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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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