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Viewing changes to test/primer_internal1_output

  • 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_output
 
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
PRIMER_LEFT_EXPLAIN=considered 35, too many Ns 33, ok 2
 
28
PRIMER_RIGHT_EXPLAIN=considered 35, too many Ns 33, ok 2
 
29
PRIMER_INTERNAL_OLIGO_EXPLAIN=considered 60, too many Ns 57, ok 3
 
30
PRIMER_PAIR_EXPLAIN=considered 4, unacceptable product size 1, no internal oligo 2, ok 1
 
31
PRIMER_PAIR_PENALTY=3.3813
 
32
PRIMER_LEFT_PENALTY=2.731673
 
33
PRIMER_RIGHT_PENALTY=0.649600
 
34
PRIMER_INTERNAL_OLIGO_PENALTY=11.495378
 
35
PRIMER_LEFT_SEQUENCE=CACGTCATCTCATCAAATTTGATTG
 
36
PRIMER_RIGHT_SEQUENCE=GAATTGTTTGGAAATGACAGTGAGT
 
37
PRIMER_INTERNAL_OLIGO_SEQUENCE=ACGTACGTACGTTGCAGTCGACGCA
 
38
PRIMER_LEFT=3,25
 
39
PRIMER_RIGHT=82,25
 
40
PRIMER_INTERNAL_OLIGO=31,25
 
41
PRIMER_LEFT_TM=62.732
 
42
PRIMER_RIGHT_TM=60.650
 
43
PRIMER_INTERNAL_OLIGO_TM=71.495
 
44
PRIMER_LEFT_GC_PERCENT=36.000
 
45
PRIMER_RIGHT_GC_PERCENT=36.000
 
46
PRIMER_INTERNAL_OLIGO_GC_PERCENT=56.000
 
47
PRIMER_LEFT_SELF_ANY=12.00
 
48
PRIMER_RIGHT_SELF_ANY=4.00
 
49
PRIMER_INTERNAL_OLIGO_SELF_ANY=12.00
 
50
PRIMER_LEFT_SELF_END=10.00
 
51
PRIMER_RIGHT_SELF_END=3.00
 
52
PRIMER_INTERNAL_OLIGO_SELF_END=8.00
 
53
PRIMER_LEFT_END_STABILITY=6.9000
 
54
PRIMER_RIGHT_END_STABILITY=6.4000
 
55
PRIMER_PAIR_COMPL_ANY=7.00
 
56
PRIMER_PAIR_COMPL_END=1.00
 
57
PRIMER_PRODUCT_SIZE=80
 
58
=
 
59
MARKER_NAME=boundary_test_01
 
60
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNCACGTCATCTCATCAAATTTGATTGNNNACTCACTGTCATTTCCAAACAATTCNN
 
61
PRIMER_PRODUCT_SIZE_RANGE=55-100
 
62
PRIMER_PICK_INTERNAL_OLIGO=1
 
63
PRIMER_LEFT_EXPLAIN=considered 30, too many Ns 28, ok 2
 
64
PRIMER_RIGHT_EXPLAIN=considered 30, too many Ns 29, ok 1
 
65
PRIMER_INTERNAL_OLIGO_EXPLAIN=considered 60, too many Ns 57, ok 3
 
66
PRIMER_PAIR_EXPLAIN=considered 2, unacceptable product size 1, ok 1
 
67
PRIMER_PAIR_PENALTY=3.3813
 
68
PRIMER_LEFT_PENALTY=2.731673
 
69
PRIMER_RIGHT_PENALTY=0.649600
 
70
PRIMER_INTERNAL_OLIGO_PENALTY=2.731673
 
71
PRIMER_LEFT_SEQUENCE=CACGTCATCTCATCAAATTTGATTG
 
72
PRIMER_RIGHT_SEQUENCE=GAATTGTTTGGAAATGACAGTGAGT
 
73
PRIMER_INTERNAL_OLIGO_SEQUENCE=CACGTCATCTCATCAAATTTGATTG
 
74
PRIMER_LEFT=3,25
 
75
PRIMER_RIGHT=82,25
 
76
PRIMER_INTERNAL_OLIGO=30,25
 
77
PRIMER_LEFT_TM=62.732
 
78
PRIMER_RIGHT_TM=60.650
 
79
PRIMER_INTERNAL_OLIGO_TM=62.732
 
80
PRIMER_LEFT_GC_PERCENT=36.000
 
81
PRIMER_RIGHT_GC_PERCENT=36.000
 
82
PRIMER_INTERNAL_OLIGO_GC_PERCENT=36.000
 
83
PRIMER_LEFT_SELF_ANY=12.00
 
84
PRIMER_RIGHT_SELF_ANY=4.00
 
85
PRIMER_INTERNAL_OLIGO_SELF_ANY=12.00
 
86
PRIMER_LEFT_SELF_END=10.00
 
87
PRIMER_RIGHT_SELF_END=3.00
 
88
PRIMER_INTERNAL_OLIGO_SELF_END=10.00
 
89
PRIMER_LEFT_END_STABILITY=6.9000
 
90
PRIMER_RIGHT_END_STABILITY=6.4000
 
91
PRIMER_PAIR_COMPL_ANY=7.00
 
92
PRIMER_PAIR_COMPL_END=1.00
 
93
PRIMER_PRODUCT_SIZE=80
 
94
=
 
95
MARKER_NAME=boundary_test_02
 
96
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNCACGTCATCTCATCAAATTTGATTGNNNACTCACTGTCATTTCCAAACAATTCNN
 
97
PRIMER_PRODUCT_SIZE_RANGE=80-80
 
98
PRIMER_PICK_INTERNAL_OLIGO=1
 
99
PRIMER_LEFT_EXPLAIN=considered 5, too many Ns 4, ok 1
 
100
PRIMER_RIGHT_EXPLAIN=considered 5, too many Ns 4, ok 1
 
101
PRIMER_INTERNAL_OLIGO_EXPLAIN=considered 60, too many Ns 57, ok 3
 
102
PRIMER_PAIR_EXPLAIN=considered 1, ok 1
 
103
PRIMER_PAIR_PENALTY=3.3813
 
104
PRIMER_LEFT_PENALTY=2.731673
 
105
PRIMER_RIGHT_PENALTY=0.649600
 
106
PRIMER_INTERNAL_OLIGO_PENALTY=2.731673
 
107
PRIMER_LEFT_SEQUENCE=CACGTCATCTCATCAAATTTGATTG
 
108
PRIMER_RIGHT_SEQUENCE=GAATTGTTTGGAAATGACAGTGAGT
 
109
PRIMER_INTERNAL_OLIGO_SEQUENCE=CACGTCATCTCATCAAATTTGATTG
 
110
PRIMER_LEFT=3,25
 
111
PRIMER_RIGHT=82,25
 
112
PRIMER_INTERNAL_OLIGO=30,25
 
113
PRIMER_LEFT_TM=62.732
 
114
PRIMER_RIGHT_TM=60.650
 
115
PRIMER_INTERNAL_OLIGO_TM=62.732
 
116
PRIMER_LEFT_GC_PERCENT=36.000
 
117
PRIMER_RIGHT_GC_PERCENT=36.000
 
118
PRIMER_INTERNAL_OLIGO_GC_PERCENT=36.000
 
119
PRIMER_LEFT_SELF_ANY=12.00
 
120
PRIMER_RIGHT_SELF_ANY=4.00
 
121
PRIMER_INTERNAL_OLIGO_SELF_ANY=12.00
 
122
PRIMER_LEFT_SELF_END=10.00
 
123
PRIMER_RIGHT_SELF_END=3.00
 
124
PRIMER_INTERNAL_OLIGO_SELF_END=10.00
 
125
PRIMER_LEFT_END_STABILITY=6.9000
 
126
PRIMER_RIGHT_END_STABILITY=6.4000
 
127
PRIMER_PAIR_COMPL_ANY=7.00
 
128
PRIMER_PAIR_COMPL_END=1.00
 
129
PRIMER_PRODUCT_SIZE=80
 
130
=
 
131
MARKER_NAME=boundary_test_05
 
132
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNCACGTCATCTCATCAAATTTGATTGNNNACTCACTGTCATTTCCAAACAATTCNN
 
133
PRIMER_PRODUCT_SIZE_RANGE=80-80
 
134
PRIMER_MIN_SIZE=24
 
135
PRIMER_MAX_SIZE=24
 
136
PRIMER_OPT_SIZE=24
 
137
PRIMER_PICK_INTERNAL_OLIGO=1
 
138
PRIMER_LEFT_EXPLAIN=considered 5, too many Ns 3, ok 2
 
139
PRIMER_RIGHT_EXPLAIN=considered 5, too many Ns 3, ok 2
 
140
PRIMER_INTERNAL_OLIGO_EXPLAIN=considered 60, too many Ns 57, ok 3
 
141
PRIMER_PAIR_EXPLAIN=considered 4, unacceptable product size 3, ok 1
 
142
PRIMER_PAIR_PENALTY=0.3310
 
143
PRIMER_LEFT_PENALTY=0.243965
 
144
PRIMER_RIGHT_PENALTY=0.087031
 
145
PRIMER_INTERNAL_OLIGO_PENALTY=2.731673
 
146
PRIMER_LEFT_SEQUENCE=CACGTCATCTCATCAAATTTGATT
 
147
PRIMER_RIGHT_SEQUENCE=GAATTGTTTGGAAATGACAGTGAG
 
148
PRIMER_INTERNAL_OLIGO_SEQUENCE=CACGTCATCTCATCAAATTTGATTG
 
149
PRIMER_LEFT=3,24
 
150
PRIMER_RIGHT=82,24
 
151
PRIMER_INTERNAL_OLIGO=30,25
 
152
PRIMER_LEFT_TM=60.244
 
153
PRIMER_RIGHT_TM=59.913
 
154
PRIMER_INTERNAL_OLIGO_TM=62.732
 
155
PRIMER_LEFT_GC_PERCENT=33.333
 
156
PRIMER_RIGHT_GC_PERCENT=37.500
 
157
PRIMER_INTERNAL_OLIGO_GC_PERCENT=36.000
 
158
PRIMER_LEFT_SELF_ANY=12.00
 
159
PRIMER_RIGHT_SELF_ANY=4.00
 
160
PRIMER_INTERNAL_OLIGO_SELF_ANY=12.00
 
161
PRIMER_LEFT_SELF_END=10.00
 
162
PRIMER_RIGHT_SELF_END=1.00
 
163
PRIMER_INTERNAL_OLIGO_SELF_END=10.00
 
164
PRIMER_LEFT_END_STABILITY=6.9000
 
165
PRIMER_RIGHT_END_STABILITY=6.4000
 
166
PRIMER_PAIR_COMPL_ANY=7.00
 
167
PRIMER_PAIR_COMPL_END=2.00
 
168
PRIMER_PRODUCT_SIZE=80
 
169
=
 
170
MARKER_NAME=boundary_test_11
 
171
PRIMER_NUM_NS_ACCEPTED=1
 
172
SEQUENCE=NNCACGTCATCTNATCAAATTTGATTGNNCACGTCATCTNATCAAATTTGATTGNNNACTCACTGTCATTTCCAAACAATTCNN
 
173
PRIMER_PICK_INTERNAL_OLIGO=1
 
174
PRIMER_LEFT_EXPLAIN=considered 5, too many Ns 3, ok 2
 
175
PRIMER_RIGHT_EXPLAIN=considered 5, too many Ns 1, ok 4
 
176
PRIMER_INTERNAL_OLIGO_EXPLAIN=considered 60, too many Ns 59, ok 1
 
177
PRIMER_PAIR_EXPLAIN=considered 8, unacceptable product size 6, no internal oligo 2, ok 0
 
178
=
 
179
MARKER_NAME=boundary_test_11
 
180
PRIMER_NUM_NS_ACCEPTED=2
 
181
PRIMER_INTERNAL_OLIGO_NUM_NS=2
 
182
SEQUENCE=NNCACGTCATCNNATCAAATTTGATTGNNCACGTCATCNNATCAAATTTGATTGNNNACTCACTGTCATTTCCAAACAATTCNN
 
183
PRIMER_PICK_INTERNAL_OLIGO=1
 
184
PRIMER_LEFT_EXPLAIN=considered 5, too many Ns 3, ok 2
 
185
PRIMER_RIGHT_EXPLAIN=considered 5, ok 5
 
186
PRIMER_INTERNAL_OLIGO_EXPLAIN=considered 60, too many Ns 52, ok 8
 
187
PRIMER_PAIR_EXPLAIN=considered 10, unacceptable product size 8, ok 2
 
188
PRIMER_PAIR_PENALTY=0.8938
 
189
PRIMER_LEFT_PENALTY=0.806819
 
190
PRIMER_RIGHT_PENALTY=0.087031
 
191
PRIMER_INTERNAL_OLIGO_PENALTY=3.221174
 
192
PRIMER_LEFT_SEQUENCE=CACGTCATCNNATCAAATTTGATT
 
193
PRIMER_RIGHT_SEQUENCE=GAATTGTTTGGAAATGACAGTGAG
 
194
PRIMER_INTERNAL_OLIGO_SEQUENCE=CACGTCATCNNATCAAATTTGATTG
 
195
PRIMER_LEFT=3,24
 
196
PRIMER_RIGHT=82,24
 
197
PRIMER_INTERNAL_OLIGO=30,25
 
198
PRIMER_LEFT_TM=60.807
 
199
PRIMER_RIGHT_TM=59.913
 
200
PRIMER_INTERNAL_OLIGO_TM=63.221
 
201
PRIMER_LEFT_GC_PERCENT=31.818
 
202
PRIMER_RIGHT_GC_PERCENT=37.500
 
203
PRIMER_INTERNAL_OLIGO_GC_PERCENT=34.783
 
204
PRIMER_LEFT_SELF_ANY=12.00
 
205
PRIMER_RIGHT_SELF_ANY=4.00
 
206
PRIMER_INTERNAL_OLIGO_SELF_ANY=12.00
 
207
PRIMER_LEFT_SELF_END=11.50
 
208
PRIMER_RIGHT_SELF_END=1.00
 
209
PRIMER_INTERNAL_OLIGO_SELF_END=11.00
 
210
PRIMER_LEFT_END_STABILITY=6.9000
 
211
PRIMER_RIGHT_END_STABILITY=6.4000
 
212
PRIMER_PAIR_COMPL_ANY=6.00
 
213
PRIMER_PAIR_COMPL_END=2.00
 
214
PRIMER_PRODUCT_SIZE=80
 
215
PRIMER_PAIR_PENALTY_1=2.5470
 
216
PRIMER_LEFT_1_PENALTY=0.806819
 
217
PRIMER_RIGHT_1_PENALTY=1.740140
 
218
PRIMER_INTERNAL_OLIGO_1_PENALTY=3.221174
 
219
PRIMER_LEFT_1_SEQUENCE=ACGTCATCNNATCAAATTTGATTG
 
220
PRIMER_RIGHT_1_SEQUENCE=NGAATTGTTTGGAAATGACAGTGA
 
221
PRIMER_INTERNAL_OLIGO_1_SEQUENCE=CACGTCATCNNATCAAATTTGATTG
 
222
PRIMER_LEFT_1=4,24
 
223
PRIMER_RIGHT_1=83,24
 
224
PRIMER_INTERNAL_OLIGO_1=30,25
 
225
PRIMER_LEFT_1_TM=60.807
 
226
PRIMER_RIGHT_1_TM=61.740
 
227
PRIMER_INTERNAL_OLIGO_1_TM=63.221
 
228
PRIMER_LEFT_1_GC_PERCENT=31.818
 
229
PRIMER_RIGHT_1_GC_PERCENT=34.783
 
230
PRIMER_INTERNAL_OLIGO_1_GC_PERCENT=34.783
 
231
PRIMER_LEFT_1_SELF_ANY=12.00
 
232
PRIMER_RIGHT_1_SELF_ANY=4.00
 
233
PRIMER_INTERNAL_OLIGO_1_SELF_ANY=12.00
 
234
PRIMER_LEFT_1_SELF_END=11.00
 
235
PRIMER_RIGHT_1_SELF_END=3.00
 
236
PRIMER_INTERNAL_OLIGO_1_SELF_END=11.00
 
237
PRIMER_LEFT_1_END_STABILITY=6.9000
 
238
PRIMER_RIGHT_1_END_STABILITY=6.4000
 
239
PRIMER_PAIR_1_COMPL_ANY=5.00
 
240
PRIMER_PAIR_1_COMPL_END=2.00
 
241
PRIMER_PRODUCT_SIZE_1=80
 
242
=
 
243
MARKER_NAME=boundary_test_12
 
244
PRIMER_NUM_NS_ACCEPTED=2
 
245
SEQUENCE=NNCACGTCATCNNATCAAATTTGATTGNNCACGTCATCNNATCAAATTTGATTGNNNACTCACTGTCATTTCCAAACAATTCNN
 
246
PRIMER_PICK_INTERNAL_OLIGO=1
 
247
PRIMER_LEFT_EXPLAIN=considered 5, too many Ns 3, ok 2
 
248
PRIMER_RIGHT_EXPLAIN=considered 5, ok 5
 
249
PRIMER_INTERNAL_OLIGO_EXPLAIN=considered 60, too many Ns 52, ok 8
 
250
PRIMER_PAIR_EXPLAIN=considered 10, unacceptable product size 8, ok 2
 
251
PRIMER_PAIR_PENALTY=0.8938
 
252
PRIMER_LEFT_PENALTY=0.806819
 
253
PRIMER_RIGHT_PENALTY=0.087031
 
254
PRIMER_INTERNAL_OLIGO_PENALTY=3.221174
 
255
PRIMER_LEFT_SEQUENCE=CACGTCATCNNATCAAATTTGATT
 
256
PRIMER_RIGHT_SEQUENCE=GAATTGTTTGGAAATGACAGTGAG
 
257
PRIMER_INTERNAL_OLIGO_SEQUENCE=CACGTCATCNNATCAAATTTGATTG
 
258
PRIMER_LEFT=3,24
 
259
PRIMER_RIGHT=82,24
 
260
PRIMER_INTERNAL_OLIGO=30,25
 
261
PRIMER_LEFT_TM=60.807
 
262
PRIMER_RIGHT_TM=59.913
 
263
PRIMER_INTERNAL_OLIGO_TM=63.221
 
264
PRIMER_LEFT_GC_PERCENT=31.818
 
265
PRIMER_RIGHT_GC_PERCENT=37.500
 
266
PRIMER_INTERNAL_OLIGO_GC_PERCENT=34.783
 
267
PRIMER_LEFT_SELF_ANY=12.00
 
268
PRIMER_RIGHT_SELF_ANY=4.00
 
269
PRIMER_INTERNAL_OLIGO_SELF_ANY=12.00
 
270
PRIMER_LEFT_SELF_END=11.50
 
271
PRIMER_RIGHT_SELF_END=1.00
 
272
PRIMER_INTERNAL_OLIGO_SELF_END=11.00
 
273
PRIMER_LEFT_END_STABILITY=6.9000
 
274
PRIMER_RIGHT_END_STABILITY=6.4000
 
275
PRIMER_PAIR_COMPL_ANY=6.00
 
276
PRIMER_PAIR_COMPL_END=2.00
 
277
PRIMER_PRODUCT_SIZE=80
 
278
PRIMER_PAIR_PENALTY_1=2.5470
 
279
PRIMER_LEFT_1_PENALTY=0.806819
 
280
PRIMER_RIGHT_1_PENALTY=1.740140
 
281
PRIMER_INTERNAL_OLIGO_1_PENALTY=3.221174
 
282
PRIMER_LEFT_1_SEQUENCE=ACGTCATCNNATCAAATTTGATTG
 
283
PRIMER_RIGHT_1_SEQUENCE=NGAATTGTTTGGAAATGACAGTGA
 
284
PRIMER_INTERNAL_OLIGO_1_SEQUENCE=CACGTCATCNNATCAAATTTGATTG
 
285
PRIMER_LEFT_1=4,24
 
286
PRIMER_RIGHT_1=83,24
 
287
PRIMER_INTERNAL_OLIGO_1=30,25
 
288
PRIMER_LEFT_1_TM=60.807
 
289
PRIMER_RIGHT_1_TM=61.740
 
290
PRIMER_INTERNAL_OLIGO_1_TM=63.221
 
291
PRIMER_LEFT_1_GC_PERCENT=31.818
 
292
PRIMER_RIGHT_1_GC_PERCENT=34.783
 
293
PRIMER_INTERNAL_OLIGO_1_GC_PERCENT=34.783
 
294
PRIMER_LEFT_1_SELF_ANY=12.00
 
295
PRIMER_RIGHT_1_SELF_ANY=4.00
 
296
PRIMER_INTERNAL_OLIGO_1_SELF_ANY=12.00
 
297
PRIMER_LEFT_1_SELF_END=11.00
 
298
PRIMER_RIGHT_1_SELF_END=3.00
 
299
PRIMER_INTERNAL_OLIGO_1_SELF_END=11.00
 
300
PRIMER_LEFT_1_END_STABILITY=6.9000
 
301
PRIMER_RIGHT_1_END_STABILITY=6.4000
 
302
PRIMER_PAIR_1_COMPL_ANY=5.00
 
303
PRIMER_PAIR_1_COMPL_END=2.00
 
304
PRIMER_PRODUCT_SIZE_1=80
 
305
=
 
306
MARKER_NAME=boundary_test_13
 
307
PRIMER_NUM_NS_ACCEPTED=0
 
308
PRIMER_MIN_GC=0
 
309
SEQUENCE=NNAAAAAAAAAAAAAAAAAAAAAAAAANNTTTTTTTTTTTTTTTTTTTTTTTTTNNNACTCACTGTCATTTCCAAACAATTCNN
 
310
PRIMER_LEFT_EXPLAIN=considered 5, too many Ns 3, ok 2
 
311
PRIMER_RIGHT_EXPLAIN=considered 5, too many Ns 3, ok 2
 
312
PRIMER_INTERNAL_OLIGO_EXPLAIN=considered 60, too many Ns 23, ok 37
 
313
PRIMER_PAIR_EXPLAIN=considered 4, unacceptable product size 3, ok 1
 
314
PRIMER_PAIR_PENALTY=5.3942
 
315
PRIMER_LEFT_PENALTY=5.307199
 
316
PRIMER_RIGHT_PENALTY=0.087031
 
317
PRIMER_INTERNAL_OLIGO_PENALTY=3.800256
 
318
PRIMER_LEFT_SEQUENCE=AAAAAAAAAAAAAAAAAAAAAAAA
 
319
PRIMER_RIGHT_SEQUENCE=GAATTGTTTGGAAATGACAGTGAG
 
320
PRIMER_INTERNAL_OLIGO_SEQUENCE=TTTTTTTTTTTTTTTTTTTTTTTNN
 
321
PRIMER_LEFT=3,24
 
322
PRIMER_RIGHT=82,24
 
323
PRIMER_INTERNAL_OLIGO=32,25
 
324
PRIMER_LEFT_TM=54.693
 
325
PRIMER_RIGHT_TM=59.913
 
326
PRIMER_INTERNAL_OLIGO_TM=56.200
 
327
PRIMER_LEFT_GC_PERCENT=0.000
 
328
PRIMER_RIGHT_GC_PERCENT=37.500
 
329
PRIMER_INTERNAL_OLIGO_GC_PERCENT=0.000
 
330
PRIMER_LEFT_SELF_ANY=0.00
 
331
PRIMER_RIGHT_SELF_ANY=4.00
 
332
PRIMER_INTERNAL_OLIGO_SELF_ANY=0.00
 
333
PRIMER_LEFT_SELF_END=0.00
 
334
PRIMER_RIGHT_SELF_END=1.00
 
335
PRIMER_INTERNAL_OLIGO_SELF_END=0.00
 
336
PRIMER_LEFT_END_STABILITY=7.6000
 
337
PRIMER_RIGHT_END_STABILITY=6.4000
 
338
PRIMER_PAIR_COMPL_ANY=4.00
 
339
PRIMER_PAIR_COMPL_END=0.00
 
340
PRIMER_PRODUCT_SIZE=80
 
341
=
 
342
MARKER_NAME=boundary_test_14
 
343
PRIMER_NUM_NS_ACCEPTED=0
 
344
PRIMER_MIN_GC=.0001
 
345
SEQUENCE=NNAAAAAAAAAAAAAAAAACAAAAAAATTTTTTTTTTTTTTTTTTTTTTTTTNNNNNACTCACTGTCATTTCCAAACAATTCNN
 
346
PRIMER_LEFT_EXPLAIN=considered 5, too many Ns 2, ok 3
 
347
PRIMER_RIGHT_EXPLAIN=considered 5, too many Ns 3, ok 2
 
348
PRIMER_INTERNAL_OLIGO_EXPLAIN=considered 60, too many Ns 25, ok 35
 
349
PRIMER_PAIR_EXPLAIN=considered 6, unacceptable product size 5, ok 1
 
350
PRIMER_PAIR_PENALTY=4.8436
 
351
PRIMER_LEFT_PENALTY=4.756523
 
352
PRIMER_RIGHT_PENALTY=0.087031
 
353
PRIMER_INTERNAL_OLIGO_PENALTY=3.800256
 
354
PRIMER_LEFT_SEQUENCE=AAAAAAAAAAAAAAAAACAAAAAA
 
355
PRIMER_RIGHT_SEQUENCE=GAATTGTTTGGAAATGACAGTGAG
 
356
PRIMER_INTERNAL_OLIGO_SEQUENCE=TTTTTTTTTTTTTTTTTTTTTTTNN
 
357
PRIMER_LEFT=3,24
 
358
PRIMER_RIGHT=82,24
 
359
PRIMER_INTERNAL_OLIGO=30,25
 
360
PRIMER_LEFT_TM=55.243
 
361
PRIMER_RIGHT_TM=59.913
 
362
PRIMER_INTERNAL_OLIGO_TM=56.200
 
363
PRIMER_LEFT_GC_PERCENT=4.167
 
364
PRIMER_RIGHT_GC_PERCENT=37.500
 
365
PRIMER_INTERNAL_OLIGO_GC_PERCENT=0.000
 
366
PRIMER_LEFT_SELF_ANY=0.00
 
367
PRIMER_RIGHT_SELF_ANY=4.00
 
368
PRIMER_INTERNAL_OLIGO_SELF_ANY=0.00
 
369
PRIMER_LEFT_SELF_END=0.00
 
370
PRIMER_RIGHT_SELF_END=1.00
 
371
PRIMER_INTERNAL_OLIGO_SELF_END=0.00
 
372
PRIMER_LEFT_END_STABILITY=7.6000
 
373
PRIMER_RIGHT_END_STABILITY=6.4000
 
374
PRIMER_PAIR_COMPL_ANY=6.00
 
375
PRIMER_PAIR_COMPL_END=0.00
 
376
PRIMER_PRODUCT_SIZE=80
 
377
=
 
378
MARKER_NAME=boundary_test_15
 
379
PRIMER_NUM_NS_ACCEPTED=0
 
380
PRIMER_MIN_GC=20
 
381
PRIMER_MAX_GC=100
 
382
SEQUENCE=NNGGGGGGGGGGGGGGGGGGGGGGGGGNNNNNTTTTTTTTTTTTTTTTTTTTTTTTTACTCACTGTCATTTCCAAACAATTCNN
 
383
PRIMER_LEFT_EXPLAIN=considered 5, too many Ns 3, ok 2
 
384
PRIMER_RIGHT_EXPLAIN=considered 5, too many Ns 2, ok 3
 
385
PRIMER_INTERNAL_OLIGO_EXPLAIN=considered 60, too many Ns 25, ok 35
 
386
PRIMER_PAIR_EXPLAIN=considered 6, unacceptable product size 5, ok 1
 
387
PRIMER_PAIR_PENALTY=29.3957
 
388
PRIMER_LEFT_PENALTY=29.308664
 
389
PRIMER_RIGHT_PENALTY=0.087031
 
390
PRIMER_INTERNAL_OLIGO_PENALTY=4.161950
 
391
PRIMER_LEFT_SEQUENCE=GGGGGGGGGGGGGGGGGGGGGGGG
 
392
PRIMER_RIGHT_SEQUENCE=GAATTGTTTGGAAATGACAGTGAG
 
393
PRIMER_INTERNAL_OLIGO_SEQUENCE=TTTTTTTTTTTTTTTTTTTTTTTTT
 
394
PRIMER_LEFT=3,24
 
395
PRIMER_RIGHT=82,24
 
396
PRIMER_INTERNAL_OLIGO=33,25
 
397
PRIMER_LEFT_TM=89.309
 
398
PRIMER_RIGHT_TM=59.913
 
399
PRIMER_INTERNAL_OLIGO_TM=55.838
 
400
PRIMER_LEFT_GC_PERCENT=100.000
 
401
PRIMER_RIGHT_GC_PERCENT=37.500
 
402
PRIMER_INTERNAL_OLIGO_GC_PERCENT=0.000
 
403
PRIMER_LEFT_SELF_ANY=0.00
 
404
PRIMER_RIGHT_SELF_ANY=4.00
 
405
PRIMER_INTERNAL_OLIGO_SELF_ANY=0.00
 
406
PRIMER_LEFT_SELF_END=0.00
 
407
PRIMER_RIGHT_SELF_END=1.00
 
408
PRIMER_INTERNAL_OLIGO_SELF_END=0.00
 
409
PRIMER_LEFT_END_STABILITY=12.4000
 
410
PRIMER_RIGHT_END_STABILITY=6.4000
 
411
PRIMER_PAIR_COMPL_ANY=1.00
 
412
PRIMER_PAIR_COMPL_END=0.00
 
413
PRIMER_PRODUCT_SIZE=80
 
414
=
 
415
MARKER_NAME=boundary_test_16
 
416
PRIMER_NUM_NS_ACCEPTED=0
 
417
PRIMER_PRODUCT_SIZE_RANGE=50-200
 
418
PRIMER_INTERNAL_OLIGO_NUM_NS=5
 
419
SEQUENCE=NNGGGGGGGGGGGGGGGGGGGGGGGGGNNNNNACTCACTGTCATTTCCAAACAATTCNN
 
420
PRIMER_LEFT_EXPLAIN=considered 10, too many Ns 8, ok 2
 
421
PRIMER_RIGHT_EXPLAIN=considered 10, too many Ns 8, ok 2
 
422
PRIMER_INTERNAL_OLIGO_EXPLAIN=considered 35, ok 35
 
423
PRIMER_PAIR_EXPLAIN=considered 4, no internal oligo 4, ok 0
 
424
=
 
425
MARKER_NAME=boundary_test_17
 
426
PRIMER_NUM_NS_ACCEPTED=0
 
427
PRIMER_MIN_GC=0
 
428
PRIMER_MAX_GC=100
 
429
PRIMER_INTERNAL_OLIGO_MIN_GC=20
 
430
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNTTTTTTTTTTTTTTTTTTTTTTTTGNNNACTCACTGTCATTTCCAAACAATTCNN
 
431
PRIMER_LEFT_EXPLAIN=considered 35, too many Ns 31, ok 4
 
432
PRIMER_RIGHT_EXPLAIN=considered 35, too many Ns 31, ok 4
 
433
PRIMER_INTERNAL_OLIGO_EXPLAIN=considered 60, GC content failed 29, ok 31
 
434
PRIMER_PAIR_EXPLAIN=considered 16, unacceptable product size 4, no internal oligo 12, ok 0
 
435
=
 
436
MARKER_NAME=boundary_test_18
 
437
PRIMER_NUM_NS_ACCEPTED=0
 
438
PRIMER_MIN_GC=0
 
439
PRIMER_MAX_GC=100
 
440
PRIMER_INTERNAL_OLIGO_EXCLUDED_REGION=11,50
 
441
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNACCGCTATTGGGCCATTTGCCCATTGCATGNNNNNNNNNNNNNNNNNNNNNNNNNACTCACTGTCATTTCCAAACAATTCNN
 
442
PRIMER_LEFT_EXPLAIN=considered 62, too many Ns 53, ok 9
 
443
PRIMER_RIGHT_EXPLAIN=considered 62, too many Ns 53, ok 9
 
444
PRIMER_INTERNAL_OLIGO_EXPLAIN=considered 87, too many Ns 39, overlap excluded region 40, ok 8
 
445
PRIMER_PAIR_EXPLAIN=considered 81, unacceptable product size 49, no internal oligo 32, ok 0
 
446
=
 
447
MARKER_NAME=boundary_test_19
 
448
PRIMER_NUM_NS_ACCEPTED=0
 
449
PRIMER_MIN_GC=0
 
450
PRIMER_MAX_GC=100
 
451
PRIMER_INTERNAL_OLIGO_NUM_NS=0
 
452
PRIMER_INTERNAL_OLIGO_EXCLUDED_REGION=11,50
 
453
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNAAGCTAAGCTTGCCCGTATCCCCTGGATNNNCCGTTAGGTGCTAGCCGTGTAGATTNNNACTCACTGTCATTTCCAAACAATTCNN
 
454
PRIMER_LEFT_EXPLAIN=considered 66, too many Ns 57, ok 9
 
455
PRIMER_RIGHT_EXPLAIN=considered 66, too many Ns 57, ok 9
 
456
PRIMER_INTERNAL_OLIGO_EXPLAIN=considered 91, too many Ns 84, overlap excluded region 5, ok 2
 
457
PRIMER_PAIR_EXPLAIN=considered 18, unacceptable product size 3, no internal oligo 8, ok 7
 
458
PRIMER_PAIR_PENALTY=0.3310
 
459
PRIMER_LEFT_PENALTY=0.243965
 
460
PRIMER_RIGHT_PENALTY=0.087031
 
461
PRIMER_INTERNAL_OLIGO_PENALTY=5.578209
 
462
PRIMER_LEFT_SEQUENCE=ACGTCATCTCATCAAATTTGATTG
 
463
PRIMER_RIGHT_SEQUENCE=GAATTGTTTGGAAATGACAGTGAG
 
464
PRIMER_INTERNAL_OLIGO_SEQUENCE=CCGTTAGGTGCTAGCCGTGTAGATT
 
465
PRIMER_LEFT=4,24
 
466
PRIMER_RIGHT=113,24
 
467
PRIMER_INTERNAL_OLIGO=61,25
 
468
PRIMER_LEFT_TM=60.244
 
469
PRIMER_RIGHT_TM=59.913
 
470
PRIMER_INTERNAL_OLIGO_TM=65.578
 
471
PRIMER_LEFT_GC_PERCENT=33.333
 
472
PRIMER_RIGHT_GC_PERCENT=37.500
 
473
PRIMER_INTERNAL_OLIGO_GC_PERCENT=52.000
 
474
PRIMER_LEFT_SELF_ANY=12.00
 
475
PRIMER_RIGHT_SELF_ANY=4.00
 
476
PRIMER_INTERNAL_OLIGO_SELF_ANY=6.00
 
477
PRIMER_LEFT_SELF_END=10.00
 
478
PRIMER_RIGHT_SELF_END=1.00
 
479
PRIMER_INTERNAL_OLIGO_SELF_END=1.00
 
480
PRIMER_LEFT_END_STABILITY=6.9000
 
481
PRIMER_RIGHT_END_STABILITY=6.4000
 
482
PRIMER_PAIR_COMPL_ANY=6.00
 
483
PRIMER_PAIR_COMPL_END=1.00
 
484
PRIMER_PRODUCT_SIZE=110
 
485
PRIMER_PAIR_PENALTY_1=0.3310
 
486
PRIMER_LEFT_1_PENALTY=0.243965
 
487
PRIMER_RIGHT_1_PENALTY=0.087031
 
488
PRIMER_INTERNAL_OLIGO_1_PENALTY=5.578209
 
489
PRIMER_LEFT_1_SEQUENCE=CACGTCATCTCATCAAATTTGATT
 
490
PRIMER_RIGHT_1_SEQUENCE=GAATTGTTTGGAAATGACAGTGAG
 
491
PRIMER_INTERNAL_OLIGO_1_SEQUENCE=CCGTTAGGTGCTAGCCGTGTAGATT
 
492
PRIMER_LEFT_1=3,24
 
493
PRIMER_RIGHT_1=113,24
 
494
PRIMER_INTERNAL_OLIGO_1=61,25
 
495
PRIMER_LEFT_1_TM=60.244
 
496
PRIMER_RIGHT_1_TM=59.913
 
497
PRIMER_INTERNAL_OLIGO_1_TM=65.578
 
498
PRIMER_LEFT_1_GC_PERCENT=33.333
 
499
PRIMER_RIGHT_1_GC_PERCENT=37.500
 
500
PRIMER_INTERNAL_OLIGO_1_GC_PERCENT=52.000
 
501
PRIMER_LEFT_1_SELF_ANY=12.00
 
502
PRIMER_RIGHT_1_SELF_ANY=4.00
 
503
PRIMER_INTERNAL_OLIGO_1_SELF_ANY=6.00
 
504
PRIMER_LEFT_1_SELF_END=10.00
 
505
PRIMER_RIGHT_1_SELF_END=1.00
 
506
PRIMER_INTERNAL_OLIGO_1_SELF_END=1.00
 
507
PRIMER_LEFT_1_END_STABILITY=6.9000
 
508
PRIMER_RIGHT_1_END_STABILITY=6.4000
 
509
PRIMER_PAIR_1_COMPL_ANY=7.00
 
510
PRIMER_PAIR_1_COMPL_END=2.00
 
511
PRIMER_PRODUCT_SIZE_1=111
 
512
PRIMER_PAIR_PENALTY_2=1.2615
 
513
PRIMER_LEFT_2_PENALTY=0.243965
 
514
PRIMER_RIGHT_2_PENALTY=1.017510
 
515
PRIMER_INTERNAL_OLIGO_2_PENALTY=5.578209
 
516
PRIMER_LEFT_2_SEQUENCE=ACGTCATCTCATCAAATTTGATTG
 
517
PRIMER_RIGHT_2_SEQUENCE=AATTGTTTGGAAATGACAGTGAGT
 
518
PRIMER_INTERNAL_OLIGO_2_SEQUENCE=CCGTTAGGTGCTAGCCGTGTAGATT
 
519
PRIMER_LEFT_2=4,24
 
520
PRIMER_RIGHT_2=112,24
 
521
PRIMER_INTERNAL_OLIGO_2=61,25
 
522
PRIMER_LEFT_2_TM=60.244
 
523
PRIMER_RIGHT_2_TM=58.982
 
524
PRIMER_INTERNAL_OLIGO_2_TM=65.578
 
525
PRIMER_LEFT_2_GC_PERCENT=33.333
 
526
PRIMER_RIGHT_2_GC_PERCENT=33.333
 
527
PRIMER_INTERNAL_OLIGO_2_GC_PERCENT=52.000
 
528
PRIMER_LEFT_2_SELF_ANY=12.00
 
529
PRIMER_RIGHT_2_SELF_ANY=4.00
 
530
PRIMER_INTERNAL_OLIGO_2_SELF_ANY=6.00
 
531
PRIMER_LEFT_2_SELF_END=10.00
 
532
PRIMER_RIGHT_2_SELF_END=3.00
 
533
PRIMER_INTERNAL_OLIGO_2_SELF_END=1.00
 
534
PRIMER_LEFT_2_END_STABILITY=6.9000
 
535
PRIMER_RIGHT_2_END_STABILITY=6.4000
 
536
PRIMER_PAIR_2_COMPL_ANY=6.00
 
537
PRIMER_PAIR_2_COMPL_END=1.00
 
538
PRIMER_PRODUCT_SIZE_2=109
 
539
PRIMER_PAIR_PENALTY_3=1.2615
 
540
PRIMER_LEFT_3_PENALTY=0.243965
 
541
PRIMER_RIGHT_3_PENALTY=1.017510
 
542
PRIMER_INTERNAL_OLIGO_3_PENALTY=5.578209
 
543
PRIMER_LEFT_3_SEQUENCE=CACGTCATCTCATCAAATTTGATT
 
544
PRIMER_RIGHT_3_SEQUENCE=AATTGTTTGGAAATGACAGTGAGT
 
545
PRIMER_INTERNAL_OLIGO_3_SEQUENCE=CCGTTAGGTGCTAGCCGTGTAGATT
 
546
PRIMER_LEFT_3=3,24
 
547
PRIMER_RIGHT_3=112,24
 
548
PRIMER_INTERNAL_OLIGO_3=61,25
 
549
PRIMER_LEFT_3_TM=60.244
 
550
PRIMER_RIGHT_3_TM=58.982
 
551
PRIMER_INTERNAL_OLIGO_3_TM=65.578
 
552
PRIMER_LEFT_3_GC_PERCENT=33.333
 
553
PRIMER_RIGHT_3_GC_PERCENT=33.333
 
554
PRIMER_INTERNAL_OLIGO_3_GC_PERCENT=52.000
 
555
PRIMER_LEFT_3_SELF_ANY=12.00
 
556
PRIMER_RIGHT_3_SELF_ANY=4.00
 
557
PRIMER_INTERNAL_OLIGO_3_SELF_ANY=6.00
 
558
PRIMER_LEFT_3_SELF_END=10.00
 
559
PRIMER_RIGHT_3_SELF_END=3.00
 
560
PRIMER_INTERNAL_OLIGO_3_SELF_END=1.00
 
561
PRIMER_LEFT_3_END_STABILITY=6.9000
 
562
PRIMER_RIGHT_3_END_STABILITY=6.4000
 
563
PRIMER_PAIR_3_COMPL_ANY=7.00
 
564
PRIMER_PAIR_3_COMPL_END=2.00
 
565
PRIMER_PRODUCT_SIZE_3=110
 
566
PRIMER_PAIR_PENALTY_4=8.0059
 
567
PRIMER_LEFT_4_PENALTY=7.918829
 
568
PRIMER_RIGHT_4_PENALTY=0.087031
 
569
PRIMER_INTERNAL_OLIGO_4_PENALTY=5.578209
 
570
PRIMER_LEFT_4_SEQUENCE=AAGCTAAGCTTGCCCGTATCCCCT
 
571
PRIMER_RIGHT_4_SEQUENCE=GAATTGTTTGGAAATGACAGTGAG
 
572
PRIMER_INTERNAL_OLIGO_4_SEQUENCE=CCGTTAGGTGCTAGCCGTGTAGATT
 
573
PRIMER_LEFT_4=30,24
 
574
PRIMER_RIGHT_4=113,24
 
575
PRIMER_INTERNAL_OLIGO_4=61,25
 
576
PRIMER_LEFT_4_TM=67.919
 
577
PRIMER_RIGHT_4_TM=59.913
 
578
PRIMER_INTERNAL_OLIGO_4_TM=65.578
 
579
PRIMER_LEFT_4_GC_PERCENT=54.167
 
580
PRIMER_RIGHT_4_GC_PERCENT=37.500
 
581
PRIMER_INTERNAL_OLIGO_4_GC_PERCENT=52.000
 
582
PRIMER_LEFT_4_SELF_ANY=9.00
 
583
PRIMER_RIGHT_4_SELF_ANY=4.00
 
584
PRIMER_INTERNAL_OLIGO_4_SELF_ANY=6.00
 
585
PRIMER_LEFT_4_SELF_END=0.00
 
586
PRIMER_RIGHT_4_SELF_END=1.00
 
587
PRIMER_INTERNAL_OLIGO_4_SELF_END=1.00
 
588
PRIMER_LEFT_4_END_STABILITY=10.9000
 
589
PRIMER_RIGHT_4_END_STABILITY=6.4000
 
590
PRIMER_PAIR_4_COMPL_ANY=3.00
 
591
PRIMER_PAIR_4_COMPL_END=2.00
 
592
PRIMER_PRODUCT_SIZE_4=84
 
593
=
 
594
MARKER_NAME=boundary_test_20
 
595
PRIMER_NUM_NS_ACCEPTED=0
 
596
PRIMER_MIN_GC=0
 
597
PRIMER_MAX_GC=100
 
598
PRIMER_PRODUCT_SIZE_RANGE=100-300
 
599
PRIMER_INTERNAL_OLIGO_EXCLUDED_REGION=6,50
 
600
PRIMER_INTERNAL_OLIGO_EXCLUDED_REGION=61,15
 
601
INCLUDED_REGION=3,250
 
602
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNAAGCTAAGCTGTCGATGCGGTGGAGACGATACGGTAAGCTAGCTAACTGGTCAAAGCTAGCGGTAGCTTAGCTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNACTCACTGTCATTTCCAAACAATTCATCTCTCTCTCATATATATATATATATATATATATATAT
 
603
PRIMER_LEFT_EXPLAIN=considered 151, too many Ns 99, ok 52
 
604
PRIMER_RIGHT_EXPLAIN=considered 151, too many Ns 148, ok 3
 
605
PRIMER_INTERNAL_OLIGO_EXPLAIN=considered 226, too many Ns 175, overlap excluded region 47, ok 4
 
606
PRIMER_PAIR_EXPLAIN=considered 23, no internal oligo 15, ok 8
 
607
PRIMER_PAIR_PENALTY=0.3310
 
608
PRIMER_LEFT_PENALTY=0.243965
 
609
PRIMER_RIGHT_PENALTY=0.087031
 
610
PRIMER_INTERNAL_OLIGO_PENALTY=3.811648
 
611
PRIMER_LEFT_SEQUENCE=ACGTCATCTCATCAAATTTGATTG
 
612
PRIMER_RIGHT_SEQUENCE=GAATTGTTTGGAAATGACAGTGAG
 
613
PRIMER_INTERNAL_OLIGO_SEQUENCE=CTGGTCAAAGCTAGCGGTAGCTTAG
 
614
PRIMER_LEFT=4,24
 
615
PRIMER_RIGHT=252,24
 
616
PRIMER_INTERNAL_OLIGO=76,25
 
617
PRIMER_LEFT_TM=60.244
 
618
PRIMER_RIGHT_TM=59.913
 
619
PRIMER_INTERNAL_OLIGO_TM=63.812
 
620
PRIMER_LEFT_GC_PERCENT=33.333
 
621
PRIMER_RIGHT_GC_PERCENT=37.500
 
622
PRIMER_INTERNAL_OLIGO_GC_PERCENT=52.000
 
623
PRIMER_LEFT_SELF_ANY=12.00
 
624
PRIMER_RIGHT_SELF_ANY=4.00
 
625
PRIMER_INTERNAL_OLIGO_SELF_ANY=12.00
 
626
PRIMER_LEFT_SELF_END=10.00
 
627
PRIMER_RIGHT_SELF_END=1.00
 
628
PRIMER_INTERNAL_OLIGO_SELF_END=12.00
 
629
PRIMER_LEFT_END_STABILITY=6.9000
 
630
PRIMER_RIGHT_END_STABILITY=6.4000
 
631
PRIMER_PAIR_COMPL_ANY=6.00
 
632
PRIMER_PAIR_COMPL_END=1.00
 
633
PRIMER_PRODUCT_SIZE=249
 
634
PRIMER_PAIR_PENALTY_1=0.3310
 
635
PRIMER_LEFT_1_PENALTY=0.243965
 
636
PRIMER_RIGHT_1_PENALTY=0.087031
 
637
PRIMER_INTERNAL_OLIGO_1_PENALTY=3.811648
 
638
PRIMER_LEFT_1_SEQUENCE=CACGTCATCTCATCAAATTTGATT
 
639
PRIMER_RIGHT_1_SEQUENCE=GAATTGTTTGGAAATGACAGTGAG
 
640
PRIMER_INTERNAL_OLIGO_1_SEQUENCE=CTGGTCAAAGCTAGCGGTAGCTTAG
 
641
PRIMER_LEFT_1=3,24
 
642
PRIMER_RIGHT_1=252,24
 
643
PRIMER_INTERNAL_OLIGO_1=76,25
 
644
PRIMER_LEFT_1_TM=60.244
 
645
PRIMER_RIGHT_1_TM=59.913
 
646
PRIMER_INTERNAL_OLIGO_1_TM=63.812
 
647
PRIMER_LEFT_1_GC_PERCENT=33.333
 
648
PRIMER_RIGHT_1_GC_PERCENT=37.500
 
649
PRIMER_INTERNAL_OLIGO_1_GC_PERCENT=52.000
 
650
PRIMER_LEFT_1_SELF_ANY=12.00
 
651
PRIMER_RIGHT_1_SELF_ANY=4.00
 
652
PRIMER_INTERNAL_OLIGO_1_SELF_ANY=12.00
 
653
PRIMER_LEFT_1_SELF_END=10.00
 
654
PRIMER_RIGHT_1_SELF_END=1.00
 
655
PRIMER_INTERNAL_OLIGO_1_SELF_END=12.00
 
656
PRIMER_LEFT_1_END_STABILITY=6.9000
 
657
PRIMER_RIGHT_1_END_STABILITY=6.4000
 
658
PRIMER_PAIR_1_COMPL_ANY=7.00
 
659
PRIMER_PAIR_1_COMPL_END=2.00
 
660
PRIMER_PRODUCT_SIZE_1=250
 
661
PRIMER_PAIR_PENALTY_2=0.3864
 
662
PRIMER_LEFT_2_PENALTY=0.299404
 
663
PRIMER_RIGHT_2_PENALTY=0.087031
 
664
PRIMER_INTERNAL_OLIGO_2_PENALTY=3.811648
 
665
PRIMER_LEFT_2_SEQUENCE=GGAGACGATACGGTAAGCTAGCTA
 
666
PRIMER_RIGHT_2_SEQUENCE=GAATTGTTTGGAAATGACAGTGAG
 
667
PRIMER_INTERNAL_OLIGO_2_SEQUENCE=CTGGTCAAAGCTAGCGGTAGCTTAG
 
668
PRIMER_LEFT_2=51,24
 
669
PRIMER_RIGHT_2=252,24
 
670
PRIMER_INTERNAL_OLIGO_2=76,25
 
671
PRIMER_LEFT_2_TM=60.299
 
672
PRIMER_RIGHT_2_TM=59.913
 
673
PRIMER_INTERNAL_OLIGO_2_TM=63.812
 
674
PRIMER_LEFT_2_GC_PERCENT=50.000
 
675
PRIMER_RIGHT_2_GC_PERCENT=37.500
 
676
PRIMER_INTERNAL_OLIGO_2_GC_PERCENT=52.000
 
677
PRIMER_LEFT_2_SELF_ANY=8.00
 
678
PRIMER_RIGHT_2_SELF_ANY=4.00
 
679
PRIMER_INTERNAL_OLIGO_2_SELF_ANY=12.00
 
680
PRIMER_LEFT_2_SELF_END=6.00
 
681
PRIMER_RIGHT_2_SELF_END=1.00
 
682
PRIMER_INTERNAL_OLIGO_2_SELF_END=12.00
 
683
PRIMER_LEFT_2_END_STABILITY=7.2000
 
684
PRIMER_RIGHT_2_END_STABILITY=6.4000
 
685
PRIMER_PAIR_2_COMPL_ANY=3.00
 
686
PRIMER_PAIR_2_COMPL_END=1.00
 
687
PRIMER_PRODUCT_SIZE_2=202
 
688
PRIMER_PAIR_PENALTY_3=1.2615
 
689
PRIMER_LEFT_3_PENALTY=0.243965
 
690
PRIMER_RIGHT_3_PENALTY=1.017510
 
691
PRIMER_INTERNAL_OLIGO_3_PENALTY=3.811648
 
692
PRIMER_LEFT_3_SEQUENCE=ACGTCATCTCATCAAATTTGATTG
 
693
PRIMER_RIGHT_3_SEQUENCE=AATTGTTTGGAAATGACAGTGAGT
 
694
PRIMER_INTERNAL_OLIGO_3_SEQUENCE=CTGGTCAAAGCTAGCGGTAGCTTAG
 
695
PRIMER_LEFT_3=4,24
 
696
PRIMER_RIGHT_3=251,24
 
697
PRIMER_INTERNAL_OLIGO_3=76,25
 
698
PRIMER_LEFT_3_TM=60.244
 
699
PRIMER_RIGHT_3_TM=58.982
 
700
PRIMER_INTERNAL_OLIGO_3_TM=63.812
 
701
PRIMER_LEFT_3_GC_PERCENT=33.333
 
702
PRIMER_RIGHT_3_GC_PERCENT=33.333
 
703
PRIMER_INTERNAL_OLIGO_3_GC_PERCENT=52.000
 
704
PRIMER_LEFT_3_SELF_ANY=12.00
 
705
PRIMER_RIGHT_3_SELF_ANY=4.00
 
706
PRIMER_INTERNAL_OLIGO_3_SELF_ANY=12.00
 
707
PRIMER_LEFT_3_SELF_END=10.00
 
708
PRIMER_RIGHT_3_SELF_END=3.00
 
709
PRIMER_INTERNAL_OLIGO_3_SELF_END=12.00
 
710
PRIMER_LEFT_3_END_STABILITY=6.9000
 
711
PRIMER_RIGHT_3_END_STABILITY=6.4000
 
712
PRIMER_PAIR_3_COMPL_ANY=6.00
 
713
PRIMER_PAIR_3_COMPL_END=1.00
 
714
PRIMER_PRODUCT_SIZE_3=248
 
715
PRIMER_PAIR_PENALTY_4=1.2615
 
716
PRIMER_LEFT_4_PENALTY=0.243965
 
717
PRIMER_RIGHT_4_PENALTY=1.017510
 
718
PRIMER_INTERNAL_OLIGO_4_PENALTY=3.811648
 
719
PRIMER_LEFT_4_SEQUENCE=CACGTCATCTCATCAAATTTGATT
 
720
PRIMER_RIGHT_4_SEQUENCE=AATTGTTTGGAAATGACAGTGAGT
 
721
PRIMER_INTERNAL_OLIGO_4_SEQUENCE=CTGGTCAAAGCTAGCGGTAGCTTAG
 
722
PRIMER_LEFT_4=3,24
 
723
PRIMER_RIGHT_4=251,24
 
724
PRIMER_INTERNAL_OLIGO_4=76,25
 
725
PRIMER_LEFT_4_TM=60.244
 
726
PRIMER_RIGHT_4_TM=58.982
 
727
PRIMER_INTERNAL_OLIGO_4_TM=63.812
 
728
PRIMER_LEFT_4_GC_PERCENT=33.333
 
729
PRIMER_RIGHT_4_GC_PERCENT=33.333
 
730
PRIMER_INTERNAL_OLIGO_4_GC_PERCENT=52.000
 
731
PRIMER_LEFT_4_SELF_ANY=12.00
 
732
PRIMER_RIGHT_4_SELF_ANY=4.00
 
733
PRIMER_INTERNAL_OLIGO_4_SELF_ANY=12.00
 
734
PRIMER_LEFT_4_SELF_END=10.00
 
735
PRIMER_RIGHT_4_SELF_END=3.00
 
736
PRIMER_INTERNAL_OLIGO_4_SELF_END=12.00
 
737
PRIMER_LEFT_4_END_STABILITY=6.9000
 
738
PRIMER_RIGHT_4_END_STABILITY=6.4000
 
739
PRIMER_PAIR_4_COMPL_ANY=7.00
 
740
PRIMER_PAIR_4_COMPL_END=2.00
 
741
PRIMER_PRODUCT_SIZE_4=249
 
742
=
 
743
MARKER_NAME=boundary_test_21
 
744
PRIMER_NUM_NS_ACCEPTED=0
 
745
PRIMER_MIN_GC=0
 
746
PRIMER_MAX_GC=100
 
747
PRIMER_INTERNAL_OLIGO_MIN_GC=0
 
748
PRIMER_INTERNAL_OLIGO_MIN_TM=55.7
 
749
PRIMER_INTERNAL_OLIGO_MAX_TM=55.9
 
750
PRIMER_INTERNAL_OLIGO_OPT_TM=55.8
 
751
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGAAAAAAAAAAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGNNNACTCACTGTCATTTCCAAACAATTCNN
 
752
PRIMER_LEFT_EXPLAIN=considered 77, too many Ns 27, ok 50
 
753
PRIMER_RIGHT_EXPLAIN=considered 77, too many Ns 28, ok 49
 
754
PRIMER_INTERNAL_OLIGO_EXPLAIN=considered 152, too many Ns 57, low tm 1, high tm 93, ok 1
 
755
PRIMER_PAIR_EXPLAIN=considered 323, unacceptable product size 223, no internal oligo 87, ok 13
 
756
PRIMER_PAIR_PENALTY=0.3310
 
757
PRIMER_LEFT_PENALTY=0.243965
 
758
PRIMER_RIGHT_PENALTY=0.087031
 
759
PRIMER_INTERNAL_OLIGO_PENALTY=0.038050
 
760
PRIMER_LEFT_SEQUENCE=ACGTCATCTCATCAAATTTGATTG
 
761
PRIMER_RIGHT_SEQUENCE=GAATTGTTTGGAAATGACAGTGAG
 
762
PRIMER_INTERNAL_OLIGO_SEQUENCE=AAAAAAAAAAAAAAAAAAAAAAAAA
 
763
PRIMER_LEFT=4,24
 
764
PRIMER_RIGHT=174,24
 
765
PRIMER_INTERNAL_OLIGO=62,25
 
766
PRIMER_LEFT_TM=60.244
 
767
PRIMER_RIGHT_TM=59.913
 
768
PRIMER_INTERNAL_OLIGO_TM=55.838
 
769
PRIMER_LEFT_GC_PERCENT=33.333
 
770
PRIMER_RIGHT_GC_PERCENT=37.500
 
771
PRIMER_INTERNAL_OLIGO_GC_PERCENT=0.000
 
772
PRIMER_LEFT_SELF_ANY=12.00
 
773
PRIMER_RIGHT_SELF_ANY=4.00
 
774
PRIMER_INTERNAL_OLIGO_SELF_ANY=0.00
 
775
PRIMER_LEFT_SELF_END=10.00
 
776
PRIMER_RIGHT_SELF_END=1.00
 
777
PRIMER_INTERNAL_OLIGO_SELF_END=0.00
 
778
PRIMER_LEFT_END_STABILITY=6.9000
 
779
PRIMER_RIGHT_END_STABILITY=6.4000
 
780
PRIMER_PAIR_COMPL_ANY=6.00
 
781
PRIMER_PAIR_COMPL_END=1.00
 
782
PRIMER_PRODUCT_SIZE=171
 
783
PRIMER_PAIR_PENALTY_1=0.3310
 
784
PRIMER_LEFT_1_PENALTY=0.243965
 
785
PRIMER_RIGHT_1_PENALTY=0.087031
 
786
PRIMER_INTERNAL_OLIGO_1_PENALTY=0.038050
 
787
PRIMER_LEFT_1_SEQUENCE=CACGTCATCTCATCAAATTTGATT
 
788
PRIMER_RIGHT_1_SEQUENCE=GAATTGTTTGGAAATGACAGTGAG
 
789
PRIMER_INTERNAL_OLIGO_1_SEQUENCE=AAAAAAAAAAAAAAAAAAAAAAAAA
 
790
PRIMER_LEFT_1=3,24
 
791
PRIMER_RIGHT_1=174,24
 
792
PRIMER_INTERNAL_OLIGO_1=62,25
 
793
PRIMER_LEFT_1_TM=60.244
 
794
PRIMER_RIGHT_1_TM=59.913
 
795
PRIMER_INTERNAL_OLIGO_1_TM=55.838
 
796
PRIMER_LEFT_1_GC_PERCENT=33.333
 
797
PRIMER_RIGHT_1_GC_PERCENT=37.500
 
798
PRIMER_INTERNAL_OLIGO_1_GC_PERCENT=0.000
 
799
PRIMER_LEFT_1_SELF_ANY=12.00
 
800
PRIMER_RIGHT_1_SELF_ANY=4.00
 
801
PRIMER_INTERNAL_OLIGO_1_SELF_ANY=0.00
 
802
PRIMER_LEFT_1_SELF_END=10.00
 
803
PRIMER_RIGHT_1_SELF_END=1.00
 
804
PRIMER_INTERNAL_OLIGO_1_SELF_END=0.00
 
805
PRIMER_LEFT_1_END_STABILITY=6.9000
 
806
PRIMER_RIGHT_1_END_STABILITY=6.4000
 
807
PRIMER_PAIR_1_COMPL_ANY=7.00
 
808
PRIMER_PAIR_1_COMPL_END=2.00
 
809
PRIMER_PRODUCT_SIZE_1=172
 
810
PRIMER_PAIR_PENALTY_2=1.2615
 
811
PRIMER_LEFT_2_PENALTY=0.243965
 
812
PRIMER_RIGHT_2_PENALTY=1.017510
 
813
PRIMER_INTERNAL_OLIGO_2_PENALTY=0.038050
 
814
PRIMER_LEFT_2_SEQUENCE=ACGTCATCTCATCAAATTTGATTG
 
815
PRIMER_RIGHT_2_SEQUENCE=AATTGTTTGGAAATGACAGTGAGT
 
816
PRIMER_INTERNAL_OLIGO_2_SEQUENCE=AAAAAAAAAAAAAAAAAAAAAAAAA
 
817
PRIMER_LEFT_2=4,24
 
818
PRIMER_RIGHT_2=173,24
 
819
PRIMER_INTERNAL_OLIGO_2=62,25
 
820
PRIMER_LEFT_2_TM=60.244
 
821
PRIMER_RIGHT_2_TM=58.982
 
822
PRIMER_INTERNAL_OLIGO_2_TM=55.838
 
823
PRIMER_LEFT_2_GC_PERCENT=33.333
 
824
PRIMER_RIGHT_2_GC_PERCENT=33.333
 
825
PRIMER_INTERNAL_OLIGO_2_GC_PERCENT=0.000
 
826
PRIMER_LEFT_2_SELF_ANY=12.00
 
827
PRIMER_RIGHT_2_SELF_ANY=4.00
 
828
PRIMER_INTERNAL_OLIGO_2_SELF_ANY=0.00
 
829
PRIMER_LEFT_2_SELF_END=10.00
 
830
PRIMER_RIGHT_2_SELF_END=3.00
 
831
PRIMER_INTERNAL_OLIGO_2_SELF_END=0.00
 
832
PRIMER_LEFT_2_END_STABILITY=6.9000
 
833
PRIMER_RIGHT_2_END_STABILITY=6.4000
 
834
PRIMER_PAIR_2_COMPL_ANY=6.00
 
835
PRIMER_PAIR_2_COMPL_END=1.00
 
836
PRIMER_PRODUCT_SIZE_2=170
 
837
PRIMER_PAIR_PENALTY_3=1.2615
 
838
PRIMER_LEFT_3_PENALTY=0.243965
 
839
PRIMER_RIGHT_3_PENALTY=1.017510
 
840
PRIMER_INTERNAL_OLIGO_3_PENALTY=0.038050
 
841
PRIMER_LEFT_3_SEQUENCE=CACGTCATCTCATCAAATTTGATT
 
842
PRIMER_RIGHT_3_SEQUENCE=AATTGTTTGGAAATGACAGTGAGT
 
843
PRIMER_INTERNAL_OLIGO_3_SEQUENCE=AAAAAAAAAAAAAAAAAAAAAAAAA
 
844
PRIMER_LEFT_3=3,24
 
845
PRIMER_RIGHT_3=173,24
 
846
PRIMER_INTERNAL_OLIGO_3=62,25
 
847
PRIMER_LEFT_3_TM=60.244
 
848
PRIMER_RIGHT_3_TM=58.982
 
849
PRIMER_INTERNAL_OLIGO_3_TM=55.838
 
850
PRIMER_LEFT_3_GC_PERCENT=33.333
 
851
PRIMER_RIGHT_3_GC_PERCENT=33.333
 
852
PRIMER_INTERNAL_OLIGO_3_GC_PERCENT=0.000
 
853
PRIMER_LEFT_3_SELF_ANY=12.00
 
854
PRIMER_RIGHT_3_SELF_ANY=4.00
 
855
PRIMER_INTERNAL_OLIGO_3_SELF_ANY=0.00
 
856
PRIMER_LEFT_3_SELF_END=10.00
 
857
PRIMER_RIGHT_3_SELF_END=3.00
 
858
PRIMER_INTERNAL_OLIGO_3_SELF_END=0.00
 
859
PRIMER_LEFT_3_END_STABILITY=6.9000
 
860
PRIMER_RIGHT_3_END_STABILITY=6.4000
 
861
PRIMER_PAIR_3_COMPL_ANY=7.00
 
862
PRIMER_PAIR_3_COMPL_END=2.00
 
863
PRIMER_PRODUCT_SIZE_3=171
 
864
PRIMER_PAIR_PENALTY_4=29.3957
 
865
PRIMER_LEFT_4_PENALTY=29.308664
 
866
PRIMER_RIGHT_4_PENALTY=0.087031
 
867
PRIMER_INTERNAL_OLIGO_4_PENALTY=0.038050
 
868
PRIMER_LEFT_4_SEQUENCE=GGGGGGGGGGGGGGGGGGGGGGGG
 
869
PRIMER_RIGHT_4_SEQUENCE=GAATTGTTTGGAAATGACAGTGAG
 
870
PRIMER_INTERNAL_OLIGO_4_SEQUENCE=AAAAAAAAAAAAAAAAAAAAAAAAA
 
871
PRIMER_LEFT_4=38,24
 
872
PRIMER_RIGHT_4=174,24
 
873
PRIMER_INTERNAL_OLIGO_4=62,25
 
874
PRIMER_LEFT_4_TM=89.309
 
875
PRIMER_RIGHT_4_TM=59.913
 
876
PRIMER_INTERNAL_OLIGO_4_TM=55.838
 
877
PRIMER_LEFT_4_GC_PERCENT=100.000
 
878
PRIMER_RIGHT_4_GC_PERCENT=37.500
 
879
PRIMER_INTERNAL_OLIGO_4_GC_PERCENT=0.000
 
880
PRIMER_LEFT_4_SELF_ANY=0.00
 
881
PRIMER_RIGHT_4_SELF_ANY=4.00
 
882
PRIMER_INTERNAL_OLIGO_4_SELF_ANY=0.00
 
883
PRIMER_LEFT_4_SELF_END=0.00
 
884
PRIMER_RIGHT_4_SELF_END=1.00
 
885
PRIMER_INTERNAL_OLIGO_4_SELF_END=0.00
 
886
PRIMER_LEFT_4_END_STABILITY=12.4000
 
887
PRIMER_RIGHT_4_END_STABILITY=6.4000
 
888
PRIMER_PAIR_4_COMPL_ANY=1.00
 
889
PRIMER_PAIR_4_COMPL_END=0.00
 
890
PRIMER_PRODUCT_SIZE_4=137
 
891
=
 
892
MARKER_NAME=boundary_test_22
 
893
PRIMER_EXPLAIN_FLAG=1
 
894
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNACGTACGTACGTTGCAGTCGACGCANNACTCACTGTCATTTCCAAACAATTCNN
 
895
PRIMER_PRODUCT_SIZE_RANGE=80-80
 
896
PRIMER_MIN_TM=0.0
 
897
PRIMER_MAX_TM=100.0
 
898
PRIMER_MIN_SIZE=25
 
899
PRIMER_MAX_SIZE=25
 
900
PRIMER_INTERNAL_OLIGO_MIN_SIZE=25
 
901
PRIMER_INTERNAL_OLIGO_MAX_SIZE=25
 
902
PRIMER_INTERNAL_OLIGO_OPT_SIZE=25
 
903
PRIMER_OPT_SIZE=25
 
904
PRIMER_MAX_GC=100
 
905
PRIMER_MIN_GC=0
 
906
PRIMER_SELF_END=100
 
907
PRIMER_SELF_ANY=100
 
908
PRIMER_INTERNAL_OLIGO_SELF_ANY=100
 
909
PRIMER_INTERNAL_OLIGO_SELF_END=100 
 
910
PRIMER_INTERNAL_OLIGO_MAX_TM=100
 
911
PRIMER_INTERNAL_OLIGO_MIN_TM=30
 
912
PRIMER_INTERNAL_OLIGO_MAX_GC=100
 
913
PRIMER_INTERNAL_OLIGO_MIN_GC=0
 
914
PRIMER_PICK_INTERNAL_OLIGO=1
 
915
COMMENT=should succeed
 
916
PRIMER_LEFT_EXPLAIN=considered 5, too many Ns 4, ok 1
 
917
PRIMER_RIGHT_EXPLAIN=considered 5, too many Ns 4, ok 1
 
918
PRIMER_INTERNAL_OLIGO_EXPLAIN=considered 60, too many Ns 57, ok 3
 
919
PRIMER_PAIR_EXPLAIN=considered 1, ok 1
 
920
PRIMER_PAIR_PENALTY=3.3813
 
921
PRIMER_LEFT_PENALTY=2.731673
 
922
PRIMER_RIGHT_PENALTY=0.649600
 
923
PRIMER_INTERNAL_OLIGO_PENALTY=15.695378
 
924
PRIMER_LEFT_SEQUENCE=CACGTCATCTCATCAAATTTGATTG
 
925
PRIMER_RIGHT_SEQUENCE=GAATTGTTTGGAAATGACAGTGAGT
 
926
PRIMER_INTERNAL_OLIGO_SEQUENCE=ACGTACGTACGTTGCAGTCGACGCA
 
927
PRIMER_LEFT=3,25
 
928
PRIMER_RIGHT=82,25
 
929
PRIMER_INTERNAL_OLIGO=31,25
 
930
PRIMER_LEFT_TM=62.732
 
931
PRIMER_RIGHT_TM=60.650
 
932
PRIMER_INTERNAL_OLIGO_TM=71.495
 
933
PRIMER_LEFT_GC_PERCENT=36.000
 
934
PRIMER_RIGHT_GC_PERCENT=36.000
 
935
PRIMER_INTERNAL_OLIGO_GC_PERCENT=56.000
 
936
PRIMER_LEFT_SELF_ANY=12.00
 
937
PRIMER_RIGHT_SELF_ANY=4.00
 
938
PRIMER_INTERNAL_OLIGO_SELF_ANY=12.00
 
939
PRIMER_LEFT_SELF_END=10.00
 
940
PRIMER_RIGHT_SELF_END=3.00
 
941
PRIMER_INTERNAL_OLIGO_SELF_END=8.00
 
942
PRIMER_LEFT_END_STABILITY=6.9000
 
943
PRIMER_RIGHT_END_STABILITY=6.4000
 
944
PRIMER_PAIR_COMPL_ANY=7.00
 
945
PRIMER_PAIR_COMPL_END=1.00
 
946
PRIMER_PRODUCT_SIZE=80
 
947
=
 
948
MARKER_NAME=boundary_test_23
 
949
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNACGTACGTACGTTGCAGTCGACGCANNACTCACTGTCATTTCCAAACAATTCNN
 
950
INCLUDED_REGION=3,80
 
951
PRIMER_INTERNAL_OLIGO_EXCLUDED_REGION=2,1
 
952
COMMENT=should succeed with warning (internal oligo excluded region outside of included region)
 
953
PRIMER_WARNING=PRIMER_INTERNAL_OLIGO_EXCLUDED_REGION outside of INCLUDED_REGION
 
954
PRIMER_LEFT_EXPLAIN=considered 1, ok 1
 
955
PRIMER_RIGHT_EXPLAIN=considered 1, ok 1
 
956
PRIMER_INTERNAL_OLIGO_EXPLAIN=considered 56, too many Ns 53, ok 3
 
957
PRIMER_PAIR_EXPLAIN=considered 1, ok 1
 
958
PRIMER_PAIR_PENALTY=3.3813
 
959
PRIMER_LEFT_PENALTY=2.731673
 
960
PRIMER_RIGHT_PENALTY=0.649600
 
961
PRIMER_INTERNAL_OLIGO_PENALTY=15.695378
 
962
PRIMER_LEFT_SEQUENCE=CACGTCATCTCATCAAATTTGATTG
 
963
PRIMER_RIGHT_SEQUENCE=GAATTGTTTGGAAATGACAGTGAGT
 
964
PRIMER_INTERNAL_OLIGO_SEQUENCE=ACGTACGTACGTTGCAGTCGACGCA
 
965
PRIMER_LEFT=3,25
 
966
PRIMER_RIGHT=82,25
 
967
PRIMER_INTERNAL_OLIGO=31,25
 
968
PRIMER_LEFT_TM=62.732
 
969
PRIMER_RIGHT_TM=60.650
 
970
PRIMER_INTERNAL_OLIGO_TM=71.495
 
971
PRIMER_LEFT_GC_PERCENT=36.000
 
972
PRIMER_RIGHT_GC_PERCENT=36.000
 
973
PRIMER_INTERNAL_OLIGO_GC_PERCENT=56.000
 
974
PRIMER_LEFT_SELF_ANY=12.00
 
975
PRIMER_RIGHT_SELF_ANY=4.00
 
976
PRIMER_INTERNAL_OLIGO_SELF_ANY=12.00
 
977
PRIMER_LEFT_SELF_END=10.00
 
978
PRIMER_RIGHT_SELF_END=3.00
 
979
PRIMER_INTERNAL_OLIGO_SELF_END=8.00
 
980
PRIMER_LEFT_END_STABILITY=6.9000
 
981
PRIMER_RIGHT_END_STABILITY=6.4000
 
982
PRIMER_PAIR_COMPL_ANY=7.00
 
983
PRIMER_PAIR_COMPL_END=1.00
 
984
PRIMER_PRODUCT_SIZE=80
 
985
=
 
986
MARKER_NAME=boundary_test_24
 
987
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNACGTACGTACGTTGCAGTCGACGCANNACTCACTGTCATTTCCAAACAATTCNN
 
988
INCLUDED_REGION=3,80
 
989
PRIMER_INTERNAL_OLIGO_EXCLUDED_REGION=3,1
 
990
COMMENT=should succeed
 
991
PRIMER_LEFT_EXPLAIN=considered 1, ok 1
 
992
PRIMER_RIGHT_EXPLAIN=considered 1, ok 1
 
993
PRIMER_INTERNAL_OLIGO_EXPLAIN=considered 56, too many Ns 53, overlap excluded region 1, ok 2
 
994
PRIMER_PAIR_EXPLAIN=considered 1, ok 1
 
995
PRIMER_PAIR_PENALTY=3.3813
 
996
PRIMER_LEFT_PENALTY=2.731673
 
997
PRIMER_RIGHT_PENALTY=0.649600
 
998
PRIMER_INTERNAL_OLIGO_PENALTY=15.695378
 
999
PRIMER_LEFT_SEQUENCE=CACGTCATCTCATCAAATTTGATTG
 
1000
PRIMER_RIGHT_SEQUENCE=GAATTGTTTGGAAATGACAGTGAGT
 
1001
PRIMER_INTERNAL_OLIGO_SEQUENCE=ACGTACGTACGTTGCAGTCGACGCA
 
1002
PRIMER_LEFT=3,25
 
1003
PRIMER_RIGHT=82,25
 
1004
PRIMER_INTERNAL_OLIGO=31,25
 
1005
PRIMER_LEFT_TM=62.732
 
1006
PRIMER_RIGHT_TM=60.650
 
1007
PRIMER_INTERNAL_OLIGO_TM=71.495
 
1008
PRIMER_LEFT_GC_PERCENT=36.000
 
1009
PRIMER_RIGHT_GC_PERCENT=36.000
 
1010
PRIMER_INTERNAL_OLIGO_GC_PERCENT=56.000
 
1011
PRIMER_LEFT_SELF_ANY=12.00
 
1012
PRIMER_RIGHT_SELF_ANY=4.00
 
1013
PRIMER_INTERNAL_OLIGO_SELF_ANY=12.00
 
1014
PRIMER_LEFT_SELF_END=10.00
 
1015
PRIMER_RIGHT_SELF_END=3.00
 
1016
PRIMER_INTERNAL_OLIGO_SELF_END=8.00
 
1017
PRIMER_LEFT_END_STABILITY=6.9000
 
1018
PRIMER_RIGHT_END_STABILITY=6.4000
 
1019
PRIMER_PAIR_COMPL_ANY=7.00
 
1020
PRIMER_PAIR_COMPL_END=1.00
 
1021
PRIMER_PRODUCT_SIZE=80
 
1022
=
 
1023
MARKER_NAME=boundary_test_25
 
1024
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNACGTACGTACGTTGCAGTCGACGCANNACTCACTGTCATTTCCAAACAATTCNN
 
1025
INCLUDED_REGION=3,80
 
1026
PRIMER_INTERNAL_OLIGO_EXCLUDED_REGION=1,3
 
1027
COMMENT=should succeed with warning (internal oligo excluded region outside of included region)
 
1028
PRIMER_WARNING=PRIMER_INTERNAL_OLIGO_EXCLUDED_REGION outside of INCLUDED_REGION
 
1029
PRIMER_LEFT_EXPLAIN=considered 1, ok 1
 
1030
PRIMER_RIGHT_EXPLAIN=considered 1, ok 1
 
1031
PRIMER_INTERNAL_OLIGO_EXPLAIN=considered 56, too many Ns 53, overlap excluded region 1, ok 2
 
1032
PRIMER_PAIR_EXPLAIN=considered 1, ok 1
 
1033
PRIMER_PAIR_PENALTY=3.3813
 
1034
PRIMER_LEFT_PENALTY=2.731673
 
1035
PRIMER_RIGHT_PENALTY=0.649600
 
1036
PRIMER_INTERNAL_OLIGO_PENALTY=15.695378
 
1037
PRIMER_LEFT_SEQUENCE=CACGTCATCTCATCAAATTTGATTG
 
1038
PRIMER_RIGHT_SEQUENCE=GAATTGTTTGGAAATGACAGTGAGT
 
1039
PRIMER_INTERNAL_OLIGO_SEQUENCE=ACGTACGTACGTTGCAGTCGACGCA
 
1040
PRIMER_LEFT=3,25
 
1041
PRIMER_RIGHT=82,25
 
1042
PRIMER_INTERNAL_OLIGO=31,25
 
1043
PRIMER_LEFT_TM=62.732
 
1044
PRIMER_RIGHT_TM=60.650
 
1045
PRIMER_INTERNAL_OLIGO_TM=71.495
 
1046
PRIMER_LEFT_GC_PERCENT=36.000
 
1047
PRIMER_RIGHT_GC_PERCENT=36.000
 
1048
PRIMER_INTERNAL_OLIGO_GC_PERCENT=56.000
 
1049
PRIMER_LEFT_SELF_ANY=12.00
 
1050
PRIMER_RIGHT_SELF_ANY=4.00
 
1051
PRIMER_INTERNAL_OLIGO_SELF_ANY=12.00
 
1052
PRIMER_LEFT_SELF_END=10.00
 
1053
PRIMER_RIGHT_SELF_END=3.00
 
1054
PRIMER_INTERNAL_OLIGO_SELF_END=8.00
 
1055
PRIMER_LEFT_END_STABILITY=6.9000
 
1056
PRIMER_RIGHT_END_STABILITY=6.4000
 
1057
PRIMER_PAIR_COMPL_ANY=7.00
 
1058
PRIMER_PAIR_COMPL_END=1.00
 
1059
PRIMER_PRODUCT_SIZE=80
 
1060
=
 
1061
MARKER_NAME=boundary_test_26
 
1062
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNACGTACGTACGTTGCAGTCGACGCANNACTCACTGTCATTTCCAAACAATTCNN
 
1063
INCLUDED_REGION=3,80
 
1064
PRIMER_INTERNAL_OLIGO_EXCLUDED_REGION=30,1
 
1065
COMMENT=should succeed
 
1066
PRIMER_LEFT_EXPLAIN=considered 1, ok 1
 
1067
PRIMER_RIGHT_EXPLAIN=considered 1, ok 1
 
1068
PRIMER_INTERNAL_OLIGO_EXPLAIN=considered 56, too many Ns 53, ok 3
 
1069
PRIMER_PAIR_EXPLAIN=considered 1, ok 1
 
1070
PRIMER_PAIR_PENALTY=3.3813
 
1071
PRIMER_LEFT_PENALTY=2.731673
 
1072
PRIMER_RIGHT_PENALTY=0.649600
 
1073
PRIMER_INTERNAL_OLIGO_PENALTY=15.695378
 
1074
PRIMER_LEFT_SEQUENCE=CACGTCATCTCATCAAATTTGATTG
 
1075
PRIMER_RIGHT_SEQUENCE=GAATTGTTTGGAAATGACAGTGAGT
 
1076
PRIMER_INTERNAL_OLIGO_SEQUENCE=ACGTACGTACGTTGCAGTCGACGCA
 
1077
PRIMER_LEFT=3,25
 
1078
PRIMER_RIGHT=82,25
 
1079
PRIMER_INTERNAL_OLIGO=31,25
 
1080
PRIMER_LEFT_TM=62.732
 
1081
PRIMER_RIGHT_TM=60.650
 
1082
PRIMER_INTERNAL_OLIGO_TM=71.495
 
1083
PRIMER_LEFT_GC_PERCENT=36.000
 
1084
PRIMER_RIGHT_GC_PERCENT=36.000
 
1085
PRIMER_INTERNAL_OLIGO_GC_PERCENT=56.000
 
1086
PRIMER_LEFT_SELF_ANY=12.00
 
1087
PRIMER_RIGHT_SELF_ANY=4.00
 
1088
PRIMER_INTERNAL_OLIGO_SELF_ANY=12.00
 
1089
PRIMER_LEFT_SELF_END=10.00
 
1090
PRIMER_RIGHT_SELF_END=3.00
 
1091
PRIMER_INTERNAL_OLIGO_SELF_END=8.00
 
1092
PRIMER_LEFT_END_STABILITY=6.9000
 
1093
PRIMER_RIGHT_END_STABILITY=6.4000
 
1094
PRIMER_PAIR_COMPL_ANY=7.00
 
1095
PRIMER_PAIR_COMPL_END=1.00
 
1096
PRIMER_PRODUCT_SIZE=80
 
1097
=
 
1098
MARKER_NAME=boundary_test_27
 
1099
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNACGTACGTACGTTGCAGTCGACGCANNACTCACTGTCATTTCCAAACAATTCNN
 
1100
INCLUDED_REGION=3,80
 
1101
PRIMER_INTERNAL_OLIGO_EXCLUDED_REGION=31,1
 
1102
COMMENT=should fail w/ no legal internal oligo
 
1103
PRIMER_LEFT_EXPLAIN=considered 1, ok 1
 
1104
PRIMER_RIGHT_EXPLAIN=considered 1, ok 1
 
1105
PRIMER_INTERNAL_OLIGO_EXPLAIN=considered 56, too many Ns 53, overlap excluded region 1, ok 2
 
1106
PRIMER_PAIR_EXPLAIN=considered 1, no internal oligo 1, ok 0
 
1107
=
 
1108
MARKER_NAME=boundary_test_28
 
1109
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNACGTACGTACGTTGCAGTCGACGCANNACTCACTGTCATTTCCAAACAATTCNN
 
1110
INCLUDED_REGION=3,80
 
1111
PRIMER_INTERNAL_OLIGO_EXCLUDED_REGION=55,1
 
1112
COMMENT=should fail w/ no legal internal oligo
 
1113
PRIMER_LEFT_EXPLAIN=considered 1, ok 1
 
1114
PRIMER_RIGHT_EXPLAIN=considered 1, ok 1
 
1115
PRIMER_INTERNAL_OLIGO_EXPLAIN=considered 56, too many Ns 53, overlap excluded region 1, ok 2
 
1116
PRIMER_PAIR_EXPLAIN=considered 1, no internal oligo 1, ok 0
 
1117
=
 
1118
MARKER_NAME=boundary_test_29
 
1119
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNACGTACGTACGTTGCAGTCGACGCANNACTCACTGTCATTTCCAAACAATTCNN
 
1120
INCLUDED_REGION=3,80
 
1121
PRIMER_INTERNAL_OLIGO_EXCLUDED_REGION=56,1
 
1122
COMMENT=should succeed
 
1123
PRIMER_LEFT_EXPLAIN=considered 1, ok 1
 
1124
PRIMER_RIGHT_EXPLAIN=considered 1, ok 1
 
1125
PRIMER_INTERNAL_OLIGO_EXPLAIN=considered 56, too many Ns 53, ok 3
 
1126
PRIMER_PAIR_EXPLAIN=considered 1, ok 1
 
1127
PRIMER_PAIR_PENALTY=3.3813
 
1128
PRIMER_LEFT_PENALTY=2.731673
 
1129
PRIMER_RIGHT_PENALTY=0.649600
 
1130
PRIMER_INTERNAL_OLIGO_PENALTY=15.695378
 
1131
PRIMER_LEFT_SEQUENCE=CACGTCATCTCATCAAATTTGATTG
 
1132
PRIMER_RIGHT_SEQUENCE=GAATTGTTTGGAAATGACAGTGAGT
 
1133
PRIMER_INTERNAL_OLIGO_SEQUENCE=ACGTACGTACGTTGCAGTCGACGCA
 
1134
PRIMER_LEFT=3,25
 
1135
PRIMER_RIGHT=82,25
 
1136
PRIMER_INTERNAL_OLIGO=31,25
 
1137
PRIMER_LEFT_TM=62.732
 
1138
PRIMER_RIGHT_TM=60.650
 
1139
PRIMER_INTERNAL_OLIGO_TM=71.495
 
1140
PRIMER_LEFT_GC_PERCENT=36.000
 
1141
PRIMER_RIGHT_GC_PERCENT=36.000
 
1142
PRIMER_INTERNAL_OLIGO_GC_PERCENT=56.000
 
1143
PRIMER_LEFT_SELF_ANY=12.00
 
1144
PRIMER_RIGHT_SELF_ANY=4.00
 
1145
PRIMER_INTERNAL_OLIGO_SELF_ANY=12.00
 
1146
PRIMER_LEFT_SELF_END=10.00
 
1147
PRIMER_RIGHT_SELF_END=3.00
 
1148
PRIMER_INTERNAL_OLIGO_SELF_END=8.00
 
1149
PRIMER_LEFT_END_STABILITY=6.9000
 
1150
PRIMER_RIGHT_END_STABILITY=6.4000
 
1151
PRIMER_PAIR_COMPL_ANY=7.00
 
1152
PRIMER_PAIR_COMPL_END=1.00
 
1153
PRIMER_PRODUCT_SIZE=80
 
1154
=
 
1155
MARKER_NAME=boundary_test_30
 
1156
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNACGTACGTACGTTGCAGTCGACGCANNACTCACTGTCATTTCCAAACAATTCNN
 
1157
INCLUDED_REGION=3,80
 
1158
PRIMER_INTERNAL_OLIGO_EXCLUDED_REGION=82,1
 
1159
COMMENT=should succeed
 
1160
PRIMER_LEFT_EXPLAIN=considered 1, ok 1
 
1161
PRIMER_RIGHT_EXPLAIN=considered 1, ok 1
 
1162
PRIMER_INTERNAL_OLIGO_EXPLAIN=considered 56, too many Ns 53, overlap excluded region 1, ok 2
 
1163
PRIMER_PAIR_EXPLAIN=considered 1, ok 1
 
1164
PRIMER_PAIR_PENALTY=3.3813
 
1165
PRIMER_LEFT_PENALTY=2.731673
 
1166
PRIMER_RIGHT_PENALTY=0.649600
 
1167
PRIMER_INTERNAL_OLIGO_PENALTY=15.695378
 
1168
PRIMER_LEFT_SEQUENCE=CACGTCATCTCATCAAATTTGATTG
 
1169
PRIMER_RIGHT_SEQUENCE=GAATTGTTTGGAAATGACAGTGAGT
 
1170
PRIMER_INTERNAL_OLIGO_SEQUENCE=ACGTACGTACGTTGCAGTCGACGCA
 
1171
PRIMER_LEFT=3,25
 
1172
PRIMER_RIGHT=82,25
 
1173
PRIMER_INTERNAL_OLIGO=31,25
 
1174
PRIMER_LEFT_TM=62.732
 
1175
PRIMER_RIGHT_TM=60.650
 
1176
PRIMER_INTERNAL_OLIGO_TM=71.495
 
1177
PRIMER_LEFT_GC_PERCENT=36.000
 
1178
PRIMER_RIGHT_GC_PERCENT=36.000
 
1179
PRIMER_INTERNAL_OLIGO_GC_PERCENT=56.000
 
1180
PRIMER_LEFT_SELF_ANY=12.00
 
1181
PRIMER_RIGHT_SELF_ANY=4.00
 
1182
PRIMER_INTERNAL_OLIGO_SELF_ANY=12.00
 
1183
PRIMER_LEFT_SELF_END=10.00
 
1184
PRIMER_RIGHT_SELF_END=3.00
 
1185
PRIMER_INTERNAL_OLIGO_SELF_END=8.00
 
1186
PRIMER_LEFT_END_STABILITY=6.9000
 
1187
PRIMER_RIGHT_END_STABILITY=6.4000
 
1188
PRIMER_PAIR_COMPL_ANY=7.00
 
1189
PRIMER_PAIR_COMPL_END=1.00
 
1190
PRIMER_PRODUCT_SIZE=80
 
1191
=
 
1192
MARKER_NAME=boundary_test_31
 
1193
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNACGTACGTACGTTGCAGTCGACGCANNACTCACTGTCATTTCCAAACAATTCNN
 
1194
INCLUDED_REGION=3,80
 
1195
PRIMER_INTERNAL_OLIGO_EXCLUDED_REGION=83,1
 
1196
COMMENT=should generate warning (external oligo excluded region outside of included region)
 
1197
PRIMER_WARNING=PRIMER_INTERNAL_OLIGO_EXCLUDED_REGION outside of INCLUDED_REGION
 
1198
PRIMER_LEFT_EXPLAIN=considered 1, ok 1
 
1199
PRIMER_RIGHT_EXPLAIN=considered 1, ok 1
 
1200
PRIMER_INTERNAL_OLIGO_EXPLAIN=considered 56, too many Ns 53, ok 3
 
1201
PRIMER_PAIR_EXPLAIN=considered 1, ok 1
 
1202
PRIMER_PAIR_PENALTY=3.3813
 
1203
PRIMER_LEFT_PENALTY=2.731673
 
1204
PRIMER_RIGHT_PENALTY=0.649600
 
1205
PRIMER_INTERNAL_OLIGO_PENALTY=15.695378
 
1206
PRIMER_LEFT_SEQUENCE=CACGTCATCTCATCAAATTTGATTG
 
1207
PRIMER_RIGHT_SEQUENCE=GAATTGTTTGGAAATGACAGTGAGT
 
1208
PRIMER_INTERNAL_OLIGO_SEQUENCE=ACGTACGTACGTTGCAGTCGACGCA
 
1209
PRIMER_LEFT=3,25
 
1210
PRIMER_RIGHT=82,25
 
1211
PRIMER_INTERNAL_OLIGO=31,25
 
1212
PRIMER_LEFT_TM=62.732
 
1213
PRIMER_RIGHT_TM=60.650
 
1214
PRIMER_INTERNAL_OLIGO_TM=71.495
 
1215
PRIMER_LEFT_GC_PERCENT=36.000
 
1216
PRIMER_RIGHT_GC_PERCENT=36.000
 
1217
PRIMER_INTERNAL_OLIGO_GC_PERCENT=56.000
 
1218
PRIMER_LEFT_SELF_ANY=12.00
 
1219
PRIMER_RIGHT_SELF_ANY=4.00
 
1220
PRIMER_INTERNAL_OLIGO_SELF_ANY=12.00
 
1221
PRIMER_LEFT_SELF_END=10.00
 
1222
PRIMER_RIGHT_SELF_END=3.00
 
1223
PRIMER_INTERNAL_OLIGO_SELF_END=8.00
 
1224
PRIMER_LEFT_END_STABILITY=6.9000
 
1225
PRIMER_RIGHT_END_STABILITY=6.4000
 
1226
PRIMER_PAIR_COMPL_ANY=7.00
 
1227
PRIMER_PAIR_COMPL_END=1.00
 
1228
PRIMER_PRODUCT_SIZE=80
 
1229
=
 
1230
MARKER_NAME=boundary_test_32
 
1231
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNACGTACGTACGTTGCAGTCGACGCANNACTCACTGTCATTTCCAAACAATTCNN
 
1232
INCLUDED_REGION=3,80
 
1233
PRIMER_INTERNAL_OLIGO_EXCLUDED_REGION=82,2
 
1234
COMMENT=should generate warning (external oligo excluded region outside of included region)
 
1235
PRIMER_WARNING=PRIMER_INTERNAL_OLIGO_EXCLUDED_REGION outside of INCLUDED_REGION
 
1236
PRIMER_LEFT_EXPLAIN=considered 1, ok 1
 
1237
PRIMER_RIGHT_EXPLAIN=considered 1, ok 1
 
1238
PRIMER_INTERNAL_OLIGO_EXPLAIN=considered 56, too many Ns 53, overlap excluded region 1, ok 2
 
1239
PRIMER_PAIR_EXPLAIN=considered 1, ok 1
 
1240
PRIMER_PAIR_PENALTY=3.3813
 
1241
PRIMER_LEFT_PENALTY=2.731673
 
1242
PRIMER_RIGHT_PENALTY=0.649600
 
1243
PRIMER_INTERNAL_OLIGO_PENALTY=15.695378
 
1244
PRIMER_LEFT_SEQUENCE=CACGTCATCTCATCAAATTTGATTG
 
1245
PRIMER_RIGHT_SEQUENCE=GAATTGTTTGGAAATGACAGTGAGT
 
1246
PRIMER_INTERNAL_OLIGO_SEQUENCE=ACGTACGTACGTTGCAGTCGACGCA
 
1247
PRIMER_LEFT=3,25
 
1248
PRIMER_RIGHT=82,25
 
1249
PRIMER_INTERNAL_OLIGO=31,25
 
1250
PRIMER_LEFT_TM=62.732
 
1251
PRIMER_RIGHT_TM=60.650
 
1252
PRIMER_INTERNAL_OLIGO_TM=71.495
 
1253
PRIMER_LEFT_GC_PERCENT=36.000
 
1254
PRIMER_RIGHT_GC_PERCENT=36.000
 
1255
PRIMER_INTERNAL_OLIGO_GC_PERCENT=56.000
 
1256
PRIMER_LEFT_SELF_ANY=12.00
 
1257
PRIMER_RIGHT_SELF_ANY=4.00
 
1258
PRIMER_INTERNAL_OLIGO_SELF_ANY=12.00
 
1259
PRIMER_LEFT_SELF_END=10.00
 
1260
PRIMER_RIGHT_SELF_END=3.00
 
1261
PRIMER_INTERNAL_OLIGO_SELF_END=8.00
 
1262
PRIMER_LEFT_END_STABILITY=6.9000
 
1263
PRIMER_RIGHT_END_STABILITY=6.4000
 
1264
PRIMER_PAIR_COMPL_ANY=7.00
 
1265
PRIMER_PAIR_COMPL_END=1.00
 
1266
PRIMER_PRODUCT_SIZE=80
 
1267
=
 
1268
MARKER_NAME=boundary_test_33
 
1269
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNACGTACGTACGTTGCAGTCGACGCANNACTCACTGTCATTTCCAAACAATTCNN
 
1270
INCLUDED_REGION=3,80
 
1271
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
 
1272
COMMENT=should succeed (testing number of internal oligo excluded regions)
 
1273
PRIMER_LEFT_EXPLAIN=considered 1, ok 1
 
1274
PRIMER_RIGHT_EXPLAIN=considered 1, ok 1
 
1275
PRIMER_INTERNAL_OLIGO_EXPLAIN=considered 56, too many Ns 53, overlap excluded region 1, ok 2
 
1276
PRIMER_PAIR_EXPLAIN=considered 1, ok 1
 
1277
PRIMER_PAIR_PENALTY=3.3813
 
1278
PRIMER_LEFT_PENALTY=2.731673
 
1279
PRIMER_RIGHT_PENALTY=0.649600
 
1280
PRIMER_INTERNAL_OLIGO_PENALTY=15.695378
 
1281
PRIMER_LEFT_SEQUENCE=CACGTCATCTCATCAAATTTGATTG
 
1282
PRIMER_RIGHT_SEQUENCE=GAATTGTTTGGAAATGACAGTGAGT
 
1283
PRIMER_INTERNAL_OLIGO_SEQUENCE=ACGTACGTACGTTGCAGTCGACGCA
 
1284
PRIMER_LEFT=3,25
 
1285
PRIMER_RIGHT=82,25
 
1286
PRIMER_INTERNAL_OLIGO=31,25
 
1287
PRIMER_LEFT_TM=62.732
 
1288
PRIMER_RIGHT_TM=60.650
 
1289
PRIMER_INTERNAL_OLIGO_TM=71.495
 
1290
PRIMER_LEFT_GC_PERCENT=36.000
 
1291
PRIMER_RIGHT_GC_PERCENT=36.000
 
1292
PRIMER_INTERNAL_OLIGO_GC_PERCENT=56.000
 
1293
PRIMER_LEFT_SELF_ANY=12.00
 
1294
PRIMER_RIGHT_SELF_ANY=4.00
 
1295
PRIMER_INTERNAL_OLIGO_SELF_ANY=12.00
 
1296
PRIMER_LEFT_SELF_END=10.00
 
1297
PRIMER_RIGHT_SELF_END=3.00
 
1298
PRIMER_INTERNAL_OLIGO_SELF_END=8.00
 
1299
PRIMER_LEFT_END_STABILITY=6.9000
 
1300
PRIMER_RIGHT_END_STABILITY=6.4000
 
1301
PRIMER_PAIR_COMPL_ANY=7.00
 
1302
PRIMER_PAIR_COMPL_END=1.00
 
1303
PRIMER_PRODUCT_SIZE=80
 
1304
=
 
1305
MARKER_NAME=boundary_test_34
 
1306
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNACGTACGTACGTTGCAGTCGACGCANNACTCACTGTCATTTCCAAACAATTCNN
 
1307
INCLUDED_REGION=3,80
 
1308
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
 
1309
COMMENT=should fail (testing number of internal oligo excluded regions)
 
1310
PRIMER_ERROR=Too many elements for tag PRIMER_INTERNAL_OLIGO_EXCLUDED_REGION
 
1311
=