNAL_OLIGO_TM=23.029
PRIMER_LEFT_GC_PERCENT=50.000
PRIMER_RIGHT_GC_PERCENT=50.000
PRIMER_INTERNAL_OLIGO_GC_PERCENT=41.667
PRIMER_LEFT_SELF_ANY=4.00
PRIMER_RIGHT_SELF_ANY=4.00
PRIMER_INTERNAL_OLIGO_SELF_ANY=4.00
PRIMER_LEFT_SELF_END=2.00
PRIMER_RIGHT_SELF_END=2.00
PRIMER_INTERNAL_OLIGO_SELF_END=2.00
PRIMER_LEFT_MIN_SEQ_QUALITY=60
PRIMER_RIGHT_MIN_SEQ_QUALITY=60
PRIMER_LEFT_END_STABILITY=8.2000
PRIMER_RIGHT_END_STABILITY=5.4000
PRIMER_INTERNAL_OLIGO_MIN_SEQ_QUALITY=55
PRIMER_PAIR_COMPL_ANY=3.00
PRIMER_PAIR_COMPL_END=3.00
PRIMER_PRODUCT_SIZE=121
=
PRIMER_SEQUENCE_ID=quality_test11
COMMENT=Should fail as high quality pairs are not in the included region
PRIMER_PICK_INTERNAL_OLIGO=1
PRIMER_INTERNAL_OLIGO_MIN_QUALITY=55
PRIMER_INTERNAL_OLIGO_MIN_SIZE=12
PRIMER_MIN_END_QUALITY=61
INCLUDED_REGION=2,115
SEQUENCE=ATCGTAGCTGATCGTAGCTGATCGTAGCTAGTCAGTCTACTACTGATCTAGCTGATCATCGTAGCTAGCTAGTCATCATCGTACTACGTAGCTACTAGTCATCTAGCTAGCTAGTCGATGC
PRIMER_SEQUENCE_QUALITY=60 60 60 60 60 61 61 61 61 61 61 61 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 55 55 55 55 55 55 55 55 55 55 55 55 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 61 61 61 61 61 60 60 60 60 60 
PRIMER_LEFT_EXPLAIN=considered 83,low sequence quality 82, ok 1
PRIMER_RIGHT_EXPLAIN=considered 83,low sequence quality 83, ok 0
PRIMER_INTERNAL_OLIGO_EXPLAIN=considered 0, ok 0
PRIMER_PAIR_EXPLAIN=considered 0, ok 0
=
PRIMER_SEQUENCE_ID=quality_test12
COMMENT=Should return exactly one pair
PRIMER_PICK_INTERNAL_OLIGO=1
PRIMER_INTERNAL_OLIGO_MIN_QUALITY=55
PRIMER_INTERNAL_OLIGO_MIN_SIZE=12
PRIMER_MIN_END_QUALITY=61
INCLUDED_REGION=2,115
SEQUENCE=ATCGTAGCTGATCGTAGCTGATCGTAGCTAGTCAGTCTACTACTGATCTAGCTGATCATCGTAGCTAGCTAGTCATCATCGTACTACGTAGCTACTAGTCATCTAGCTAGCTAGTCGATGC
PRIMER_SEQUENCE_QUALITY=60 60 60 60 60 61 61 61 61 61 61 61 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 55 55 55 55 55 55 55 55 55 55 55 55 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 61 61 61 61 61 61 61 61 61 60 50 50 50 50 
PRIMER_LEFT_EXPLAIN=considered 83,low sequence quality 82, ok 1
PRIMER_RIGHT_EXPLAIN=considered 83,low sequence quality 82, ok 1
PRIMER_INTERNAL_OLIGO_EXPLAIN=considered 105,low sequence quality 104, ok 1
PRIMER_PAIR_EXPLAIN=considered 4, unacceptable product size 3, ok 1
PRIMER_PAIR_PENALTY=108.4571
PRIMER_LEFT_PENALTY=52.299978
PRIMER_RIGHT_PENALTY=56.157144
PRIMER_INTERNAL_OLIGO_PENALTY=44.970813
PRIMER_LEFT_SEQUENCE=CGTAGCTGAT
PRIMER_RIGHT_SEQUENCE=CGACTAGCTA
PRIMER_INTERNAL_OLIGO_SEQUENCE=CATCATCGTACT
PRIMER_LEFT=2,10
PRIMER_RIGHT=116,10
PRIMER_INTERNAL_OLIGO=73,12
PRIMER_LEFT_TM=17.700
PRIMER_RIGHT_TM=13.843
PRIMER_INTERNAL_OLIGO_TM=23.029
PRIMER_LEFT_GC_PERCENT=50.000
PRIMER_RIGHT_GC_PERCENT=50.000
PRIMER_INTERNAL_OLIGO_GC_PERCENT=41.667
PRIMER_LEFT_SELF_ANY=4.00
PRIMER_RIGHT_SELF_ANY=6.00
PRIMER_INTERNAL_OLIGO_SELF_ANY=4.00
PRIMER_LEFT_SELF_END=2.00
PRIMER_RIGHT_SELF_END=6.00
PRIMER_INTERNAL_OLIGO_SELF_END=2.00
PRIMER_LEFT_MIN_SEQ_QUALITY=60
PRIMER_RIGHT_MIN_SEQ_QUALITY=60
PRIMER_LEFT_END_STABILITY=6.6000
PRIMER_RIGHT_END_STABILITY=7.2000
PRIMER_INTERNAL_OLIGO_MIN_SEQ_QUALITY=55
PRIMER_PAIR_COMPL_ANY=5.00
PRIMER_PAIR_COMPL_END=4.00
PRIMER_PRODUCT_SIZE=115
=
