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Viewing changes to test/primer_internal1_input

  • Committer: Bazaar Package Importer
  • Author(s): Charles Plessy
  • Date: 2006-09-28 20:18:54 UTC
  • Revision ID: james.westby@ubuntu.com-20060928201854-45pwapz5e3a6d684
Tags: upstream-1.0b
Import upstream version 1.0b

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Lines of Context:
test/primer_internal1_input
 
1
PRIMER_FIRST_BASE_INDEX=1
 
2
MARKER_NAME=boundary_test_00
 
3
PRIMER_MAX_POLY_X=0
 
4
PRIMER_INTERNAL_OLIGO_MAX_POLY_X=0
 
5
PRIMER_EXPLAIN_FLAG=1
 
6
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNACGTACGTACGTTGCAGTCGACGCANNACTCACTGTCATTTCCAAACAATTCNN
 
7
PRIMER_PRODUCT_SIZE_RANGE=50-100
 
8
PRIMER_MIN_TM=0.0
 
9
PRIMER_MAX_TM=100.0
 
10
PRIMER_MIN_SIZE=25
 
11
PRIMER_MAX_SIZE=25
 
12
PRIMER_INTERNAL_OLIGO_MIN_SIZE=25
 
13
PRIMER_INTERNAL_OLIGO_MAX_SIZE=25
 
14
PRIMER_INTERNAL_OLIGO_OPT_SIZE=25
 
15
PRIMER_OPT_SIZE=25
 
16
PRIMER_MAX_GC=100
 
17
PRIMER_MIN_GC=0
 
18
PRIMER_SELF_END=100
 
19
PRIMER_SELF_ANY=100
 
20
PRIMER_INTERNAL_OLIGO_SELF_ANY=100
 
21
PRIMER_INTERNAL_OLIGO_SELF_END=100 
 
22
PRIMER_INTERNAL_OLIGO_MAX_TM=100
 
23
PRIMER_INTERNAL_OLIGO_MIN_TM=30
 
24
PRIMER_INTERNAL_OLIGO_MAX_GC=100
 
25
PRIMER_INTERNAL_OLIGO_MIN_GC=0
 
26
PRIMER_PICK_INTERNAL_OLIGO=1
 
27
=
 
28
MARKER_NAME=boundary_test_01
 
29
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNCACGTCATCTCATCAAATTTGATTGNNNACTCACTGTCATTTCCAAACAATTCNN
 
30
PRIMER_PRODUCT_SIZE_RANGE=55-100
 
31
PRIMER_PICK_INTERNAL_OLIGO=1
 
32
=
 
33
MARKER_NAME=boundary_test_02
 
34
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNCACGTCATCTCATCAAATTTGATTGNNNACTCACTGTCATTTCCAAACAATTCNN
 
35
PRIMER_PRODUCT_SIZE_RANGE=80-80
 
36
PRIMER_PICK_INTERNAL_OLIGO=1
 
37
=
 
38
MARKER_NAME=boundary_test_05
 
39
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNCACGTCATCTCATCAAATTTGATTGNNNACTCACTGTCATTTCCAAACAATTCNN
 
40
PRIMER_PRODUCT_SIZE_RANGE=80-80
 
41
PRIMER_MIN_SIZE=24
 
42
PRIMER_MAX_SIZE=24
 
43
PRIMER_OPT_SIZE=24
 
44
PRIMER_PICK_INTERNAL_OLIGO=1
 
45
=
 
46
MARKER_NAME=boundary_test_11
 
47
PRIMER_NUM_NS_ACCEPTED=1
 
48
SEQUENCE=NNCACGTCATCTNATCAAATTTGATTGNNCACGTCATCTNATCAAATTTGATTGNNNACTCACTGTCATTTCCAAACAATTCNN
 
49
PRIMER_PICK_INTERNAL_OLIGO=1
 
50
=
 
51
MARKER_NAME=boundary_test_11
 
52
PRIMER_NUM_NS_ACCEPTED=2
 
53
PRIMER_INTERNAL_OLIGO_NUM_NS=2
 
54
SEQUENCE=NNCACGTCATCNNATCAAATTTGATTGNNCACGTCATCNNATCAAATTTGATTGNNNACTCACTGTCATTTCCAAACAATTCNN
 
55
PRIMER_PICK_INTERNAL_OLIGO=1
 
56
=
 
57
MARKER_NAME=boundary_test_12
 
58
PRIMER_NUM_NS_ACCEPTED=2
 
59
SEQUENCE=NNCACGTCATCNNATCAAATTTGATTGNNCACGTCATCNNATCAAATTTGATTGNNNACTCACTGTCATTTCCAAACAATTCNN
 
60
PRIMER_PICK_INTERNAL_OLIGO=1
 
61
=
 
62
MARKER_NAME=boundary_test_13
 
63
PRIMER_NUM_NS_ACCEPTED=0
 
64
PRIMER_MIN_GC=0
 
65
SEQUENCE=NNAAAAAAAAAAAAAAAAAAAAAAAAANNTTTTTTTTTTTTTTTTTTTTTTTTTNNNACTCACTGTCATTTCCAAACAATTCNN
 
66
=
 
67
MARKER_NAME=boundary_test_14
 
68
PRIMER_NUM_NS_ACCEPTED=0
 
69
PRIMER_MIN_GC=.0001
 
70
SEQUENCE=NNAAAAAAAAAAAAAAAAACAAAAAAATTTTTTTTTTTTTTTTTTTTTTTTTNNNNNACTCACTGTCATTTCCAAACAATTCNN
 
71
=
 
72
MARKER_NAME=boundary_test_15
 
73
PRIMER_NUM_NS_ACCEPTED=0
 
74
PRIMER_MIN_GC=20
 
75
PRIMER_MAX_GC=100
 
76
SEQUENCE=NNGGGGGGGGGGGGGGGGGGGGGGGGGNNNNNTTTTTTTTTTTTTTTTTTTTTTTTTACTCACTGTCATTTCCAAACAATTCNN
 
77
=
 
78
MARKER_NAME=boundary_test_16
 
79
PRIMER_NUM_NS_ACCEPTED=0
 
80
PRIMER_PRODUCT_SIZE_RANGE=50-200
 
81
PRIMER_INTERNAL_OLIGO_NUM_NS=5
 
82
SEQUENCE=NNGGGGGGGGGGGGGGGGGGGGGGGGGNNNNNACTCACTGTCATTTCCAAACAATTCNN
 
83
=
 
84
MARKER_NAME=boundary_test_17
 
85
PRIMER_NUM_NS_ACCEPTED=0
 
86
PRIMER_MIN_GC=0
 
87
PRIMER_MAX_GC=100
 
88
PRIMER_INTERNAL_OLIGO_MIN_GC=20
 
89
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNTTTTTTTTTTTTTTTTTTTTTTTTGNNNACTCACTGTCATTTCCAAACAATTCNN
 
90
=
 
91
MARKER_NAME=boundary_test_18
 
92
PRIMER_NUM_NS_ACCEPTED=0
 
93
PRIMER_MIN_GC=0
 
94
PRIMER_MAX_GC=100
 
95
PRIMER_INTERNAL_OLIGO_EXCLUDED_REGION=11,50
 
96
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNACCGCTATTGGGCCATTTGCCCATTGCATGNNNNNNNNNNNNNNNNNNNNNNNNNACTCACTGTCATTTCCAAACAATTCNN
 
97
=
 
98
MARKER_NAME=boundary_test_19
 
99
PRIMER_NUM_NS_ACCEPTED=0
 
100
PRIMER_MIN_GC=0
 
101
PRIMER_MAX_GC=100
 
102
PRIMER_INTERNAL_OLIGO_NUM_NS=0
 
103
PRIMER_INTERNAL_OLIGO_EXCLUDED_REGION=11,50
 
104
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNAAGCTAAGCTTGCCCGTATCCCCTGGATNNNCCGTTAGGTGCTAGCCGTGTAGATTNNNACTCACTGTCATTTCCAAACAATTCNN
 
105
=
 
106
MARKER_NAME=boundary_test_20
 
107
PRIMER_NUM_NS_ACCEPTED=0
 
108
PRIMER_MIN_GC=0
 
109
PRIMER_MAX_GC=100
 
110
PRIMER_PRODUCT_SIZE_RANGE=100-300
 
111
PRIMER_INTERNAL_OLIGO_EXCLUDED_REGION=6,50
 
112
PRIMER_INTERNAL_OLIGO_EXCLUDED_REGION=61,15
 
113
INCLUDED_REGION=3,250
 
114
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNAAGCTAAGCTGTCGATGCGGTGGAGACGATACGGTAAGCTAGCTAACTGGTCAAAGCTAGCGGTAGCTTAGCTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNACTCACTGTCATTTCCAAACAATTCATCTCTCTCTCATATATATATATATATATATATATATAT
 
115
=
 
116
MARKER_NAME=boundary_test_21
 
117
PRIMER_NUM_NS_ACCEPTED=0
 
118
PRIMER_MIN_GC=0
 
119
PRIMER_MAX_GC=100
 
120
PRIMER_INTERNAL_OLIGO_MIN_GC=0
 
121
PRIMER_INTERNAL_OLIGO_MIN_TM=55.7
 
122
PRIMER_INTERNAL_OLIGO_MAX_TM=55.9
 
123
PRIMER_INTERNAL_OLIGO_OPT_TM=55.8
 
124
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGAAAAAAAAAAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGNNNACTCACTGTCATTTCCAAACAATTCNN
 
125
=
 
126
MARKER_NAME=boundary_test_22
 
127
PRIMER_EXPLAIN_FLAG=1
 
128
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNACGTACGTACGTTGCAGTCGACGCANNACTCACTGTCATTTCCAAACAATTCNN
 
129
PRIMER_PRODUCT_SIZE_RANGE=80-80
 
130
PRIMER_MIN_TM=0.0
 
131
PRIMER_MAX_TM=100.0
 
132
PRIMER_MIN_SIZE=25
 
133
PRIMER_MAX_SIZE=25
 
134
PRIMER_INTERNAL_OLIGO_MIN_SIZE=25
 
135
PRIMER_INTERNAL_OLIGO_MAX_SIZE=25
 
136
PRIMER_INTERNAL_OLIGO_OPT_SIZE=25
 
137
PRIMER_OPT_SIZE=25
 
138
PRIMER_MAX_GC=100
 
139
PRIMER_MIN_GC=0
 
140
PRIMER_SELF_END=100
 
141
PRIMER_SELF_ANY=100
 
142
PRIMER_INTERNAL_OLIGO_SELF_ANY=100
 
143
PRIMER_INTERNAL_OLIGO_SELF_END=100 
 
144
PRIMER_INTERNAL_OLIGO_MAX_TM=100
 
145
PRIMER_INTERNAL_OLIGO_MIN_TM=30
 
146
PRIMER_INTERNAL_OLIGO_MAX_GC=100
 
147
PRIMER_INTERNAL_OLIGO_MIN_GC=0
 
148
PRIMER_PICK_INTERNAL_OLIGO=1
 
149
COMMENT=should succeed
 
150
=
 
151
MARKER_NAME=boundary_test_23
 
152
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNACGTACGTACGTTGCAGTCGACGCANNACTCACTGTCATTTCCAAACAATTCNN
 
153
INCLUDED_REGION=3,80
 
154
PRIMER_INTERNAL_OLIGO_EXCLUDED_REGION=2,1
 
155
COMMENT=should succeed with warning (internal oligo excluded region outside of included region)
 
156
=
 
157
MARKER_NAME=boundary_test_24
 
158
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNACGTACGTACGTTGCAGTCGACGCANNACTCACTGTCATTTCCAAACAATTCNN
 
159
INCLUDED_REGION=3,80
 
160
PRIMER_INTERNAL_OLIGO_EXCLUDED_REGION=3,1
 
161
COMMENT=should succeed
 
162
=
 
163
MARKER_NAME=boundary_test_25
 
164
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNACGTACGTACGTTGCAGTCGACGCANNACTCACTGTCATTTCCAAACAATTCNN
 
165
INCLUDED_REGION=3,80
 
166
PRIMER_INTERNAL_OLIGO_EXCLUDED_REGION=1,3
 
167
COMMENT=should succeed with warning (internal oligo excluded region outside of included region)
 
168
=
 
169
MARKER_NAME=boundary_test_26
 
170
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNACGTACGTACGTTGCAGTCGACGCANNACTCACTGTCATTTCCAAACAATTCNN
 
171
INCLUDED_REGION=3,80
 
172
PRIMER_INTERNAL_OLIGO_EXCLUDED_REGION=30,1
 
173
COMMENT=should succeed
 
174
=
 
175
MARKER_NAME=boundary_test_27
 
176
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNACGTACGTACGTTGCAGTCGACGCANNACTCACTGTCATTTCCAAACAATTCNN
 
177
INCLUDED_REGION=3,80
 
178
PRIMER_INTERNAL_OLIGO_EXCLUDED_REGION=31,1
 
179
COMMENT=should fail w/ no legal internal oligo
 
180
=
 
181
MARKER_NAME=boundary_test_28
 
182
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNACGTACGTACGTTGCAGTCGACGCANNACTCACTGTCATTTCCAAACAATTCNN
 
183
INCLUDED_REGION=3,80
 
184
PRIMER_INTERNAL_OLIGO_EXCLUDED_REGION=55,1
 
185
COMMENT=should fail w/ no legal internal oligo
 
186
=
 
187
MARKER_NAME=boundary_test_29
 
188
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNACGTACGTACGTTGCAGTCGACGCANNACTCACTGTCATTTCCAAACAATTCNN
 
189
INCLUDED_REGION=3,80
 
190
PRIMER_INTERNAL_OLIGO_EXCLUDED_REGION=56,1
 
191
COMMENT=should succeed
 
192
=
 
193
MARKER_NAME=boundary_test_30
 
194
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNACGTACGTACGTTGCAGTCGACGCANNACTCACTGTCATTTCCAAACAATTCNN
 
195
INCLUDED_REGION=3,80
 
196
PRIMER_INTERNAL_OLIGO_EXCLUDED_REGION=82,1
 
197
COMMENT=should succeed
 
198
=
 
199
MARKER_NAME=boundary_test_31
 
200
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNACGTACGTACGTTGCAGTCGACGCANNACTCACTGTCATTTCCAAACAATTCNN
 
201
INCLUDED_REGION=3,80
 
202
PRIMER_INTERNAL_OLIGO_EXCLUDED_REGION=83,1
 
203
COMMENT=should generate warning (external oligo excluded region outside of included region)
 
204
=
 
205
MARKER_NAME=boundary_test_32
 
206
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNACGTACGTACGTTGCAGTCGACGCANNACTCACTGTCATTTCCAAACAATTCNN
 
207
INCLUDED_REGION=3,80
 
208
PRIMER_INTERNAL_OLIGO_EXCLUDED_REGION=82,2
 
209
COMMENT=should generate warning (external oligo excluded region outside of included region)
 
210
=
 
211
MARKER_NAME=boundary_test_33
 
212
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNACGTACGTACGTTGCAGTCGACGCANNACTCACTGTCATTTCCAAACAATTCNN
 
213
INCLUDED_REGION=3,80
 
214
PRIMER_INTERNAL_OLIGO_EXCLUDED_REGION=82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1
 
215
COMMENT=should succeed (testing number of internal oligo excluded regions)
 
216
=
 
217
MARKER_NAME=boundary_test_34
 
218
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNACGTACGTACGTTGCAGTCGACGCANNACTCACTGTCATTTCCAAACAATTCNN
 
219
INCLUDED_REGION=3,80
 
220
PRIMER_INTERNAL_OLIGO_EXCLUDED_REGION=82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1 82,1
 
221
COMMENT=should fail (testing number of internal oligo excluded regions)
 
222
=