PRIMER_TM_FORMULA=0
PRIMER_SALT_CORRECTIONS=0
PRIMER_LOWERCASE_MASKING=0
PRIMER_NUM_RETURN=1
PRIMER_TASK=pick_left_only
PRIMER_EXPLAIN_FLAG=1
PRIMER_MIN_SIZE=10
PRIMER_MAX_SIZE=10
PRIMER_OPT_SIZE=10
PRIMER_MIN_TM=0
PRIMER_MAX_TM=70
P3_COMMENT=nomasking_Breslauer_Schildkraut
SEQUENCE_ID=000
SEQUENCE_TEMPLATE=TCCTTGTGAT
PRIMER_LEFT_EXPLAIN=considered 1, ok 1
PRIMER_LEFT_NUM_RETURNED=1
PRIMER_RIGHT_NUM_RETURNED=0
PRIMER_INTERNAL_NUM_RETURNED=0
PRIMER_PAIR_NUM_RETURNED=0
PRIMER_LEFT_0_PENALTY=44.893723
PRIMER_LEFT_0_SEQUENCE=TCCTTGTGAT
PRIMER_LEFT_0=0,10
PRIMER_LEFT_0_TM=15.106
PRIMER_LEFT_0_GC_PERCENT=40.000
PRIMER_LEFT_0_SELF_ANY=2.00
PRIMER_LEFT_0_SELF_END=2.00
PRIMER_LEFT_0_END_STABILITY=6.3000
=
PRIMER_TM_FORMULA=0
PRIMER_SALT_CORRECTIONS=1
PRIMER_LOWERCASE_MASKING=0
P3_COMMENT=nomasking_Breslauer_SantaLucia
SEQUENCE_ID=001
SEQUENCE_TEMPLATE=TCCTTGTGAT
PRIMER_LEFT_EXPLAIN=considered 1, ok 1
PRIMER_LEFT_NUM_RETURNED=1
PRIMER_RIGHT_NUM_RETURNED=0
PRIMER_INTERNAL_NUM_RETURNED=0
PRIMER_PAIR_NUM_RETURNED=0
PRIMER_LEFT_0_PENALTY=37.127461
PRIMER_LEFT_0_SEQUENCE=TCCTTGTGAT
PRIMER_LEFT_0=0,10
PRIMER_LEFT_0_TM=22.873
PRIMER_LEFT_0_GC_PERCENT=40.000
PRIMER_LEFT_0_SELF_ANY=2.00
PRIMER_LEFT_0_SELF_END=2.00
PRIMER_LEFT_0_END_STABILITY=6.3000
=
PRIMER_TM_FORMULA=0
PRIMER_SALT_CORRECTIONS=2
PRIMER_LOWERCASE_MASKING=0
P3_COMMENT=nomasking_Breslauer_Owczarzy
SEQUENCE_ID=002
SEQUENCE_TEMPLATE=TCCTTGTGAT
PRIMER_LEFT_EXPLAIN=considered 1, ok 1
PRIMER_LEFT_NUM_RETURNED=1
PRIMER_RIGHT_NUM_RETURNED=0
PRIMER_INTERNAL_NUM_RETURNED=0
PRIMER_PAIR_NUM_RETURNED=0
PRIMER_LEFT_0_PENALTY=37.175756
PRIMER_LEFT_0_SEQUENCE=TCCTTGTGAT
PRIMER_LEFT_0=0,10
PRIMER_LEFT_0_TM=22.824
PRIMER_LEFT_0_GC_PERCENT=40.000
PRIMER_LEFT_0_SELF_ANY=2.00
PRIMER_LEFT_0_SELF_END=2.00
PRIMER_LEFT_0_END_STABILITY=6.3000
=
PRIMER_TM_FORMULA=0
PRIMER_SALT_CORRECTIONS=0
PRIMER_LOWERCASE_MASKING=1
P3_COMMENT=masking_Breslauer_Schildkraut
P3_COMMENT=Should fail
SEQUENCE_ID=100
SEQUENCE_TEMPLATE=TCCTTGTGAt
PRIMER_LEFT_EXPLAIN=considered 1, lowercase masking of 3' end 1, ok 0
PRIMER_LEFT_NUM_RETURNED=0
PRIMER_RIGHT_NUM_RETURNED=0
PRIMER_INTERNAL_NUM_RETURNED=0
PRIMER_PAIR_NUM_RETURNED=0
=
PRIMER_TM_FORMULA=0
PRIMER_SALT_CORRECTIONS=1
PRIMER_LOWERCASE_MASKING=1
SEQUENCE_ID=101
P3_COMMENT=masking_Breslauer_SantaLucia
P3_COMMENT=Should succeed
SEQUENCE_TEMPLATE=TCCTTGTGaT
PRIMER_LEFT_EXPLAIN=considered 1, ok 1
PRIMER_LEFT_NUM_RETURNED=1
PRIMER_RIGHT_NUM_RETURNED=0
PRIMER_INTERNAL_NUM_RETURNED=0
PRIMER_PAIR_NUM_RETURNED=0
PRIMER_LEFT_0_PENALTY=37.127461
PRIMER_LEFT_0_SEQUENCE=TCCTTGTGaT
PRIMER_LEFT_0=0,10
PRIMER_LEFT_0_TM=22.873
PRIMER_LEFT_0_GC_PERCENT=40.000
PRIMER_LEFT_0_SELF_ANY=2.00
PRIMER_LEFT_0_SELF_END=2.00
PRIMER_LEFT_0_END_STABILITY=6.3000
=
PRIMER_TM_FORMULA=0
PRIMER_SALT_CORRECTIONS=2
PRIMER_LOWERCASE_MASKING=0
P3_COMMENT=masking_Breslauer_Owczarzy
P3_COMMENT=Should succeed
SEQUENCE_ID=102
SEQUENCE_TEMPLATE=tccttgtgat
PRIMER_LEFT_EXPLAIN=considered 1, ok 1
PRIMER_LEFT_NUM_RETURNED=1
PRIMER_RIGHT_NUM_RETURNED=0
PRIMER_INTERNAL_NUM_RETURNED=0
PRIMER_PAIR_NUM_RETURNED=0
PRIMER_LEFT_0_PENALTY=37.175756
PRIMER_LEFT_0_SEQUENCE=tccttgtgat
PRIMER_LEFT_0=0,10
PRIMER_LEFT_0_TM=22.824
PRIMER_LEFT_0_GC_PERCENT=40.000
PRIMER_LEFT_0_SELF_ANY=2.00
PRIMER_LEFT_0_SELF_END=2.00
PRIMER_LEFT_0_END_STABILITY=6.3000
=
PRIMER_TM_FORMULA=1
PRIMER_SALT_CORRECTIONS=0
PRIMER_LOWERCASE_MASKING=0
P3_COMMENT=nomasking_SantaLucia_Schildkraut
SEQUENCE_ID=010
SEQUENCE_TEMPLATE=TCCTTGTGAT
PRIMER_LEFT_EXPLAIN=considered 1, ok 1
PRIMER_LEFT_NUM_RETURNED=1
PRIMER_RIGHT_NUM_RETURNED=0
PRIMER_INTERNAL_NUM_RETURNED=0
PRIMER_PAIR_NUM_RETURNED=0
PRIMER_LEFT_0_PENALTY=50.265050
PRIMER_LEFT_0_SEQUENCE=TCCTTGTGAT
PRIMER_LEFT_0=0,10
PRIMER_LEFT_0_TM=9.735
PRIMER_LEFT_0_GC_PERCENT=40.000
PRIMER_LEFT_0_SELF_ANY=2.00
PRIMER_LEFT_0_SELF_END=2.00
PRIMER_LEFT_0_END_STABILITY=3.0600
=
PRIMER_TM_FORMULA=1
PRIMER_SALT_CORRECTIONS=1
PRIMER_LOWERCASE_MASKING=0
P3_COMMENT=nomasking_SantaLucia_SantaLucia
SEQUENCE_ID=011
SEQUENCE_TEMPLATE=TCCTTGTGAG
PRIMER_LEFT_EXPLAIN=considered 1, ok 1
PRIMER_LEFT_NUM_RETURNED=1
PRIMER_RIGHT_NUM_RETURNED=0
PRIMER_INTERNAL_NUM_RETURNED=0
PRIMER_PAIR_NUM_RETURNED=0
PRIMER_LEFT_0_PENALTY=39.057206
PRIMER_LEFT_0_SEQUENCE=TCCTTGTGAG
PRIMER_LEFT_0=0,10
PRIMER_LEFT_0_TM=20.943
PRIMER_LEFT_0_GC_PERCENT=50.000
PRIMER_LEFT_0_SELF_ANY=2.00
PRIMER_LEFT_0_SELF_END=0.00
PRIMER_LEFT_0_END_STABILITY=3.5100
=
PRIMER_TM_FORMULA=1
PRIMER_SALT_CORRECTIONS=2
PRIMER_LOWERCASE_MASKING=0
P3_COMMENT=nomasking_SantaLucia_Owczarzy
SEQUENCE_ID=012
SEQUENCE_TEMPLATE=GCCTTGTGAG
PRIMER_LEFT_EXPLAIN=considered 1, ok 1
PRIMER_LEFT_NUM_RETURNED=1
PRIMER_RIGHT_NUM_RETURNED=0
PRIMER_INTERNAL_NUM_RETURNED=0
PRIMER_PAIR_NUM_RETURNED=0
PRIMER_LEFT_0_PENALTY=33.922737
PRIMER_LEFT_0_SEQUENCE=GCCTTGTGAG
PRIMER_LEFT_0=0,10
PRIMER_LEFT_0_TM=26.077
PRIMER_LEFT_0_GC_PERCENT=60.000
PRIMER_LEFT_0_SELF_ANY=2.00
PRIMER_LEFT_0_SELF_END=0.00
PRIMER_LEFT_0_END_STABILITY=3.5100
=
PRIMER_TM_FORMULA=1
PRIMER_SALT_CORRECTIONS=0
PRIMER_LOWERCASE_MASKING=1
P3_COMMENT=masking_SantaLucia_Schildkraut
P3_COMMENT=Should fail
SEQUENCE_ID=110
SEQUENCE_TEMPLATE=TCCTTGTGAt
PRIMER_LEFT_EXPLAIN=considered 1, lowercase masking of 3' end 1, ok 0
PRIMER_LEFT_NUM_RETURNED=0
PRIMER_RIGHT_NUM_RETURNED=0
PRIMER_INTERNAL_NUM_RETURNED=0
PRIMER_PAIR_NUM_RETURNED=0
=
PRIMER_TM_FORMULA=1
PRIMER_SALT_CORRECTIONS=1
PRIMER_LOWERCASE_MASKING=1
P3_COMMENT=masking_SantaLucia_SantaLucia
P3_COMMENT=Should succeed
SEQUENCE_ID=111
SEQUENCE_TEMPLATE=TCCTTGTGaT
PRIMER_LEFT_EXPLAIN=considered 1, ok 1
PRIMER_LEFT_NUM_RETURNED=1
PRIMER_RIGHT_NUM_RETURNED=0
PRIMER_INTERNAL_NUM_RETURNED=0
PRIMER_PAIR_NUM_RETURNED=0
PRIMER_LEFT_0_PENALTY=41.601530
PRIMER_LEFT_0_SEQUENCE=TCCTTGTGaT
PRIMER_LEFT_0=0,10
PRIMER_LEFT_0_TM=18.398
PRIMER_LEFT_0_GC_PERCENT=40.000
PRIMER_LEFT_0_SELF_ANY=2.00
PRIMER_LEFT_0_SELF_END=2.00
PRIMER_LEFT_0_END_STABILITY=3.0600
=
PRIMER_TM_FORMULA=1
PRIMER_SALT_CORRECTIONS=2
PRIMER_LOWERCASE_MASKING=0
P3_COMMENT=nomasking_SantaLucia_Owczarzy
P3_COMMENT=Should succeed
SEQUENCE_ID=112
SEQUENCE_TEMPLATE=tccttgtgat
PRIMER_LEFT_EXPLAIN=considered 1, ok 1
PRIMER_LEFT_NUM_RETURNED=1
PRIMER_RIGHT_NUM_RETURNED=0
PRIMER_INTERNAL_NUM_RETURNED=0
PRIMER_PAIR_NUM_RETURNED=0
PRIMER_LEFT_0_PENALTY=42.080319
PRIMER_LEFT_0_SEQUENCE=tccttgtgat
PRIMER_LEFT_0=0,10
PRIMER_LEFT_0_TM=17.920
PRIMER_LEFT_0_GC_PERCENT=40.000
PRIMER_LEFT_0_SELF_ANY=2.00
PRIMER_LEFT_0_SELF_END=2.00
PRIMER_LEFT_0_END_STABILITY=3.0600
=
SEQUENCE_ID=masking_001
PRIMER_LOWERCASE_MASKING=1
PRIMER_PRODUCT_SIZE_RANGE=40-300
PRIMER_TASK=pick_pcr_primers
PRIMER_MAX_SIZE=20
PRIMER_MIN_SIZE=20
PRIMER_OPT_SIZE=20
SEQUENCE_TEMPLATE=GCCTTCATTAGAAAGTGACANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAATCACACCTGGGTACTAAT
PRIMER_LEFT_EXPLAIN=considered 31, too many Ns 30, ok 1
PRIMER_RIGHT_EXPLAIN=considered 31, too many Ns 30, ok 1
PRIMER_PAIR_EXPLAIN=considered 1, ok 1
PRIMER_LEFT_NUM_RETURNED=1
PRIMER_RIGHT_NUM_RETURNED=1
PRIMER_INTERNAL_NUM_RETURNED=0
PRIMER_PAIR_NUM_RETURNED=1
PRIMER_PAIR_0_PENALTY=27.371182
PRIMER_LEFT_0_PENALTY=13.856830
PRIMER_RIGHT_0_PENALTY=13.514352
PRIMER_LEFT_0_SEQUENCE=GCCTTCATTAGAAAGTGACA
PRIMER_RIGHT_0_SEQUENCE=ATTAGTACCCAGGTGTGATT
PRIMER_LEFT_0=0,20
PRIMER_RIGHT_0=69,20
PRIMER_LEFT_0_TM=46.143
PRIMER_RIGHT_0_TM=46.486
PRIMER_LEFT_0_GC_PERCENT=40.000
PRIMER_RIGHT_0_GC_PERCENT=40.000
PRIMER_LEFT_0_SELF_ANY=3.00
PRIMER_RIGHT_0_SELF_ANY=4.00
PRIMER_LEFT_0_SELF_END=3.00
PRIMER_RIGHT_0_SELF_END=1.00
PRIMER_LEFT_0_END_STABILITY=3.5800
PRIMER_RIGHT_0_END_STABILITY=2.5700
PRIMER_PAIR_0_COMPL_ANY=3.00
PRIMER_PAIR_0_COMPL_END=3.00
PRIMER_PAIR_0_PRODUCT_SIZE=70
PRIMER_PAIR_0_PRODUCT_TM=60.7
=
SEQUENCE_ID=masking_002
SEQUENCE_TEMPLATE=GCCTTCATTAGAAAGTGACANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNaATCACACCTGGGTACTAAT
PRIMER_LEFT_EXPLAIN=considered 31, too many Ns 30, ok 1
PRIMER_RIGHT_EXPLAIN=considered 31, too many Ns 30, lowercase masking of 3' end 1, ok 0
PRIMER_PAIR_EXPLAIN=considered 0, ok 0
PRIMER_LEFT_NUM_RETURNED=0
PRIMER_RIGHT_NUM_RETURNED=0
PRIMER_INTERNAL_NUM_RETURNED=0
PRIMER_PAIR_NUM_RETURNED=0
=
SEQUENCE_ID=masking_003
SEQUENCE_TEMPLATE=GCCTTCATTAGAAAGTGACANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAATCACACCTGGGTACTAAt
PRIMER_LEFT_EXPLAIN=considered 31, too many Ns 30, ok 1
PRIMER_RIGHT_EXPLAIN=considered 31, too many Ns 30, ok 1
PRIMER_PAIR_EXPLAIN=considered 1, ok 1
PRIMER_LEFT_NUM_RETURNED=1
PRIMER_RIGHT_NUM_RETURNED=1
PRIMER_INTERNAL_NUM_RETURNED=0
PRIMER_PAIR_NUM_RETURNED=1
PRIMER_PAIR_0_PENALTY=27.371182
PRIMER_LEFT_0_PENALTY=13.856830
PRIMER_RIGHT_0_PENALTY=13.514352
PRIMER_LEFT_0_SEQUENCE=GCCTTCATTAGAAAGTGACA
PRIMER_RIGHT_0_SEQUENCE=aTTAGTACCCAGGTGTGATT
PRIMER_LEFT_0=0,20
PRIMER_RIGHT_0=69,20
PRIMER_LEFT_0_TM=46.143
PRIMER_RIGHT_0_TM=46.486
PRIMER_LEFT_0_GC_PERCENT=40.000
PRIMER_RIGHT_0_GC_PERCENT=40.000
PRIMER_LEFT_0_SELF_ANY=3.00
PRIMER_RIGHT_0_SELF_ANY=4.00
PRIMER_LEFT_0_SELF_END=3.00
PRIMER_RIGHT_0_SELF_END=1.00
PRIMER_LEFT_0_END_STABILITY=3.5800
PRIMER_RIGHT_0_END_STABILITY=2.5700
PRIMER_PAIR_0_COMPL_ANY=3.00
PRIMER_PAIR_0_COMPL_END=3.00
PRIMER_PAIR_0_PRODUCT_SIZE=70
PRIMER_PAIR_0_PRODUCT_TM=60.7
=
SEQUENCE_ID=masking_004
SEQUENCE_TEMPLATE=gCCTTCATTAGAAAGTGACANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAATCACACCTGGGTACTAAT
PRIMER_LEFT_EXPLAIN=considered 31, too many Ns 30, ok 1
PRIMER_RIGHT_EXPLAIN=considered 31, too many Ns 30, ok 1
PRIMER_PAIR_EXPLAIN=considered 1, ok 1
PRIMER_LEFT_NUM_RETURNED=1
PRIMER_RIGHT_NUM_RETURNED=1
PRIMER_INTERNAL_NUM_RETURNED=0
PRIMER_PAIR_NUM_RETURNED=1
PRIMER_PAIR_0_PENALTY=27.371182
PRIMER_LEFT_0_PENALTY=13.856830
PRIMER_RIGHT_0_PENALTY=13.514352
PRIMER_LEFT_0_SEQUENCE=gCCTTCATTAGAAAGTGACA
PRIMER_RIGHT_0_SEQUENCE=ATTAGTACCCAGGTGTGATT
PRIMER_LEFT_0=0,20
PRIMER_RIGHT_0=69,20
PRIMER_LEFT_0_TM=46.143
PRIMER_RIGHT_0_TM=46.486
PRIMER_LEFT_0_GC_PERCENT=40.000
PRIMER_RIGHT_0_GC_PERCENT=40.000
PRIMER_LEFT_0_SELF_ANY=3.00
PRIMER_RIGHT_0_SELF_ANY=4.00
PRIMER_LEFT_0_SELF_END=3.00
PRIMER_RIGHT_0_SELF_END=1.00
PRIMER_LEFT_0_END_STABILITY=3.5800
PRIMER_RIGHT_0_END_STABILITY=2.5700
PRIMER_PAIR_0_COMPL_ANY=3.00
PRIMER_PAIR_0_COMPL_END=3.00
PRIMER_PAIR_0_PRODUCT_SIZE=70
PRIMER_PAIR_0_PRODUCT_TM=60.7
=
SEQUENCE_ID=masking_005
SEQUENCE_TEMPLATE=GCCTTCATTAGAAAGTGACaNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAATCACACCTGGGTACTAAT
PRIMER_LEFT_EXPLAIN=considered 31, too many Ns 30, lowercase masking of 3' end 1, ok 0
PRIMER_RIGHT_EXPLAIN=considered 31, too many Ns 30, ok 1
PRIMER_PAIR_EXPLAIN=considered 0, ok 0
PRIMER_LEFT_NUM_RETURNED=0
PRIMER_RIGHT_NUM_RETURNED=0
PRIMER_INTERNAL_NUM_RETURNED=0
PRIMER_PAIR_NUM_RETURNED=0
=
