1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
|
PRIMER_SECONDARY_STRUCTURE_ALIGNMENT=1
PRIMER_FIRST_BASE_INDEX=1
PRIMER_EXPLAIN_FLAG=1
PRIMER_MISPRIMING_LIBRARY=../src/humrep_and_simple.txt
PRIMER_PRODUCT_SIZE_RANGE=300-400 401-500 200-299 501-600 100-199 601-700 701-850 851-1001
PRIMER_NUM_RETURN=5
PRIMER_MAX_END_STABILITY=9.0
PRIMER_MAX_LIBRARY_MISPRIMING=12.00
PRIMER_PAIR_MAX_LIBRARY_MISPRIMING=20.00
PRIMER_MAX_SELF_ANY_TH=47.00
PRIMER_MAX_SELF_END_TH=47.00
PRIMER_MAX_HAIRPIN_TH=47.0
PRIMER_PAIR_MAX_COMPL_ANY_TH=47.00
PRIMER_PAIR_MAX_COMPL_END_TH=47.00
PRIMER_MAX_TEMPLATE_MISPRIMING_TH=47.00
PRIMER_PAIR_MAX_TEMPLATE_MISPRIMING_TH=80.00
PRIMER_MIN_TM=57.0
PRIMER_OPT_TM=59.0
PRIMER_MAX_TM=63.0
PRIMER_PAIR_MAX_DIFF_TM=5.0
PRIMER_TM_FORMULA=1
PRIMER_SALT_MONOVALENT=50.0
PRIMER_SALT_CORRECTIONS=1
PRIMER_SALT_DIVALENT=1.5
PRIMER_DNTP_CONC=0.6
PRIMER_DNA_CONC=50.0
PRIMER_THERMODYNAMIC_OLIGO_ALIGNMENT=1
PRIMER_THERMODYNAMIC_TEMPLATE_ALIGNMENT=1
PRIMER_LOWERCASE_MASKING=0
PRIMER_MIN_GC=20.0
PRIMER_MAX_GC=80.0
PRIMER_MAX_NS_ACCEPTED=0
PRIMER_MAX_POLY_X=5
PRIMER_OUTSIDE_PENALTY=0
PRIMER_GC_CLAMP=0
PRIMER_LIBERAL_BASE=1
PRIMER_LIB_AMBIGUITY_CODES_CONSENSUS=0
PRIMER_WT_TM_LT=1.0
PRIMER_WT_TM_GT=1.0
PRIMER_WT_SIZE_LT=1.0
PRIMER_WT_SIZE_GT=1.0
PRIMER_WT_GC_PERCENT_LT=0.0
PRIMER_WT_GC_PERCENT_GT=0.0
PRIMER_WT_SELF_ANY_TH=0.0
PRIMER_WT_SELF_END_TH=0.0
PRIMER_WT_HAIRPIN_TH=0.0
PRIMER_WT_NUM_NS=0.0
PRIMER_WT_LIBRARY_MISPRIMING=0.0
PRIMER_WT_SEQ_QUAL=0.0
PRIMER_WT_END_QUAL=0.0
PRIMER_WT_POS_PENALTY=0.0
PRIMER_WT_END_STABILITY=0.0
PRIMER_WT_TEMPLATE_MISPRIMING_TH=0.0
PRIMER_PAIR_WT_PRODUCT_SIZE_LT=0.0
PRIMER_PAIR_WT_PRODUCT_SIZE_GT=0.0
PRIMER_PAIR_WT_PRODUCT_TM_LT=0.0
PRIMER_PAIR_WT_PRODUCT_TM_GT=0.0
PRIMER_PAIR_WT_DIFF_TM=0.0
PRIMER_PAIR_WT_COMPL_ANY_TH=0.0
PRIMER_PAIR_WT_COMPL_END_TH=0.0
PRIMER_PAIR_WT_LIBRARY_MISPRIMING=0.0
PRIMER_PAIR_WT_PR_PENALTY=1.0
PRIMER_PAIR_WT_IO_PENALTY=0.0
PRIMER_PAIR_WT_TEMPLATE_MISPRIMING=0.0
PRIMER_PICK_ANYWAY=0
PRIMER_TASK=generic
PRIMER_OPT_SIZE=20
PRIMER_MIN_SIZE=19
PRIMER_MAX_SIZE=21
SEQUENCE_ID=start_up
SEQUENCE_TEMPLATE=GTAGTCAGTAGACATGACACTGACGATGCAGACNACACACACACACACAGCACACAGGTATTAGTGGGCCATTCGATCCCGACCCAAATCGATAGCTACGATGACG
SEQUENCE_TARGET=37,21
=
PRIMER_NUM_RETURN=1
PRIMER_MAX_SELF_ANY_TH=47.00
PRIMER_MAX_SELF_END_TH=47.00
PRIMER_MAX_HAIRPIN_TH=47.0
PRIMER_PAIR_MAX_COMPL_ANY_TH=47.00
PRIMER_PAIR_MAX_COMPL_END_TH=47.00
PRIMER_MAX_TEMPLATE_MISPRIMING_TH=47.00
PRIMER_PAIR_MAX_TEMPLATE_MISPRIMING_TH=80.00
PRIMER_PRODUCT_SIZE_RANGE=75-200
SEQUENCE_INTERNAL_EXCLUDED_REGION=37,21
PRIMER_EXPLAIN_FLAG=1
SEQUENCE_ID=pick_detection_primers_th_1
SEQUENCE_TEMPLATE=GTAGTCAGTAGACATGACACTGACGATGCAGACNACACACACACACACAGCACACAGGTATTAGTGGGCCATTCGATCCCGACCCAAATCGATAGCTACGATGACG
SEQUENCE_TARGET=37,21
=
PRIMER_PRODUCT_SIZE_RANGE=75-100
SEQUENCE_ID=pick_detection_primers_th_2
SEQUENCE_TEMPLATE=GANAATGCAGTAATGAGTTGGCAAATTATGAATCGCAATCAAATTTTTTCTATGACCTGATAGAAACGCCAACTCACTGTATGAGTCTGTTGTCAAAGTCTAACGTTGTCAAAGTCTATTCCAAAACGCAAAGCACGCTCCCGATC
=
PRIMER_TASK=pick_left_only
PRIMER_PRODUCT_SIZE_RANGE=75-200
SEQUENCE_ID=pick_left_only_th_1
SEQUENCE_TEMPLATE=GTAGTCAGTAGACATGACACTGACGATGCAGACNACACACACACACACAGCACACAGGTATTAGTGGGCCATTCGATCCCGACCCAAATCGATAGCTACGATGACG
SEQUENCE_TARGET=37,21
=
PRIMER_PRODUCT_SIZE_RANGE=75-100
SEQUENCE_ID=pick_left_only_th_2
SEQUENCE_TEMPLATE=GANAATGCAGTAATGAGTTGGCAAATTATGAATCGCAATCAAATTTTTTCTATGACCTGATAGAAACGCCAACTCACTGTATGAGTCTGTTGTCAAAGTCTAACGTTGTCAAAGTCTATTCCAAAACGCAAAGCACGCTCCCGATC
=
PRIMER_TASK=pick_right_only
PRIMER_PRODUCT_SIZE_RANGE=75-200
SEQUENCE_ID=pick_right_only_th_1
SEQUENCE_TEMPLATE=GTAGTCAGTAGACATGACACTGACGATGCAGACNACACACACACACACAGCACACAGGTATTAGTGGGCCATTCGATCCCGACCCAAATCGATAGCTACGATGACG
SEQUENCE_TARGET=37,21
=
PRIMER_PRODUCT_SIZE_RANGE=75-100
SEQUENCE_ID=pick_right_only_th_2
SEQUENCE_TEMPLATE=GANAATGCAGTAATGAGTTGGCAAATTATGAATCGCAATCAAATTTTTTCTATGACCTGATAGAAACGCCAACTCACTGTATGAGTCTGTTGTCAAAGTCTAACGTTGTCAAAGTCTATTCCAAAACGCAAAGCACGCTCCCGATC
=
PRIMER_TASK=pick_hyb_probe_only
PRIMER_PRODUCT_SIZE_RANGE=75-200
SEQUENCE_ID=pick_hyb_probe_only_th_1
SEQUENCE_TEMPLATE=GTAGTCAGTAGACATGACACTGACGATGCAGACNACACACACACACACAGCACACAGGTATTAGTGGGCCATTCGATCCCGACCCAAATCGATAGCTACGATGACG
SEQUENCE_TARGET=37,21
=
PRIMER_PRODUCT_SIZE_RANGE=75-100
SEQUENCE_ID=pick_hyb_probe_only_th_2
SEQUENCE_TEMPLATE=GANAATGCAGTAATGAGTTGGCAAATTATGAATCGCAATCAAATTTTTTCTATGACCTGATAGAAACGCCAACTCACTGTATGAGTCTGTTGTCAAAGTCTAACGTTGTCAAAGTCTATTCCAAAACGCAAAGCACGCTCCCGATC
=
PRIMER_TASK=pick_primer_list
PRIMER_NUM_RETURN=30
PRIMER_PRODUCT_SIZE_RANGE=75-200
SEQUENCE_ID=pick_primer_list_th_1
SEQUENCE_TEMPLATE=GTAGTCAGTAGACATGACACTGACGATGCAGACNACACACACACACACAGCACACAGGTATTAGTGGGCCATTCGATCCCGACCCAAATCGATAGCTACGATGACG
SEQUENCE_TARGET=37,21
=
PRIMER_PICK_LEFT_PRIMER=1
PRIMER_PICK_RIGHT_PRIMER=1
PRIMER_PICK_INTERNAL_OLIGO=1
PRIMER_PRODUCT_SIZE_RANGE=75-100
SEQUENCE_ID=pick_pick_primer_list_th_2
SEQUENCE_TEMPLATE=GANAATGCAGTAATGAGTTGGCAAATTATGAATCGCAATCAAATTTTTTCTATGACCTGATAGAAACGCCAACTCACTGTATGAGTCTGTTGTCAAAGTCTAACGTTGTCAAAGTCTATTCCAAAACGCAAAGCACGCTCCCGATC
=
PRIMER_TASK=pick_primer_list
PRIMER_PRODUCT_SIZE_RANGE=75-200
SEQUENCE_ID=pick_primer_list_and_file_flag_th_1
SEQUENCE_TEMPLATE=GTAGTCAGTAGACATGACACTGACGATGCAGACNACACACACACACACAGCACACAGGTATTAGTGGGCCATTCGATCCCGACCCAAATCGATAGCTACGATGACG
SEQUENCE_TARGET=37,21
=
PRIMER_PRODUCT_SIZE_RANGE=75-100
SEQUENCE_ID=pick_primer_list_and_file_flag_th_2
SEQUENCE_TEMPLATE=GANAATGCAGTAATGAGTTGGCAAATTATGAATCGCAATCAAATTTTTTCTATGACCTGATAGAAACGCCAACTCACTGTATGAGTCTGTTGTCAAAGTCTAACGTTGTCAAAGTCTATTCCAAAACGCAAAGCACGCTCCCGATC
=
PRIMER_TASK=pick_primer_list
PRIMER_PRODUCT_SIZE_RANGE=75-200
PRIMER_MIN_LEFT_THREE_PRIME_DISTANCE=4
PRIMER_MIN_RIGHT_THREE_PRIME_DISTANCE=4
SEQUENCE_ID=pick_primer_list_and_file_flag_th_3
SEQUENCE_TEMPLATE=GTAGTCAGTAGACATGACACTGACGATGCAGACNACACACACACACACAGCACACAGGTATTAGTGGGCCATTCGATCCCGACCCAAATCGATAGCTACGATGACG
SEQUENCE_TARGET=37,21
=
PRIMER_PRODUCT_SIZE_RANGE=75-100
SEQUENCE_ID=pick_primer_list_and_file_flag_th_4
SEQUENCE_TEMPLATE=GANAATGCAGTAATGAGTTGGCAAATTATGAATCGCAATCAAATTTTTTCTATGACCTGATAGAAACGCCAACTCACTGTATGAGTCTGTTGTCAAAGTCTAACGTTGTCAAAGTCTATTCCAAAACGCAAAGCACGCTCCCGATC
=
PRIMER_TASK=pick_sequencing_primers
PRIMER_PICK_LEFT_PRIMER=0
PRIMER_PICK_RIGHT_PRIMER=0
PRIMER_PICK_INTERNAL_OLIGO=0
PRIMER_NUM_RETURN=1
PRIMER_MIN_LEFT_THREE_PRIME_DISTANCE=-1
PRIMER_MIN_RIGHT_THREE_PRIME_DISTANCE=-1
PRIMER_PRODUCT_SIZE_RANGE=75-200
SEQUENCE_ID=pick_sequencing_primers_th_1
SEQUENCE_TEMPLATE=GTAGTCAGTAGACATGACACTGACGATGCAGACNACACACACACACACAGCACACAGGTATTAGTGGGCCATTCGATCCCGACCCAAATCGATAGCTACGATGACG
SEQUENCE_TARGET=37,21
=
PRIMER_PRODUCT_SIZE_RANGE=75-100
PRIMER_PICK_LEFT_PRIMER=1
SEQUENCE_ID=pick_sequencing_primers_th_2
SEQUENCE_TEMPLATE=GANAATGCAGTAATGAGTTGGCAAATTATGAATCGCAATCAAATTTTTTCTATGACCTGATAGAAACGCCAACTCACTGTATGAGTCTGTTGTCAAAGTCTAACGTTGTCAAAGTCTATTCCAAAACGCAAAGCACGCTCCCGATC
=
PRIMER_PRODUCT_SIZE_RANGE=75-100
PRIMER_PICK_RIGHT_PRIMER=1
SEQUENCE_ID=pick_sequencing_primers_th_3
SEQUENCE_TEMPLATE=GANAATGCAGTAATGAGTTGGCAAATTATGAATCGCAATCAAATTTTTTCTATGACCTGATAGAAACGCCAACTCACTGTATGAGTCTGTTGTCAAAGTCTAACGTTGTCAAAGTCTATTCCAAAACGCAAAGCACGCTCCCGATC
=
PRIMER_TASK=check_primers
PRIMER_PRODUCT_SIZE_RANGE=75-200
SEQUENCE_ID=check_primers_th_1
SEQUENCE_TEMPLATE=GTAGTCAGTAGACATGACACTGACGATGCAGACNACACACACACACACAGCACACAGGTATTAGTGGGCCATTCGATCCCGACCCAAATCGATAGCTACGATGACG
SEQUENCE_TARGET=37,21
SEQUENCE_PRIMER=GACATGACACTGACGATGCA
SEQUENCE_PRIMER_REVCOMP=TAGCTATCGATTTGGGTCGG
=
PRIMER_PRODUCT_SIZE_RANGE=75-100
SEQUENCE_ID=check_primers_th_2
SEQUENCE_TEMPLATE=GANAATGCAGTAATGAGTTGGCAAATTATGAATCGCAATCAAATTTTTTCTATGACCTGATAGAAACGCCAACTCACTGTATGAGTCTGTTGTCAAAGTCTAACGTTGTCAAAGTCTATTCCAAAACGCAAAGCACGCTCCCGATC
SEQUENCE_PRIMER=TGACCTGATAGAAACGCCAA
SEQUENCE_PRIMER_REVCOMP=TGCTTTGCGTTTTGGAATAG
=
PRIMER_TASK=pick_discriminative_primers
PRIMER_PRODUCT_SIZE_RANGE=75-200
SEQUENCE_ID=pick_disc_th_1
SEQUENCE_TEMPLATE=GTAGTCAGTAGACATGACACTGACGATGCAGACNACACACACACACACAGCACACAGGTATTAGTGGGCCATTCGATCCCGACCCAAATCGATAGCTACGATGACG
SEQUENCE_TARGET=37,21
PRIMER_PICK_ANYWAY=1
=
PRIMER_PRODUCT_SIZE_RANGE=75-100
SEQUENCE_ID=pick_disc_primer_th_2
SEQUENCE_TEMPLATE=GANAATGCAGTAATGAGTTGGCAAATTATGAATCGCAATCAAATTTTTTCTATGACCTGATAGAAACGCCAACTCACTGTATGAGTCTGTTGTCAAAGTCTAACGTTGTCAAAGTCTATTCCAAAACGCAAAGCACGCTCCCGATC
SEQUENCE_TARGET=37,21
=
PRIMER_TASK=pick_cloning_primers
PRIMER_PRODUCT_SIZE_RANGE=200-300
SEQUENCE_ID=pick_disc_th_1
SEQUENCE_TEMPLATE=GTAGTCAGTAGACATGACACTGACGATGCAGACNACACACACACACACAGCACACAGGTATTAGTGGGCCATTCGATCCCGACCCAAATCGATAGCTACGATGACG
SEQUENCE_TARGET=2,100
=
PRIMER_PRODUCT_SIZE_RANGE=200-300
SEQUENCE_ID=pick_disc_primer_th_2
SEQUENCE_TEMPLATE=GANAATGCAGTAATGAGTTGGCAAATTATGAATCGCAATCAAATTTTTTCTATGACCTGATAGAAACGCCAACTCACTGTATGAGTCTGTTGTCAAAGTCTAACGTTGTCAAAGTCTATTCCAAAACGCAAAGCACGCTCCCGATC
SEQUENCE_TARGET=2,120
=
|
