P3_COMMENT=Test SEQUENCE_OVERHANG_LEFT and SEQUENCE_OVERHANG_RIGHT
PRIMER_TASK=check_primers
PRIMER_PICK_ANYWAY=1
PRIMER_NUM_RETURN=1
PRIMER_EXPLAIN_FLAG=1
PRIMER_MAX_NS_ACCEPTED=100
PRIMER_MAX_SIZE=35
PRIMER_MIN_SIZE=14
PRIMER_PRODUCT_SIZE_RANGE=60-1000
PRIMER_PICK_LEFT_PRIMER=1
PRIMER_PICK_RIGHT_PRIMER=1
PRIMER_PICK_INTERNAL_OLIGO=0
PRIMER_SECONDARY_STRUCTURE_ALIGNMENT=1
SEQUENCE_ID=Overhang01
SEQUENCE_TEMPLATE=GACATACGATACTTTGCTTTCAATCATGTGGGTGAAACGACTAAACCTTACGACTACTTAAAGTGGACTGGTAGTCTTTTTAAAGGTAC
SEQUENCE_PRIMER=TGCTTTCAATCATGTGGGTGA
SEQUENCE_OVERHANG_LEFT=TCACCCAC
SEQUENCE_PRIMER_REVCOMP=GACTACCAGTCCACTTTAAG
SEQUENCE_OVERHANG_RIGHT=TAAGGATTT
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=14.515061
PRIMER_LEFT_0_PENALTY=3.431046
PRIMER_RIGHT_0_PENALTY=11.084015
PRIMER_LEFT_0_PROBLEMS= Similarity to self too high; Similary to 3' end of self too high;
PRIMER_RIGHT_0_PROBLEMS= Temperature too low; Similary to 3' end of self too high;
PRIMER_LEFT_0_SEQUENCE=TCACCCACTGCTTTCAATCATGTGGGTGA
PRIMER_RIGHT_0_SEQUENCE=TAAGGATTTGACTACCAGTCCACTTTAAG
PRIMER_LEFT_0=14,21
PRIMER_RIGHT_0=75,20
PRIMER_LEFT_0_TM=62.431
PRIMER_RIGHT_0_TM=48.916
PRIMER_LEFT_0_GC_PERCENT=42.857
PRIMER_RIGHT_0_GC_PERCENT=45.000
PRIMER_LEFT_0_SELF_ANY=16.00
PRIMER_RIGHT_0_SELF_ANY=5.00
PRIMER_LEFT_0_SELF_ANY_STUCT=5' TCACCCAC-TGCTTTCAATCATGTGGGTGA 3'\n   |||||||| || ||  || || ||||||||\n3' AGTGGGTGTACTAACTTTCGT-CACCCACT 5'\n
PRIMER_RIGHT_0_SELF_ANY_STUCT=5' TAAGGATTTGACTACCAGTCCACTTTAAG 3'\n                         ||| |||\n                      3' GAATTTCACCTGACCATCAGTTTAGGAAT 5'\n
PRIMER_LEFT_0_SELF_END=16.00
PRIMER_RIGHT_0_SELF_END=5.00
PRIMER_LEFT_0_SELF_END_STUCT=5' TCACCCAC-TGCTTTCAATCATGTGGGTGA 3'\n   |||||||| || ||  || || ||||||||\n3' AGTGGGTGTACTAACTTTCGT-CACCCACT 5'\n
PRIMER_RIGHT_0_SELF_END_STUCT=5' TAAGGATTTGACTACCAGTCCACTTTAAG 3'\n                         ||| |||\n                      3' GAATTTCACCTGACCATCAGTTTAGGAAT 5'\n
PRIMER_LEFT_0_END_STABILITY=7.9000
PRIMER_RIGHT_0_END_STABILITY=6.3000
PRIMER_PAIR_0_COMPL_ANY=5.00
PRIMER_PAIR_0_COMPL_ANY_STUCT=    5' TCACCCACTGCT-TTC-AATCATGTGGGTGA 3'\n             |||| |  || |||| |\n3' GAATTTCACCTGACCATCAGTTTAGGAAT 5'\n
PRIMER_PAIR_0_COMPL_END=0.00
PRIMER_PAIR_0_PRODUCT_SIZE=79
PRIMER_PAIR_0_PRODUCT_TM=67.4
=
SEQUENCE_ID=Overhang02
PRIMER_SECONDARY_STRUCTURE_ALIGNMENT=1
SEQUENCE_TEMPLATE=TCACCCACTGCTTTCAATCATGTGGGTGAAACGACTAAACCTTACGACTACTTAAAGTGGACTGGTAGTCAAATCCTTA
SEQUENCE_PRIMER=TCACCCACTGCTTTCAATCATGTGGGTGA
SEQUENCE_PRIMER_REVCOMP=TAAGGATTTGACTACCAGTCCACTTTAAG
P3_COMMENT=same oligos as Overhang01 but without using SEQUENCE_OVERHANG_LEFT/RIGHT
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=35.316594
PRIMER_LEFT_0_PENALTY=24.063335
PRIMER_RIGHT_0_PENALTY=11.253259
PRIMER_LEFT_0_PROBLEMS= Temperature too high; Similarity to self too high; Similary to 3' end of self too high;
PRIMER_RIGHT_0_PROBLEMS= Similary to 3' end of self too high;
PRIMER_LEFT_0_SEQUENCE=TCACCCACTGCTTTCAATCATGTGGGTGA
PRIMER_RIGHT_0_SEQUENCE=TAAGGATTTGACTACCAGTCCACTTTAAG
PRIMER_LEFT_0=0,29
PRIMER_RIGHT_0=78,29
PRIMER_LEFT_0_TM=75.063
PRIMER_RIGHT_0_TM=62.253
PRIMER_LEFT_0_GC_PERCENT=48.276
PRIMER_RIGHT_0_GC_PERCENT=37.931
PRIMER_LEFT_0_SELF_ANY=16.00
PRIMER_RIGHT_0_SELF_ANY=5.00
PRIMER_LEFT_0_SELF_ANY_STUCT=5' TCACCCAC-TGCTTTCAATCATGTGGGTGA 3'\n   |||||||| || ||  || || ||||||||\n3' AGTGGGTGTACTAACTTTCGT-CACCCACT 5'\n
PRIMER_RIGHT_0_SELF_ANY_STUCT=5' TAAGGATTTGACTACCAGTCCACTTTAAG 3'\n                         ||| |||\n                      3' GAATTTCACCTGACCATCAGTTTAGGAAT 5'\n
PRIMER_LEFT_0_SELF_END=16.00
PRIMER_RIGHT_0_SELF_END=5.00
PRIMER_LEFT_0_SELF_END_STUCT=5' TCACCCAC-TGCTTTCAATCATGTGGGTGA 3'\n   |||||||| || ||  || || ||||||||\n3' AGTGGGTGTACTAACTTTCGT-CACCCACT 5'\n
PRIMER_RIGHT_0_SELF_END_STUCT=5' TAAGGATTTGACTACCAGTCCACTTTAAG 3'\n                         ||| |||\n                      3' GAATTTCACCTGACCATCAGTTTAGGAAT 5'\n
PRIMER_LEFT_0_END_STABILITY=7.9000
PRIMER_RIGHT_0_END_STABILITY=6.3000
PRIMER_PAIR_0_COMPL_ANY=5.00
PRIMER_PAIR_0_COMPL_ANY_STUCT=    5' TCACCCACTGCT-TTC-AATCATGTGGGTGA 3'\n             |||| |  || |||| |\n3' GAATTTCACCTGACCATCAGTTTAGGAAT 5'\n
PRIMER_PAIR_0_COMPL_END=0.00
PRIMER_PAIR_0_PRODUCT_SIZE=79
PRIMER_PAIR_0_PRODUCT_TM=69.4
=
SEQUENCE_ID=Overhang03
PRIMER_SECONDARY_STRUCTURE_ALIGNMENT=0
SEQUENCE_TEMPLATE=GACATACGATACTTTGCTTTCAATCATGTGGGTGAAACGACTAAACCTTACGACTACTTAAAGTGGACTGGTAGTCTTTTTAAAGGTAC
SEQUENCE_PRIMER=TGCTTTCAATCATGTGGGTGA
SEQUENCE_OVERHANG_LEFT=TCACCCAC
SEQUENCE_PRIMER_REVCOMP=GACTACCAGTCCACTTTAAG
SEQUENCE_OVERHANG_RIGHT=TAAGGATTT
P3_COMMENT=same as Overhang01 but with PRIMER_SECONDARY_STRUCTURE_ALIGNMENT=0
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=14.515061
PRIMER_LEFT_0_PENALTY=3.431046
PRIMER_RIGHT_0_PENALTY=11.084015
PRIMER_LEFT_0_PROBLEMS= Similarity to self too high; Similary to 3' end of self too high;
PRIMER_RIGHT_0_PROBLEMS= Temperature too low; Similary to 3' end of self too high;
PRIMER_LEFT_0_SEQUENCE=TCACCCACTGCTTTCAATCATGTGGGTGA
PRIMER_RIGHT_0_SEQUENCE=TAAGGATTTGACTACCAGTCCACTTTAAG
PRIMER_LEFT_0=14,21
PRIMER_RIGHT_0=75,20
PRIMER_LEFT_0_TM=62.431
PRIMER_RIGHT_0_TM=48.916
PRIMER_LEFT_0_GC_PERCENT=42.857
PRIMER_RIGHT_0_GC_PERCENT=45.000
PRIMER_LEFT_0_SELF_ANY=16.00
PRIMER_RIGHT_0_SELF_ANY=5.00
PRIMER_LEFT_0_SELF_END=16.00
PRIMER_RIGHT_0_SELF_END=5.00
PRIMER_LEFT_0_END_STABILITY=7.9000
PRIMER_RIGHT_0_END_STABILITY=6.3000
PRIMER_PAIR_0_COMPL_ANY=5.00
PRIMER_PAIR_0_COMPL_END=0.00
PRIMER_PAIR_0_PRODUCT_SIZE=79
PRIMER_PAIR_0_PRODUCT_TM=67.4
=
SEQUENCE_ID=Overhang04
PRIMER_SECONDARY_STRUCTURE_ALIGNMENT=0
SEQUENCE_TEMPLATE=TCACCCACTGCTTTCAATCATGTGGGTGAAACGACTAAACCTTACGACTACTTAAAGTGGACTGGTAGTCAAATCCTTA
SEQUENCE_PRIMER=TCACCCACTGCTTTCAATCATGTGGGTGA
SEQUENCE_PRIMER_REVCOMP=TAAGGATTTGACTACCAGTCCACTTTAAG
P3_COMMENT=same as Overhang02 but with PRIMER_SECONDARY_STRUCTURE_ALIGNMENT=0
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=35.316594
PRIMER_LEFT_0_PENALTY=24.063335
PRIMER_RIGHT_0_PENALTY=11.253259
PRIMER_LEFT_0_PROBLEMS= Temperature too high; Similarity to self too high; Similary to 3' end of self too high;
PRIMER_RIGHT_0_PROBLEMS= Similary to 3' end of self too high;
PRIMER_LEFT_0_SEQUENCE=TCACCCACTGCTTTCAATCATGTGGGTGA
PRIMER_RIGHT_0_SEQUENCE=TAAGGATTTGACTACCAGTCCACTTTAAG
PRIMER_LEFT_0=0,29
PRIMER_RIGHT_0=78,29
PRIMER_LEFT_0_TM=75.063
PRIMER_RIGHT_0_TM=62.253
PRIMER_LEFT_0_GC_PERCENT=48.276
PRIMER_RIGHT_0_GC_PERCENT=37.931
PRIMER_LEFT_0_SELF_ANY=16.00
PRIMER_RIGHT_0_SELF_ANY=5.00
PRIMER_LEFT_0_SELF_END=16.00
PRIMER_RIGHT_0_SELF_END=5.00
PRIMER_LEFT_0_END_STABILITY=7.9000
PRIMER_RIGHT_0_END_STABILITY=6.3000
PRIMER_PAIR_0_COMPL_ANY=5.00
PRIMER_PAIR_0_COMPL_END=0.00
PRIMER_PAIR_0_PRODUCT_SIZE=79
PRIMER_PAIR_0_PRODUCT_TM=69.4
=
SEQUENCE_ID=Overhang05
PRIMER_SECONDARY_STRUCTURE_ALIGNMENT=1
SEQUENCE_TEMPLATE=GGACGTCAGCGGGTGACGTCCCCCCTTGTAAGATACGCGGGTGACGACCCCCATCAACAATCAATCGTTTATAATCCTTATTTCTGACAGGCTGAAGGACTCAGGACTCCCCATAAGAAATTGTTCGGGGGACGTCACCACTCAGTGAGA
SEQUENCE_PRIMER=GCGGGTGACGTCCCCC
SEQUENCE_OVERHANG_LEFT=GGACGTCA
SEQUENCE_PRIMER_REVCOMP=GAACAATTTCTTATGGGG
SEQUENCE_OVERHANG_RIGHT=GGTGACGTCCCCC
PRIMER_PRODUCT_SIZE_RANGE=70-1000
P3_COMMENT=overhangs and full oligos have hairpins and complementary regions
PRIMER_PAIR_EXPLAIN=considered 1, high any compl 1, high end compl 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=21.987458
PRIMER_LEFT_0_PENALTY=10.206349
PRIMER_RIGHT_0_PENALTY=11.781109
PRIMER_LEFT_0_PROBLEMS= GC content too high; Temperature too high; Similarity to self too high; Similary to 3' end of self too high;
PRIMER_RIGHT_0_PROBLEMS= Temperature too low; Similarity to self too high; Similary to 3' end of self too high;
PRIMER_LEFT_0_SEQUENCE=GGACGTCAGCGGGTGACGTCCCCC
PRIMER_RIGHT_0_SEQUENCE=GGTGACGTCCCCCGAACAATTTCTTATGGGG
PRIMER_LEFT_0=8,16
PRIMER_RIGHT_0=125,18
PRIMER_LEFT_0_TM=66.206
PRIMER_RIGHT_0_TM=50.219
PRIMER_LEFT_0_GC_PERCENT=81.250
PRIMER_RIGHT_0_GC_PERCENT=38.889
PRIMER_LEFT_0_SELF_ANY=15.00
PRIMER_RIGHT_0_SELF_ANY=9.00
PRIMER_LEFT_0_SELF_ANY_STUCT=   5' GGACGTCAGCGGGTGACGTCCCCC 3'\n      |||||||| | | ||||||||\n3' CCCCCTGCAGTGGGCGACTGCAGG 5'\n
PRIMER_RIGHT_0_SELF_ANY_STUCT=5' GGTGACGTCCCCCGAACAATTTCTTATGGGG 3'\n           ||||  || || || ||  ||||\n        3' GGGGTATTCTTTAACAAGCCCCCTGCAGTGG 5'\n
PRIMER_LEFT_0_SELF_END=10.00
PRIMER_RIGHT_0_SELF_END=9.00
PRIMER_LEFT_0_SELF_END_STUCT=5' GGACGTCAGCGGGTGACGTCCCCC 3'\n             ||| |||||| |||\n          3' CCCCCTGCAGTGGGCGACTGCAGG 5'\n
PRIMER_RIGHT_0_SELF_END_STUCT=5' GGTGACGTCCCCCGAACAATTTCTTATGGGG 3'\n           ||||  || || || ||  ||||\n        3' GGGGTATTCTTTAACAAGCCCCCTGCAGTGG 5'\n
PRIMER_LEFT_0_END_STABILITY=12.4000
PRIMER_RIGHT_0_END_STABILITY=11.2000
PRIMER_PAIR_0_COMPL_ANY=10.00
PRIMER_PAIR_0_COMPL_ANY_STUCT=        5' GGACGTCAGCGGGTGACGTCCCCC 3'\n           | |  |   |||| |||||| ||\n3' GGGGTATTCTTTAACAAGCCCCCTGCAGTGG 5'\n
PRIMER_PAIR_0_COMPL_END=5.00
PRIMER_PAIR_0_COMPL_END_STUCT=        5' GGACGTCAGCGGGTGACGTCCCCC 3'\n           | |  |   |||| ||||| | ||\n3' GGGGTATTCTTTAACAAGCCCCCTGCA-GTGG 5'\n
PRIMER_PAIR_0_PRODUCT_SIZE=139
PRIMER_PAIR_0_PRODUCT_TM=75.0
=
SEQUENCE_ID=Overhang06
PRIMER_SECONDARY_STRUCTURE_ALIGNMENT=1
SEQUENCE_TEMPLATE=GGACGTCAGCGGGTGACGTCCCCCCTTGTAAGATACGCGGGTGACGACCCCCATCAACAATCAATCGTTTATAATCCTTATTTCTGACAGGCTGAAGGACTCAGGACTCCCCATAAGAAATTGTTCGGGGGACGTCACCACTCAGTGAGA
SEQUENCE_PRIMER=GGACGTCAGCGGGTGACGTCCCCC
SEQUENCE_PRIMER_REVCOMP=GGTGACGTCCCCCGAACAATTTCTTATGGGG
P3_COMMENT=same oligos as Overhang05 but without using SEQUENCE_OVERHANG_LEFT/RIGHT
PRIMER_PAIR_EXPLAIN=considered 1, high any compl 1, high end compl 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=51.193458
PRIMER_LEFT_0_PENALTY=22.773827
PRIMER_RIGHT_0_PENALTY=28.419631
PRIMER_LEFT_0_PROBLEMS= Temperature too high; Similarity to self too high; Similary to 3' end of self too high;
PRIMER_RIGHT_0_PROBLEMS= Temperature too high; Similarity to self too high; Similary to 3' end of self too high;
PRIMER_LEFT_0_SEQUENCE=GGACGTCAGCGGGTGACGTCCCCC
PRIMER_RIGHT_0_SEQUENCE=GGTGACGTCCCCCGAACAATTTCTTATGGGG
PRIMER_LEFT_0=0,24
PRIMER_RIGHT_0=138,31
PRIMER_LEFT_0_TM=78.774
PRIMER_RIGHT_0_TM=77.420
PRIMER_LEFT_0_GC_PERCENT=75.000
PRIMER_RIGHT_0_GC_PERCENT=54.839
PRIMER_LEFT_0_SELF_ANY=15.00
PRIMER_RIGHT_0_SELF_ANY=9.00
PRIMER_LEFT_0_SELF_ANY_STUCT=   5' GGACGTCAGCGGGTGACGTCCCCC 3'\n      |||||||| | | ||||||||\n3' CCCCCTGCAGTGGGCGACTGCAGG 5'\n
PRIMER_RIGHT_0_SELF_ANY_STUCT=5' GGTGACGTCCCCCGAACAATTTCTTATGGGG 3'\n           ||||  || || || ||  ||||\n        3' GGGGTATTCTTTAACAAGCCCCCTGCAGTGG 5'\n
PRIMER_LEFT_0_SELF_END=10.00
PRIMER_RIGHT_0_SELF_END=9.00
PRIMER_LEFT_0_SELF_END_STUCT=5' GGACGTCAGCGGGTGACGTCCCCC 3'\n             ||| |||||| |||\n          3' CCCCCTGCAGTGGGCGACTGCAGG 5'\n
PRIMER_RIGHT_0_SELF_END_STUCT=5' GGTGACGTCCCCCGAACAATTTCTTATGGGG 3'\n           ||||  || || || ||  ||||\n        3' GGGGTATTCTTTAACAAGCCCCCTGCAGTGG 5'\n
PRIMER_LEFT_0_END_STABILITY=12.4000
PRIMER_RIGHT_0_END_STABILITY=11.2000
PRIMER_PAIR_0_COMPL_ANY=10.00
PRIMER_PAIR_0_COMPL_ANY_STUCT=        5' GGACGTCAGCGGGTGACGTCCCCC 3'\n           | |  |   |||| |||||| ||\n3' GGGGTATTCTTTAACAAGCCCCCTGCAGTGG 5'\n
PRIMER_PAIR_0_COMPL_END=5.00
PRIMER_PAIR_0_COMPL_END_STUCT=        5' GGACGTCAGCGGGTGACGTCCCCC 3'\n           | |  |   |||| ||||| | ||\n3' GGGGTATTCTTTAACAAGCCCCCTGCA-GTGG 5'\n
PRIMER_PAIR_0_PRODUCT_SIZE=139
PRIMER_PAIR_0_PRODUCT_TM=77.1
=
SEQUENCE_ID=Overhang07
PRIMER_SECONDARY_STRUCTURE_ALIGNMENT=0
SEQUENCE_TEMPLATE=GGACGTCAGCGGGTGACGTCCCCCCTTGTAAGATACGCGGGTGACGACCCCCATCAACAATCAATCGTTTATAATCCTTATTTCTGACAGGCTGAAGGACTCAGGACTCCCCATAAGAAATTGTTCGGGGGACGTCACCACTCAGTGAGA
SEQUENCE_PRIMER=GCGGGTGACGTCCCCC
SEQUENCE_OVERHANG_LEFT=GGACGTCA
SEQUENCE_PRIMER_REVCOMP=GAACAATTTCTTATGGGG
SEQUENCE_OVERHANG_RIGHT=GGTGACGTCCCCC
P3_COMMENT=same as Overhang05 but with PRIMER_SECONDARY_STRUCTURE_ALIGNMENT=0
PRIMER_PAIR_EXPLAIN=considered 1, high any compl 1, high end compl 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=21.987458
PRIMER_LEFT_0_PENALTY=10.206349
PRIMER_RIGHT_0_PENALTY=11.781109
PRIMER_LEFT_0_PROBLEMS= GC content too high; Temperature too high; Similarity to self too high; Similary to 3' end of self too high;
PRIMER_RIGHT_0_PROBLEMS= Temperature too low; Similarity to self too high; Similary to 3' end of self too high;
PRIMER_LEFT_0_SEQUENCE=GGACGTCAGCGGGTGACGTCCCCC
PRIMER_RIGHT_0_SEQUENCE=GGTGACGTCCCCCGAACAATTTCTTATGGGG
PRIMER_LEFT_0=8,16
PRIMER_RIGHT_0=125,18
PRIMER_LEFT_0_TM=66.206
PRIMER_RIGHT_0_TM=50.219
PRIMER_LEFT_0_GC_PERCENT=81.250
PRIMER_RIGHT_0_GC_PERCENT=38.889
PRIMER_LEFT_0_SELF_ANY=15.00
PRIMER_RIGHT_0_SELF_ANY=9.00
PRIMER_LEFT_0_SELF_END=10.00
PRIMER_RIGHT_0_SELF_END=9.00
PRIMER_LEFT_0_END_STABILITY=12.4000
PRIMER_RIGHT_0_END_STABILITY=11.2000
PRIMER_PAIR_0_COMPL_ANY=10.00
PRIMER_PAIR_0_COMPL_END=5.00
PRIMER_PAIR_0_PRODUCT_SIZE=139
PRIMER_PAIR_0_PRODUCT_TM=75.0
=
SEQUENCE_ID=Overhang08
PRIMER_SECONDARY_STRUCTURE_ALIGNMENT=0
SEQUENCE_TEMPLATE=GGACGTCAGCGGGTGACGTCCCCCCTTGTAAGATACGCGGGTGACGACCCCCATCAACAATCAATCGTTTATAATCCTTATTTCTGACAGGCTGAAGGACTCAGGACTCCCCATAAGAAATTGTTCGGGGGACGTCACCACTCAGTGAGA
SEQUENCE_PRIMER=GGACGTCAGCGGGTGACGTCCCCC
SEQUENCE_PRIMER_REVCOMP=GGTGACGTCCCCCGAACAATTTCTTATGGGG
P3_COMMENT=same oligos as Overhang07 but without using SEQUENCE_OVERHANG_LEFT/RIGHT
PRIMER_PAIR_EXPLAIN=considered 1, high any compl 1, high end compl 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=51.193458
PRIMER_LEFT_0_PENALTY=22.773827
PRIMER_RIGHT_0_PENALTY=28.419631
PRIMER_LEFT_0_PROBLEMS= Temperature too high; Similarity to self too high; Similary to 3' end of self too high;
PRIMER_RIGHT_0_PROBLEMS= Temperature too high; Similarity to self too high; Similary to 3' end of self too high;
PRIMER_LEFT_0_SEQUENCE=GGACGTCAGCGGGTGACGTCCCCC
PRIMER_RIGHT_0_SEQUENCE=GGTGACGTCCCCCGAACAATTTCTTATGGGG
PRIMER_LEFT_0=0,24
PRIMER_RIGHT_0=138,31
PRIMER_LEFT_0_TM=78.774
PRIMER_RIGHT_0_TM=77.420
PRIMER_LEFT_0_GC_PERCENT=75.000
PRIMER_RIGHT_0_GC_PERCENT=54.839
PRIMER_LEFT_0_SELF_ANY=15.00
PRIMER_RIGHT_0_SELF_ANY=9.00
PRIMER_LEFT_0_SELF_END=10.00
PRIMER_RIGHT_0_SELF_END=9.00
PRIMER_LEFT_0_END_STABILITY=12.4000
PRIMER_RIGHT_0_END_STABILITY=11.2000
PRIMER_PAIR_0_COMPL_ANY=10.00
PRIMER_PAIR_0_COMPL_END=5.00
PRIMER_PAIR_0_PRODUCT_SIZE=139
PRIMER_PAIR_0_PRODUCT_TM=77.1
=
PRIMER_LIBERAL_BASE=0
SEQUENCE_ID=Overhang09
SEQUENCE_TEMPLATE=TGCTTTCAATCATGTGGGTGATTTTATAGATTGTCATCACCATAGTAACTGTTTTAACTCACGTCCCCTGTGTGAGAACGCCATGGGCTGTCGGGCTTCGCCAACTTGCTCTCATTTCTA
SEQUENCE_PRIMER=TGCTTTCAATCATGTGGGTGA
SEQUENCE_PRIMER_REVCOMP=ATGAGAGCAAGTTGGCGAAG
SEQUENCE_OVERHANG_LEFT=Z
SEQUENCE_OVERHANG_RIGHT=ATCAG
P3_COMMENT=non-ACGT base in left overhang with PRIMER_LIBERAL_BASE=0
PRIMER_ERROR=Unrecognized base in left overhang
=
SEQUENCE_ID=Overhang10
SEQUENCE_TEMPLATE=TGCTTTCAATCATGTGGGTGATTTTATAGATTGTCATCACCATAGTAACTGTTTTAACTCACGTCCCCTGTGTGAGAACGCCATGGGCTGTCGGGCTTCGCCAACTTGCTCTCATTTCTA
SEQUENCE_PRIMER=TGCTTTCAATCATGTGGGTGA
SEQUENCE_PRIMER_REVCOMP=ATGAGAGCAAGTTGGCGAAG
SEQUENCE_OVERHANG_LEFT=GGCATGCA
SEQUENCE_OVERHANG_RIGHT=Z
P3_COMMENT=non-ACGT base in right overhang with PRIMER_LIBERAL_BASE=0
PRIMER_ERROR=Unrecognized base in right overhang
=
SEQUENCE_ID=Overhang11
SEQUENCE_TEMPLATE=TGCTTTCAATCATGTGGGTGATTTTATAGATTGTCATCACCATAGTAACTGTTTTAACTCACGTCCCCTGTGTGAGAACGCCATGGGCTGTCGGGCTTCGCCAACTTGCTCTCATTTCTA
SEQUENCE_PRIMER=TGCTTTCAATCATGTGGGTGA
SEQUENCE_PRIMER_REVCOMP=ATGAGAGCAAGTTGGCGAAG
SEQUENCE_OVERHANG_RIGHT= C G T C
P3_COMMENT=spaces in right overhang with PRIMER_LIBERAL_BASE=0
PRIMER_ERROR=Unrecognized base in right overhang
=
SEQUENCE_ID=Overhang12
SEQUENCE_TEMPLATE=TGCTTTCAATCATGTGGGTGATTTTATAGATTGTCATCACCATAGTAACTGTTTTAACTCACGTCCCCTGTGTGAGAACGCCATGGGCTGTCGGGCTTCGCCAACTTGCTCTCATTTCTA
SEQUENCE_PRIMER=TGCTTTCAATCATGTGGGTGA
SEQUENCE_PRIMER_REVCOMP=ATGAGAGCAAGTTGGCGAAG
SEQUENCE_OVERHANG_LEFT= A T C G
P3_COMMENT=spaces in left overhang with PRIMER_LIBERAL_BASE=0
PRIMER_ERROR=Unrecognized base in left overhang
=
SEQUENCE_ID=Overhang13
SEQUENCE_TEMPLATE=TGCTTTCAATCATGTGGGTGATTTTATAGATTGTCATCACCATAGTAACTGTTTTAACTCACGTCCCCTGTGTGAGAACGCCATGGGCTGTCGGGCTTCGCCAACTTGCTCTCATTTCTA
SEQUENCE_PRIMER=TGCTTTCAATCATGTGGGTGA
SEQUENCE_PRIMER_REVCOMP=ATGAGAGCAAGTTGGCGAAG
SEQUENCE_OVERHANG_LEFT=
SEQUENCE_OVERHANG_RIGHT=
P3_COMMENT=empty strings for left and right overhangs
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=3.969130
PRIMER_LEFT_0_PENALTY=3.431046
PRIMER_RIGHT_0_PENALTY=0.538083
PRIMER_LEFT_0_PROBLEMS= Similary to 3' end of self too high;
PRIMER_LEFT_0_SEQUENCE=TGCTTTCAATCATGTGGGTGA
PRIMER_RIGHT_0_SEQUENCE=ATGAGAGCAAGTTGGCGAAG
PRIMER_LEFT_0=0,21
PRIMER_RIGHT_0=114,20
PRIMER_LEFT_0_TM=62.431
PRIMER_RIGHT_0_TM=60.538
PRIMER_LEFT_0_GC_PERCENT=42.857
PRIMER_RIGHT_0_GC_PERCENT=50.000
PRIMER_LEFT_0_SELF_ANY=4.00
PRIMER_RIGHT_0_SELF_ANY=5.00
PRIMER_LEFT_0_SELF_END=4.00
PRIMER_RIGHT_0_SELF_END=2.00
PRIMER_LEFT_0_END_STABILITY=7.9000
PRIMER_RIGHT_0_END_STABILITY=8.7000
PRIMER_PAIR_0_COMPL_ANY=6.00
PRIMER_PAIR_0_COMPL_END=0.00
PRIMER_PAIR_0_PRODUCT_SIZE=115
PRIMER_PAIR_0_PRODUCT_TM=73.6
=
SEQUENCE_ID=Overhang14
PRIMER_PICK_LEFT_PRIMER=0
PRIMER_PICK_RIGHT_PRIMER=1
PRIMER_PICK_INTERNAL_OLIGO=0
PRIMER_SECONDARY_STRUCTURE_ALIGNMENT=1
SEQUENCE_PRIMER_REVCOMP=TAAGGATTTGACTACCAGTCCACTTTAAG
P3_COMMENT=calculate hairpin without using overhangs
PRIMER_LEFT_NUM_RETURNED=0
PRIMER_RIGHT_NUM_RETURNED=1
PRIMER_INTERNAL_NUM_RETURNED=0
PRIMER_PAIR_NUM_RETURNED=0
PRIMER_RIGHT_0_PENALTY=11.253259
PRIMER_RIGHT_0_PROBLEMS= Similary to 3' end of self too high;
PRIMER_RIGHT_0_SEQUENCE=TAAGGATTTGACTACCAGTCCACTTTAAG
PRIMER_RIGHT_0=929,29
PRIMER_RIGHT_0_TM=62.253
PRIMER_RIGHT_0_GC_PERCENT=37.931
PRIMER_RIGHT_0_SELF_ANY=5.00
PRIMER_RIGHT_0_SELF_ANY_STUCT=5' TAAGGATTTGACTACCAGTCCACTTTAAG 3'\n                         ||| |||\n                      3' GAATTTCACCTGACCATCAGTTTAGGAAT 5'\n
PRIMER_RIGHT_0_SELF_END=5.00
PRIMER_RIGHT_0_SELF_END_STUCT=5' TAAGGATTTGACTACCAGTCCACTTTAAG 3'\n                         ||| |||\n                      3' GAATTTCACCTGACCATCAGTTTAGGAAT 5'\n
PRIMER_RIGHT_0_END_STABILITY=6.3000
=
SEQUENCE_ID=Overhang15
PRIMER_PICK_LEFT_PRIMER=0
PRIMER_PICK_RIGHT_PRIMER=1
PRIMER_PICK_INTERNAL_OLIGO=0
PRIMER_SECONDARY_STRUCTURE_ALIGNMENT=1
SEQUENCE_PRIMER_REVCOMP=GACTACCAGTCCACTTTAAG
SEQUENCE_OVERHANG_RIGHT=TAAGGATTT
P3_COMMENT=check hairpin calculation with overhang right - same oligo as Overhang14
PRIMER_LEFT_NUM_RETURNED=0
PRIMER_RIGHT_NUM_RETURNED=1
PRIMER_INTERNAL_NUM_RETURNED=0
PRIMER_PAIR_NUM_RETURNED=0
PRIMER_RIGHT_0_PENALTY=11.084015
PRIMER_RIGHT_0_PROBLEMS= Temperature too low; Similary to 3' end of self too high;
PRIMER_RIGHT_0_SEQUENCE=TAAGGATTTGACTACCAGTCCACTTTAAG
PRIMER_RIGHT_0=929,20
PRIMER_RIGHT_0_TM=48.916
PRIMER_RIGHT_0_GC_PERCENT=45.000
PRIMER_RIGHT_0_SELF_ANY=5.00
PRIMER_RIGHT_0_SELF_ANY_STUCT=5' TAAGGATTTGACTACCAGTCCACTTTAAG 3'\n                         ||| |||\n                      3' GAATTTCACCTGACCATCAGTTTAGGAAT 5'\n
PRIMER_RIGHT_0_SELF_END=5.00
PRIMER_RIGHT_0_SELF_END_STUCT=5' TAAGGATTTGACTACCAGTCCACTTTAAG 3'\n                         ||| |||\n                      3' GAATTTCACCTGACCATCAGTTTAGGAAT 5'\n
PRIMER_RIGHT_0_END_STABILITY=6.3000
=
SEQUENCE_ID=Overhang16
PRIMER_PICK_LEFT_PRIMER=0
PRIMER_PICK_RIGHT_PRIMER=1
PRIMER_PICK_INTERNAL_OLIGO=0
PRIMER_SECONDARY_STRUCTURE_ALIGNMENT=0
SEQUENCE_PRIMER_REVCOMP=GACTACCAGTCCACTTTAAG
SEQUENCE_OVERHANG_RIGHT=TAAGGATTT
P3_COMMENT=same as Overhang15 but with PRIMER_SECONDARY_STRUCTURE_ALIGNMENT=0
PRIMER_LEFT_NUM_RETURNED=0
PRIMER_RIGHT_NUM_RETURNED=1
PRIMER_INTERNAL_NUM_RETURNED=0
PRIMER_PAIR_NUM_RETURNED=0
PRIMER_RIGHT_0_PENALTY=11.084015
PRIMER_RIGHT_0_PROBLEMS= Temperature too low; Similary to 3' end of self too high;
PRIMER_RIGHT_0_SEQUENCE=TAAGGATTTGACTACCAGTCCACTTTAAG
PRIMER_RIGHT_0=929,20
PRIMER_RIGHT_0_TM=48.916
PRIMER_RIGHT_0_GC_PERCENT=45.000
PRIMER_RIGHT_0_SELF_ANY=5.00
PRIMER_RIGHT_0_SELF_END=5.00
PRIMER_RIGHT_0_END_STABILITY=6.3000
=
SEQUENCE_ID=Overhang17
PRIMER_LIBERAL_BASE=1
PRIMER_PICK_LEFT_PRIMER=1
PRIMER_PICK_RIGHT_PRIMER=1
PRIMER_PICK_INTERNAL_OLIGO=0
SEQUENCE_TEMPLATE=TGCTTTCAATCATGTGGGTGATTTTATAGATTGTCATCACCATAGTAACTGTTTTAACTCACGTCCCCTGTGTGAGAACGCCATGGGCTGTCGGGCTTCGCCAACTTGCTCTCATTTCTA
SEQUENCE_PRIMER=TGCTTTCAATCATGTGGGTGA
SEQUENCE_PRIMER_REVCOMP=ATGAGAGCAAGTTGGCGAAG
SEQUENCE_OVERHANG_LEFT=ATZZCG
SEQUENCE_OVERHANG_RIGHT=ATZZCC
P3_COMMENT=PRIMER_LIBERAL_BASE=1 with overhangs containing non-ACGT base pairs
PRIMER_ERROR=Unrecognized base in left overhang
=
SEQUENCE_ID=Overhang18
PRIMER_TASK=generic
PRIMER_NUM_RETURN=3
PRIMER_LIBERAL_BASE=0
PRIMER_PICK_LEFT_PRIMER=1
PRIMER_PICK_RIGHT_PRIMER=1
PRIMER_PICK_INTERNAL_OLIGO=1
SEQUENCE_TEMPLATE=TGCTTTCAATCATGTGGGTGATTTTATAGATTGTCATCACCATAGTAACTGTTTTAACTCACGTCCCCTGTGTGAGAACGCCATGGGCTGTCGGGCTTCGCCAACTTGCTCTCATTTCTA
SEQUENCE_OVERHANG_LEFT=ATG
SEQUENCE_OVERHANG_RIGHT=TAA
P3_COMMENT=PRIMER_TASK=generic with overhangs
PRIMER_LEFT_EXPLAIN=considered 1122, GC content failed 7, low tm 551, high tm 316, high end compl 1, ok 247
PRIMER_RIGHT_EXPLAIN=considered 1122, low tm 145, high tm 842, high end compl 2, ok 133
PRIMER_INTERNAL_EXPLAIN=considered 985, low tm 364, high tm 423, ok 198
PRIMER_PAIR_EXPLAIN=considered 5, unacceptable product size 1, ok 4
PRIMER_LEFT_NUM_RETURNED=3
PRIMER_RIGHT_NUM_RETURNED=3
PRIMER_INTERNAL_NUM_RETURNED=3
PRIMER_PAIR_NUM_RETURNED=3
PRIMER_PAIR_0_PENALTY=1.054801
PRIMER_LEFT_0_PENALTY=0.516718
PRIMER_RIGHT_0_PENALTY=0.538083
PRIMER_INTERNAL_0_PENALTY=0.409199
PRIMER_LEFT_0_SEQUENCE=ATGTGCTTTCAATCATGTGGGTG
PRIMER_RIGHT_0_SEQUENCE=TAAATGAGAGCAAGTTGGCGAAG
PRIMER_INTERNAL_0_SEQUENCE=TAACTCACGTCCCCTGTGTG
PRIMER_LEFT_0=0,20
PRIMER_RIGHT_0=114,20
PRIMER_INTERNAL_0=54,20
PRIMER_LEFT_0_TM=60.517
PRIMER_RIGHT_0_TM=60.538
PRIMER_INTERNAL_0_TM=59.591
PRIMER_LEFT_0_GC_PERCENT=45.000
PRIMER_RIGHT_0_GC_PERCENT=50.000
PRIMER_INTERNAL_0_GC_PERCENT=55.000
PRIMER_LEFT_0_SELF_ANY=4.00
PRIMER_RIGHT_0_SELF_ANY=5.00
PRIMER_INTERNAL_0_SELF_ANY=4.00
PRIMER_LEFT_0_SELF_END=2.00
PRIMER_RIGHT_0_SELF_END=2.00
PRIMER_INTERNAL_0_SELF_END=1.00
PRIMER_LEFT_0_END_STABILITY=9.4000
PRIMER_RIGHT_0_END_STABILITY=8.7000
PRIMER_PAIR_0_COMPL_ANY=6.00
PRIMER_PAIR_0_COMPL_END=0.00
PRIMER_PAIR_0_PRODUCT_SIZE=121
PRIMER_PAIR_0_PRODUCT_TM=73.6
PRIMER_PAIR_1_PENALTY=1.430962
PRIMER_LEFT_1_PENALTY=0.516718
PRIMER_RIGHT_1_PENALTY=0.914244
PRIMER_INTERNAL_1_PENALTY=0.409199
PRIMER_LEFT_1_SEQUENCE=ATGTGCTTTCAATCATGTGGGTG
PRIMER_RIGHT_1_SEQUENCE=TAAAAATGAGAGCAAGTTGGCGA
PRIMER_INTERNAL_1_SEQUENCE=TAACTCACGTCCCCTGTGTG
PRIMER_LEFT_1=0,20
PRIMER_RIGHT_1=116,20
PRIMER_INTERNAL_1=54,20
PRIMER_LEFT_1_TM=60.517
PRIMER_RIGHT_1_TM=60.914
PRIMER_INTERNAL_1_TM=59.591
PRIMER_LEFT_1_GC_PERCENT=45.000
PRIMER_RIGHT_1_GC_PERCENT=45.000
PRIMER_INTERNAL_1_GC_PERCENT=55.000
PRIMER_LEFT_1_SELF_ANY=4.00
PRIMER_RIGHT_1_SELF_ANY=5.00
PRIMER_INTERNAL_1_SELF_ANY=4.00
PRIMER_LEFT_1_SELF_END=2.00
PRIMER_RIGHT_1_SELF_END=2.00
PRIMER_INTERNAL_1_SELF_END=1.00
PRIMER_LEFT_1_END_STABILITY=9.4000
PRIMER_RIGHT_1_END_STABILITY=11.4000
PRIMER_PAIR_1_COMPL_ANY=6.00
PRIMER_PAIR_1_COMPL_END=0.00
PRIMER_PAIR_1_PRODUCT_SIZE=123
PRIMER_PAIR_1_PRODUCT_TM=73.3
PRIMER_PAIR_2_PENALTY=1.430962
PRIMER_LEFT_2_PENALTY=0.516718
PRIMER_RIGHT_2_PENALTY=0.914244
PRIMER_INTERNAL_2_PENALTY=0.409199
PRIMER_LEFT_2_SEQUENCE=ATGTGCTTTCAATCATGTGGGTG
PRIMER_RIGHT_2_SEQUENCE=TAAGAAATGAGAGCAAGTTGGCG
PRIMER_INTERNAL_2_SEQUENCE=TAACTCACGTCCCCTGTGTG
PRIMER_LEFT_2=0,20
PRIMER_RIGHT_2=117,20
PRIMER_INTERNAL_2=54,20
PRIMER_LEFT_2_TM=60.517
PRIMER_RIGHT_2_TM=60.914
PRIMER_INTERNAL_2_TM=59.591
PRIMER_LEFT_2_GC_PERCENT=45.000
PRIMER_RIGHT_2_GC_PERCENT=50.000
PRIMER_INTERNAL_2_GC_PERCENT=55.000
PRIMER_LEFT_2_SELF_ANY=4.00
PRIMER_RIGHT_2_SELF_ANY=5.00
PRIMER_INTERNAL_2_SELF_ANY=4.00
PRIMER_LEFT_2_SELF_END=2.00
PRIMER_RIGHT_2_SELF_END=2.00
PRIMER_INTERNAL_2_SELF_END=1.00
PRIMER_LEFT_2_END_STABILITY=9.4000
PRIMER_RIGHT_2_END_STABILITY=11.7000
PRIMER_PAIR_2_COMPL_ANY=6.00
PRIMER_PAIR_2_COMPL_END=0.00
PRIMER_PAIR_2_PRODUCT_SIZE=124
PRIMER_PAIR_2_PRODUCT_TM=73.6
=
SEQUENCE_ID=Overhang19
PRIMER_TASK=pick_primer_list
PRIMER_PICK_LEFT_PRIMER=1
PRIMER_PICK_RIGHT_PRIMER=1
PRIMER_PICK_INTERNAL_OLIGO=0
SEQUENCE_TEMPLATE=TGCTTTCAATCATGTGGGTGATTTTATAGATTGTCATCACCATAGTAACTGTTTTAACTCACGTCCCCTGTGTGAGAACGCCATGGGCTGTCGGGCTTCGCCAACTTGCTCTCATTTCTA
SEQUENCE_OVERHANG_LEFT=ATCCC
SEQUENCE_OVERHANG_RIGHT=ATTAGTC
P3_COMMENT=PRIMER_TASK=pick_primer_list with overhangs
PRIMER_LEFT_EXPLAIN=considered 2093, GC content failed 7, low tm 711, high tm 1015, high any compl 5, high end compl 104, ok 251
PRIMER_RIGHT_EXPLAIN=considered 1982, GC content failed 7, low tm 711, high tm 959, high any compl 22, high end compl 93, ok 190
PRIMER_PAIR_EXPLAIN=considered 0, ok 0
PRIMER_LEFT_NUM_RETURNED=3
PRIMER_RIGHT_NUM_RETURNED=3
PRIMER_INTERNAL_NUM_RETURNED=0
PRIMER_PAIR_NUM_RETURNED=0
PRIMER_LEFT_0_PENALTY=0.409199
PRIMER_RIGHT_0_PENALTY=0.409199
PRIMER_LEFT_0_SEQUENCE=ATCCCTAACTCACGTCCCCTGTGTG
PRIMER_RIGHT_0_SEQUENCE=ATTAGTCCACACAGGGGACGTGAGTTA
PRIMER_LEFT_0=54,20
PRIMER_RIGHT_0=73,20
PRIMER_LEFT_0_TM=59.591
PRIMER_RIGHT_0_TM=59.591
PRIMER_LEFT_0_GC_PERCENT=55.000
PRIMER_RIGHT_0_GC_PERCENT=55.000
PRIMER_LEFT_0_SELF_ANY=4.00
PRIMER_RIGHT_0_SELF_ANY=5.00
PRIMER_LEFT_0_SELF_END=1.00
PRIMER_RIGHT_0_SELF_END=2.00
PRIMER_LEFT_0_END_STABILITY=6.4000
PRIMER_RIGHT_0_END_STABILITY=5.7000
PRIMER_LEFT_1_PENALTY=0.516718
PRIMER_RIGHT_1_PENALTY=0.498267
PRIMER_LEFT_1_SEQUENCE=ATCCCTGCTTTCAATCATGTGGGTG
PRIMER_RIGHT_1_SEQUENCE=ATTAGTCTCACCCACATGATTGAAAGC
PRIMER_LEFT_1=0,20
PRIMER_RIGHT_1=20,20
PRIMER_LEFT_1_TM=60.517
PRIMER_RIGHT_1_TM=59.502
PRIMER_LEFT_1_GC_PERCENT=45.000
PRIMER_RIGHT_1_GC_PERCENT=45.000
PRIMER_LEFT_1_SELF_ANY=4.00
PRIMER_RIGHT_1_SELF_ANY=4.00
PRIMER_LEFT_1_SELF_END=2.00
PRIMER_RIGHT_1_SELF_END=2.00
PRIMER_LEFT_1_END_STABILITY=9.4000
PRIMER_RIGHT_1_END_STABILITY=8.5000
PRIMER_LEFT_2_PENALTY=0.538083
PRIMER_RIGHT_2_PENALTY=0.538083
PRIMER_LEFT_2_SEQUENCE=ATCCCCTTCGCCAACTTGCTCTCAT
PRIMER_RIGHT_2_SEQUENCE=ATTAGTCATGAGAGCAAGTTGGCGAAG
PRIMER_LEFT_2=95,20
PRIMER_RIGHT_2=114,20
PRIMER_LEFT_2_TM=60.538
PRIMER_RIGHT_2_TM=60.538
PRIMER_LEFT_2_GC_PERCENT=50.000
PRIMER_RIGHT_2_GC_PERCENT=50.000
PRIMER_LEFT_2_SELF_ANY=5.00
PRIMER_RIGHT_2_SELF_ANY=6.00
PRIMER_LEFT_2_SELF_END=2.00
PRIMER_RIGHT_2_SELF_END=2.00
PRIMER_LEFT_2_END_STABILITY=6.6000
PRIMER_RIGHT_2_END_STABILITY=8.7000
=
SEQUENCE_ID=Overhang20
PRIMER_TASK=pick_sequencing_primers
PRIMER_EXPLAIN_FLAG=0
SEQUENCE_TEMPLATE=TGCTTTCAATCATGTGGGTGATTTTATAGATTGTCATCACCATAGTAACTGTTTTAACTCACGTCCCCTGTGTGAGAACGCCATGGGCTGTCGGGCTTCGCCAACTTGCTCTCATTTCTA
SEQUENCE_OVERHANG_LEFT=ATCCC
SEQUENCE_OVERHANG_RIGHT=ATTAGTC
P3_COMMENT=PRIMER_TASK=pick_sequencing_primers with overhangs
PRIMER_LEFT_NUM_RETURNED=1
PRIMER_RIGHT_NUM_RETURNED=1
PRIMER_INTERNAL_NUM_RETURNED=0
PRIMER_PAIR_NUM_RETURNED=0
PRIMER_LEFT_0_PENALTY=0.516718
PRIMER_RIGHT_0_PENALTY=0.538083
PRIMER_LEFT_0_SEQUENCE=ATCCCTGCTTTCAATCATGTGGGTG
PRIMER_RIGHT_0_SEQUENCE=ATTAGTCATGAGAGCAAGTTGGCGAAG
PRIMER_LEFT_0=0,20
PRIMER_RIGHT_0=114,20
PRIMER_LEFT_0_TM=60.517
PRIMER_RIGHT_0_TM=60.538
PRIMER_LEFT_0_GC_PERCENT=45.000
PRIMER_RIGHT_0_GC_PERCENT=50.000
PRIMER_LEFT_0_SELF_ANY=4.00
PRIMER_RIGHT_0_SELF_ANY=6.00
PRIMER_LEFT_0_SELF_END=2.00
PRIMER_RIGHT_0_SELF_END=2.00
PRIMER_LEFT_0_END_STABILITY=9.4000
PRIMER_RIGHT_0_END_STABILITY=8.7000
=
SEQUENCE_ID=Overhang21
PRIMER_TASK=pick_cloning_primers
PRIMER_EXPLAIN_FLAG=1
SEQUENCE_TEMPLATE=TGCTTTCAATCATGTGGGTGATTTTATAGATTGTCATCACCATAGTAACTGTTTTAACTCACGTCCCCTGTGTGAGAACGCCATGGGCTGTCGGGCTTCGCCAACTTGCTCTCATTTCTA
SEQUENCE_INCLUDED_REGION=25,90
SEQUENCE_OVERHANG_LEFT=ATCCC
SEQUENCE_OVERHANG_RIGHT=ATTAGTC
P3_COMMENT=PRIMER_TASK=pick_cloning_primers with overhangs
PRIMER_LEFT_EXPLAIN=considered 22, low tm 14, high tm 1, high end compl 13, ok 22
PRIMER_RIGHT_EXPLAIN=considered 22, low tm 4, high tm 15, high end compl 4, ok 22
PRIMER_PAIR_EXPLAIN=considered 3, ok 3
PRIMER_LEFT_NUM_RETURNED=3
PRIMER_RIGHT_NUM_RETURNED=3
PRIMER_INTERNAL_NUM_RETURNED=0
PRIMER_PAIR_NUM_RETURNED=3
PRIMER_PAIR_0_PENALTY=10.595526
PRIMER_LEFT_0_PENALTY=10.057443
PRIMER_RIGHT_0_PENALTY=0.538083
PRIMER_LEFT_0_SEQUENCE=ATCCCATAGATTGTCATCACCATAGTAACTGTTTT
PRIMER_RIGHT_0_SEQUENCE=ATTAGTCATGAGAGCAAGTTGGCGAAG
PRIMER_LEFT_0=25,30
PRIMER_RIGHT_0=114,20
PRIMER_LEFT_0_TM=59.943
PRIMER_RIGHT_0_TM=60.538
PRIMER_LEFT_0_GC_PERCENT=30.000
PRIMER_RIGHT_0_GC_PERCENT=50.000
PRIMER_LEFT_0_SELF_ANY=6.00
PRIMER_RIGHT_0_SELF_ANY=6.00
PRIMER_LEFT_0_SELF_END=3.00
PRIMER_RIGHT_0_SELF_END=2.00
PRIMER_LEFT_0_END_STABILITY=7.0000
PRIMER_RIGHT_0_END_STABILITY=8.7000
PRIMER_PAIR_0_COMPL_ANY=5.00
PRIMER_PAIR_0_COMPL_END=2.00
PRIMER_PAIR_0_PRODUCT_SIZE=102
PRIMER_PAIR_0_PRODUCT_TM=73.3
PRIMER_PAIR_1_PENALTY=10.626574
PRIMER_LEFT_1_PENALTY=10.088490
PRIMER_RIGHT_1_PENALTY=0.538083
PRIMER_LEFT_1_SEQUENCE=ATCCCATAGATTGTCATCACCATAGTAACTGTTT
PRIMER_RIGHT_1_SEQUENCE=ATTAGTCATGAGAGCAAGTTGGCGAAG
PRIMER_LEFT_1=25,29
PRIMER_RIGHT_1=114,20
PRIMER_LEFT_1_TM=58.912
PRIMER_RIGHT_1_TM=60.538
PRIMER_LEFT_1_GC_PERCENT=31.034
PRIMER_RIGHT_1_GC_PERCENT=50.000
PRIMER_LEFT_1_SELF_ANY=6.00
PRIMER_RIGHT_1_SELF_ANY=6.00
PRIMER_LEFT_1_SELF_END=3.00
PRIMER_RIGHT_1_SELF_END=2.00
PRIMER_LEFT_1_END_STABILITY=7.0000
PRIMER_RIGHT_1_END_STABILITY=8.7000
PRIMER_PAIR_1_COMPL_ANY=5.00
PRIMER_PAIR_1_COMPL_END=1.00
PRIMER_PAIR_1_PRODUCT_SIZE=102
PRIMER_PAIR_1_PRODUCT_TM=73.3
PRIMER_PAIR_2_PENALTY=10.748303
PRIMER_LEFT_2_PENALTY=10.210220
PRIMER_RIGHT_2_PENALTY=0.538083
PRIMER_LEFT_2_PROBLEMS= Similary to 3' end of self too high;
PRIMER_LEFT_2_SEQUENCE=ATCCCATAGATTGTCATCACCATAGTAACTGTT
PRIMER_RIGHT_2_SEQUENCE=ATTAGTCATGAGAGCAAGTTGGCGAAG
PRIMER_LEFT_2=25,28
PRIMER_RIGHT_2=114,20
PRIMER_LEFT_2_TM=57.790
PRIMER_RIGHT_2_TM=60.538
PRIMER_LEFT_2_GC_PERCENT=32.143
PRIMER_RIGHT_2_GC_PERCENT=50.000
PRIMER_LEFT_2_SELF_ANY=6.00
PRIMER_RIGHT_2_SELF_ANY=6.00
PRIMER_LEFT_2_SELF_END=5.00
PRIMER_RIGHT_2_SELF_END=2.00
PRIMER_LEFT_2_END_STABILITY=6.7000
PRIMER_RIGHT_2_END_STABILITY=8.7000
PRIMER_PAIR_2_COMPL_ANY=5.00
PRIMER_PAIR_2_COMPL_END=2.00
PRIMER_PAIR_2_PRODUCT_SIZE=102
PRIMER_PAIR_2_PRODUCT_TM=73.3
=
SEQUENCE_ID=Overhang22
PRIMER_TASK=pick_discriminative_primers
SEQUENCE_TEMPLATE=TGCTTTCAATCATGTGGGTGATTTTATAGATTGTCATCACCATAGTAACTGTTTTAACTCACGTCCCCTGTGTGAGAACGCCATGGGCTGTCGGGCTTCGCCAACTTGCTCTCATTTCTA
SEQUENCE_TARGET=25,60
SEQUENCE_OVERHANG_LEFT=ATCCC
SEQUENCE_OVERHANG_RIGHT=ATTAGTC
P3_COMMENT=PRIMER_TASK=pick_discriminative_primers with overhangs
PRIMER_LEFT_EXPLAIN=considered 12, low tm 7, high tm 2, high any compl 1, ok 12
PRIMER_RIGHT_EXPLAIN=considered 22, low tm 1, high tm 20, high end compl 1, ok 22
PRIMER_PAIR_EXPLAIN=considered 3, ok 3
PRIMER_LEFT_NUM_RETURNED=3
PRIMER_RIGHT_NUM_RETURNED=3
PRIMER_INTERNAL_NUM_RETURNED=0
PRIMER_PAIR_NUM_RETURNED=3
PRIMER_PAIR_0_PENALTY=7.824763
PRIMER_LEFT_0_PENALTY=2.818040
PRIMER_RIGHT_0_PENALTY=5.006723
PRIMER_LEFT_0_SEQUENCE=ATCCCTTTCAATCATGTGGGTGATTTT
PRIMER_RIGHT_0_SEQUENCE=ATTAGTCCGAAGCCCGACAGCC
PRIMER_LEFT_0=3,22
PRIMER_RIGHT_0=99,15
PRIMER_LEFT_0_TM=59.182
PRIMER_RIGHT_0_TM=60.007
PRIMER_LEFT_0_GC_PERCENT=31.818
PRIMER_RIGHT_0_GC_PERCENT=73.333
PRIMER_LEFT_0_SELF_ANY=5.00
PRIMER_RIGHT_0_SELF_ANY=3.00
PRIMER_LEFT_0_SELF_END=0.00
PRIMER_RIGHT_0_SELF_END=1.00
PRIMER_LEFT_0_END_STABILITY=7.2000
PRIMER_RIGHT_0_END_STABILITY=9.7000
PRIMER_PAIR_0_COMPL_ANY=4.00
PRIMER_PAIR_0_COMPL_END=0.00
PRIMER_PAIR_0_PRODUCT_SIZE=109
PRIMER_PAIR_0_PRODUCT_TM=72.3
PRIMER_PAIR_1_PENALTY=8.108930
PRIMER_LEFT_1_PENALTY=3.102207
PRIMER_RIGHT_1_PENALTY=5.006723
PRIMER_LEFT_1_SEQUENCE=ATCCCCTTTCAATCATGTGGGTGATTTT
PRIMER_RIGHT_1_SEQUENCE=ATTAGTCCGAAGCCCGACAGCC
PRIMER_LEFT_1=2,23
PRIMER_RIGHT_1=99,15
PRIMER_LEFT_1_TM=60.102
PRIMER_RIGHT_1_TM=60.007
PRIMER_LEFT_1_GC_PERCENT=34.783
PRIMER_RIGHT_1_GC_PERCENT=73.333
PRIMER_LEFT_1_SELF_ANY=5.00
PRIMER_RIGHT_1_SELF_ANY=3.00
PRIMER_LEFT_1_SELF_END=0.00
PRIMER_RIGHT_1_SELF_END=1.00
PRIMER_LEFT_1_END_STABILITY=7.2000
PRIMER_RIGHT_1_END_STABILITY=9.7000
PRIMER_PAIR_1_COMPL_ANY=4.00
PRIMER_PAIR_1_COMPL_END=0.00
PRIMER_PAIR_1_PRODUCT_SIZE=110
PRIMER_PAIR_1_PRODUCT_TM=72.6
PRIMER_PAIR_2_PENALTY=8.228612
PRIMER_LEFT_2_PENALTY=3.221889
PRIMER_RIGHT_2_PENALTY=5.006723
PRIMER_LEFT_2_SEQUENCE=ATCCCTTCAATCATGTGGGTGATTTT
PRIMER_RIGHT_2_SEQUENCE=ATTAGTCCGAAGCCCGACAGCC
PRIMER_LEFT_2=4,21
PRIMER_RIGHT_2=99,15
PRIMER_LEFT_2_TM=57.778
PRIMER_RIGHT_2_TM=60.007
PRIMER_LEFT_2_GC_PERCENT=33.333
PRIMER_RIGHT_2_GC_PERCENT=73.333
PRIMER_LEFT_2_SELF_ANY=5.00
PRIMER_RIGHT_2_SELF_ANY=3.00
PRIMER_LEFT_2_SELF_END=0.00
PRIMER_RIGHT_2_SELF_END=1.00
PRIMER_LEFT_2_END_STABILITY=7.2000
PRIMER_RIGHT_2_END_STABILITY=9.7000
PRIMER_PAIR_2_COMPL_ANY=4.00
PRIMER_PAIR_2_COMPL_END=0.00
PRIMER_PAIR_2_PRODUCT_SIZE=108
PRIMER_PAIR_2_PRODUCT_TM=72.4
=
SEQUENCE_ID=Overhang23
PRIMER_TASK=generic
PRIMER_NUM_RETURN=3
PRIMER_LIBERAL_BASE=0
PRIMER_PICK_LEFT_PRIMER=1
PRIMER_PICK_RIGHT_PRIMER=1
PRIMER_PICK_INTERNAL_OLIGO=0
PRIMER_MAX_SIZE=27
SEQUENCE_TEMPLATE=TGCTTTCAATCATGTGGGTGATTTTATAGATTGTCATCACCATAGTAACTGTTTTAACTCACGTCCCCTGTGTGAGAACGCCATGGGCTGTCGGGCTTCGCCAACTTGCTCTCATTTCTA
SEQUENCE_OVERHANG_LEFT=AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
SEQUENCE_OVERHANG_RIGHT=CCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
P3_COMMENT=PRIMER_TASK=generic with huge overhangs
PRIMER_LEFT_EXPLAIN=considered 714, GC content failed 7, low tm 545, high tm 35, high end compl 1, ok 126
PRIMER_RIGHT_EXPLAIN=considered 714, low tm 145, high tm 434, high end compl 1, ok 134
PRIMER_PAIR_EXPLAIN=considered 7, unacceptable product size 2, ok 5
PRIMER_LEFT_NUM_RETURNED=3
PRIMER_RIGHT_NUM_RETURNED=3
PRIMER_INTERNAL_NUM_RETURNED=0
PRIMER_PAIR_NUM_RETURNED=3
PRIMER_PAIR_0_PENALTY=0.925917
PRIMER_LEFT_0_PENALTY=0.516718
PRIMER_RIGHT_0_PENALTY=0.409199
PRIMER_LEFT_0_SEQUENCE=AAAAAAAAAAAAAAAAAAAAAAAAAAAAAATGCTTTCAATCATGTGGGTG
PRIMER_RIGHT_0_SEQUENCE=CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCACACAGGGGACGTGAGTTA
PRIMER_LEFT_0=0,20
PRIMER_RIGHT_0=73,20
PRIMER_LEFT_0_TM=60.517
PRIMER_RIGHT_0_TM=59.591
PRIMER_LEFT_0_GC_PERCENT=45.000
PRIMER_RIGHT_0_GC_PERCENT=55.000
PRIMER_LEFT_0_SELF_ANY=6.00
PRIMER_RIGHT_0_SELF_ANY=4.00
PRIMER_LEFT_0_SELF_END=2.00
PRIMER_RIGHT_0_SELF_END=2.00
PRIMER_LEFT_0_END_STABILITY=9.4000
PRIMER_RIGHT_0_END_STABILITY=5.7000
PRIMER_PAIR_0_COMPL_ANY=6.00
PRIMER_PAIR_0_COMPL_END=1.00
PRIMER_PAIR_0_PRODUCT_SIZE=134
PRIMER_PAIR_0_PRODUCT_TM=67.9
PRIMER_PAIR_1_PENALTY=1.054801
PRIMER_LEFT_1_PENALTY=0.516718
PRIMER_RIGHT_1_PENALTY=0.538083
PRIMER_LEFT_1_SEQUENCE=AAAAAAAAAAAAAAAAAAAAAAAAAAAAAATGCTTTCAATCATGTGGGTG
PRIMER_RIGHT_1_SEQUENCE=CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCATGAGAGCAAGTTGGCGAAG
PRIMER_LEFT_1=0,20
PRIMER_RIGHT_1=114,20
PRIMER_LEFT_1_TM=60.517
PRIMER_RIGHT_1_TM=60.538
PRIMER_LEFT_1_GC_PERCENT=45.000
PRIMER_RIGHT_1_GC_PERCENT=50.000
PRIMER_LEFT_1_SELF_ANY=6.00
PRIMER_RIGHT_1_SELF_ANY=5.00
PRIMER_LEFT_1_SELF_END=2.00
PRIMER_RIGHT_1_SELF_END=2.00
PRIMER_LEFT_1_END_STABILITY=9.4000
PRIMER_RIGHT_1_END_STABILITY=8.7000
PRIMER_PAIR_1_COMPL_ANY=8.00
PRIMER_PAIR_1_COMPL_END=0.00
PRIMER_PAIR_1_PRODUCT_SIZE=175
PRIMER_PAIR_1_PRODUCT_TM=73.6
PRIMER_PAIR_2_PENALTY=1.430962
PRIMER_LEFT_2_PENALTY=0.516718
PRIMER_RIGHT_2_PENALTY=0.914244
PRIMER_LEFT_2_SEQUENCE=AAAAAAAAAAAAAAAAAAAAAAAAAAAAAATGCTTTCAATCATGTGGGTG
PRIMER_RIGHT_2_SEQUENCE=CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCAAATGAGAGCAAGTTGGCGA
PRIMER_LEFT_2=0,20
PRIMER_RIGHT_2=116,20
PRIMER_LEFT_2_TM=60.517
PRIMER_RIGHT_2_TM=60.914
PRIMER_LEFT_2_GC_PERCENT=45.000
PRIMER_RIGHT_2_GC_PERCENT=45.000
PRIMER_LEFT_2_SELF_ANY=6.00
PRIMER_RIGHT_2_SELF_ANY=5.00
PRIMER_LEFT_2_SELF_END=2.00
PRIMER_RIGHT_2_SELF_END=2.00
PRIMER_LEFT_2_END_STABILITY=9.4000
PRIMER_RIGHT_2_END_STABILITY=11.4000
PRIMER_PAIR_2_COMPL_ANY=8.00
PRIMER_PAIR_2_COMPL_END=1.00
PRIMER_PAIR_2_PRODUCT_SIZE=177
PRIMER_PAIR_2_PRODUCT_TM=73.3
=
