[The OMP Design File is in Boulder I/O (TAG=VALUE) format. Text inside square bracket is treated as a comment.]

[project information]
NAME=16SrRNA_1-400b

NUM_RETURN=10
DEFAULT_NUM_REDUNDANT=50
GENERATE_CANDIDATES=true
OUTPUT_DIRECTORY=C:\Program Files\DNASoftware\Visual OMP

[solution conditions]
ASSAY_TEMPERATURE=45
MAGNESIUM_CONCENTRATION=0
SODIUM_CONCENTRATION=0.1

[BLAST Settings]
BLAST_DATABASE=
BLAST_EXECUTABLE=C:\Program Files\DNASoftware\BLAST\blastall.exe
BLAST_WORD_SIZE=10
DEFAULT_BLAST_STRAND_TYPE=DOUBLE
DEFAULT_BLAST_SEARCH_FOR=BINDING SITES
RUN_BLAST=FALSE

[sequences]

SEQUENCE_NAME=16SrRNA_1-400
SEQUENCE=ATCCTGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAACGGTAACAGGAAACAGCTTGCTGCTTTGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCGGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAA
SEQUENCE_TYPE=DNA
CONCENTRATION=1E-09
STRAND=SINGLE

SEQUENCE_NAME=OLIGO_1
SEQUENCE=CAATATTCCCCACTGCTGCCTC
SEQUENCE_TYPE=DNA
CONCENTRATION=1E-06
STRAND=SINGLE

SEQUENCE_NAME=OLIGO_1_2
SEQUENCE=GCAAGCTGTTTCCTGTTACCGTTC
SEQUENCE_TYPE=DNA
CONCENTRATION=1E-06
STRAND=SINGLE

SEQUENCE_NAME=OLIGO_1_3
SEQUENCE=CCACTGCTGCCTCCCGTA
SEQUENCE_TYPE=DNA
CONCENTRATION=1E-06
STRAND=SINGLE

SEQUENCE_NAME=OLIGO_1_4
SEQUENCE=CATCTGGGCACATCCGATGG
SEQUENCE_TYPE=DNA
CONCENTRATION=1E-06
STRAND=SINGLE

SEQUENCE_NAME=OLIGO_1_5
SEQUENCE=TTACTCACCCGTCCGCCACTC
SEQUENCE_TYPE=DNA
CONCENTRATION=1E-06
STRAND=SINGLE

[designs]

OLIGO_NAME=OLIGO_1
OLIGO_TYPE=PROBE
OLIGO_TARGET_NAME=16SrRNA_1-400
OLIGO_PARAMETER_PROFILE_NAME=Balanced
OLIGO_CONCENTRATION=1E-06
OLIGO_ENABLED=TRUE

OLIGO_MIN_SIZE=15
OLIGO_OPT_SIZE=20
OLIGO_MAX_SIZE=25
OLIGO_SIZE_LT_WT=1
OLIGO_SIZE_GT_WT=1
OLIGO_SIZE_WT_SCALE=LINEAR

OLIGO_MIN_TM=60
OLIGO_OPT_TM=65
OLIGO_MAX_TM=100
OLIGO_TM_LT_WT=3
OLIGO_TM_GT_WT=-3
OLIGO_TM_WT_SCALE=LINEAR

OLIGO_MIN_DG=-100
OLIGO_OPT_DG=-24
OLIGO_MAX_DG=-3
OLIGO_DG_LT_WT=-1
OLIGO_DG_GT_WT=1
OLIGO_DG_WT_SCALE=LINEAR

OLIGO_OPT_TARGET_LOCAL_TM=0
OLIGO_MAX_TARGET_LOCAL_TM=70
OLIGO_TARGET_LOCAL_TM_GT_WT=0.1
OLIGO_TARGET_LOCAL_TM_WT_SCALE=LINEAR

OLIGO_OPT_TARGET_LOCAL_DG=0
OLIGO_MIN_TARGET_LOCAL_DG=-50
OLIGO_TARGET_LOCAL_DG_LT_WT=0.1
OLIGO_TARGET_LOCAL_DG_WT_SCALE=LINEAR

OLIGO_OPT_MONOMER_TM=0
OLIGO_MAX_MONOMER_TM=65
OLIGO_MONOMER_TM_GT_WT=1
OLIGO_MONOMER_TM_WT_SCALE=LINEAR

OLIGO_OPT_MONOMER_DG=0
OLIGO_MIN_MONOMER_DG=-50
OLIGO_MONOMER_DG_LT_WT=1
OLIGO_MONOMER_DG_WT_SCALE=LINEAR

OLIGO_OPT_HOMODIMER_TM=0
OLIGO_MAX_HOMODIMER_TM=65
OLIGO_HOMODIMER_TM_GT_WT=0.1
OLIGO_HOMODIMER_TM_WT_SCALE=LINEAR

OLIGO_OPT_HOMODIMER_DG=0
OLIGO_MIN_HOMODIMER_DG=-50
OLIGO_HOMODIMER_DG_LT_WT=1
OLIGO_HOMODIMER_DG_WT_SCALE=LINEAR

OLIGO_OPT_MISHYB_TM=0
OLIGO_MAX_MISHYB_TM=50
OLIGO_MISHYB_TM_GT_WT=0.1
OLIGO_MISHYB_TM_WT_SCALE=LINEAR

OLIGO_OPT_MISHYB_DG=0
OLIGO_MIN_MISHYB_DG=-50
OLIGO_MISHYB_DG_LT_WT=1
OLIGO_MISHYB_DG_WT_SCALE=LINEAR

OLIGO_TARGET_LOCAL_LENGTH=35
OLIGO_OPT_CROSSHYB_TM=0
OLIGO_MAX_CROSSHYB_TM=50
OLIGO_CROSSHYB_TM_GT_WT=0.5
OLIGO_CROSSHYB_TM_WT_SCALE=LINEAR

OLIGO_OPT_CROSSHYB_DG=0
OLIGO_MIN_CROSSHYB_DG=-50
OLIGO_CROSSHYB_DG_LT_WT=1
OLIGO_CROSSHYB_DG_WT_SCALE=LINEAR

OLIGO_OPT_VAR_POS=LENGTH/2
OLIGO_MIN_VAR_POS=3
OLIGO_MAX_VAR_POS=LENGTH-2
OLIGO_VAR_POS_LT_WT=1
OLIGO_VAR_POS_GT_WT=1
OLIGO_VAR_POS_WT_SCALE=LINEAR

OLIGO_MAX_POLY_A=10
OLIGO_MAX_POLY_C=4
OLIGO_MAX_POLY_G=4
OLIGO_MAX_POLY_T=10

OLIGO_ALLELE_MIN_LENGTH_DIFFERENCE=0
OLIGO_ALLELE_OPT_LENGTH_DIFFERENCE=0
OLIGO_ALLELE_MAX_LENGTH_DIFFERENCE=3
OLIGO_ALLELE_LENGTH_DIFFERENCE_LT_WT=.5
OLIGO_ALLELE_LENGTH_DIFFERENCE_GT_WT=.5
OLIGO_ALLELE_LENGTH_DIFFERENCE_WT_SCALE=LINEAR

OLIGO_ALLELE_MIN_VAR_POS_DIFFERENCE=0
OLIGO_ALLELE_OPT_VAR_POS_DIFFERENCE=0
OLIGO_ALLELE_MAX_VAR_POS_DIFFERENCE=3
OLIGO_ALLELE_VAR_POS_DIFFERENCE_LT_WT=.5
OLIGO_ALLELE_VAR_POS_DIFFERENCE_GT_WT=.5
OLIGO_ALLELE_VAR_POS_DIFFERENCE_WT_SCALE=LINEAR

OLIGO_ALLELE_MIN_START_POS_DIFFERENCE=0
OLIGO_ALLELE_OPT_START_POS_DIFFERENCE=0
OLIGO_ALLELE_MAX_START_POS_DIFFERENCE=3
OLIGO_ALLELE_START_POS_DIFFERENCE_LT_WT=.5
OLIGO_ALLELE_START_POS_DIFFERENCE_GT_WT=.5
OLIGO_ALLELE_START_POS_DIFFERENCE_WT_SCALE=LINEAR

OLIGO_MIN_TM_ALLELE_DIFFERENCE=2
OLIGO_OPT_TM_ALLELE_DIFFERENCE=10
OLIGO_TM_ALLELE_DIFFERENCE_WT=3
OLIGO_TM_ALLELE_DIFFERENCE_SCALE=LINEAR

OLIGO_MIN_DG_ALLELE_DIFFERENCE=0.5
OLIGO_OPT_DG_ALLELE_DIFFERENCE=5
OLIGO_DG_ALLELE_DIFFERENCE_WT=3
OLIGO_DG_ALLELE_DIFFERENCE_SCALE=LINEAR

OLIGO_OPT_BLAST_HITS=0
OLIGO_MAX_BLAST_HITS=10
OLIGO_BLAST_HITS_GT_WT=1
OLIGO_BLAST_HITS_WT_SCALE=LINEAR

OLIGO_OPT_MATCH_LENGTH=0
OLIGO_MAX_MATCH_LENGTH=12
OLIGO_MATCH_LENGTH_GT_WT=0.2
OLIGO_MATCH_LENGTH_WT_SCALE=LINEAR

NUM_REDUNDANT=100
SOLUTION_DISTANCE=3
OLIGO_OPT_GCC=50
OLIGO_MIN_GCC=0
OLIGO_MAX_GCC=100
OLIGO_GCC_WT=0
OLIGO_GCC_GT_WT=0
OLIGO_GCC_LT_WT=0