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Viewing changes to test/primer_boundary_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_boundary_input
 
1
PRIMER_SEQUENCE_ID=boundary_test_00
 
2
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
 
3
PRIMER_EXPLAIN_FLAG=1
 
4
PRIMER_MAX_POLY_X=0
 
5
PRIMER_INTERNAL_OLIGO_MAX_POLY_X=0
 
6
PRIMER_PRODUCT_SIZE_RANGE=50-100
 
7
PRIMER_MIN_TM=0.0
 
8
PRIMER_MAX_TM=100.0
 
9
PRIMER_MIN_SIZE=25
 
10
PRIMER_MAX_SIZE=25
 
11
PRIMER_OPT_SIZE=25
 
12
PRIMER_MAX_GC=100
 
13
PRIMER_MIN_GC=0
 
14
PRIMER_SELF_END=100
 
15
PRIMER_SELF_ANY=100
 
16
PRIMER_MAX_END_STABILITY=100.0
 
17
=
 
18
PRIMER_SEQUENCE_ID=boundary_test_01
 
19
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
 
20
PRIMER_PRODUCT_SIZE_RANGE=55-100
 
21
=
 
22
PRIMER_SEQUENCE_ID=boundary_test_02
 
23
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
 
24
PRIMER_PRODUCT_SIZE_RANGE=55-55
 
25
=
 
26
PRIMER_SEQUENCE_ID=boundary_test_03
 
27
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
 
28
PRIMER_PRODUCT_SIZE_RANGE=56-100
 
29
COMMENT=should fail
 
30
=
 
31
PRIMER_SEQUENCE_ID=boundary_test_04
 
32
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
 
33
PRIMER_PRODUCT_SIZE_RANGE=50-54
 
34
COMMENT=should fail
 
35
=
 
36
PRIMER_SEQUENCE_ID=boundary_test_05
 
37
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
 
38
PRIMER_PRODUCT_SIZE_RANGE=55-55
 
39
PRIMER_MIN_SIZE=24
 
40
PRIMER_MAX_SIZE=24
 
41
PRIMER_OPT_SIZE=24
 
42
=
 
43
PRIMER_SEQUENCE_ID=boundary_test_06
 
44
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
 
45
PRIMER_PRODUCT_SIZE_RANGE=55-55
 
46
PRIMER_MIN_SIZE=26
 
47
PRIMER_MAX_SIZE=26
 
48
PRIMER_OPT_SIZE=26
 
49
COMMENT=should fail
 
50
=
 
51
PRIMER_SEQUENCE_ID=boundary_test_07
 
52
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
 
53
PRIMER_PRODUCT_SIZE_RANGE=55-55
 
54
PRIMER_MIN_SIZE=25
 
55
PRIMER_MAX_SIZE=25
 
56
PRIMER_OPT_SIZE=25
 
57
INCLUDED_REGION=2,55
 
58
=
 
59
PRIMER_SEQUENCE_ID=boundary_test_08
 
60
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
 
61
PRIMER_PRODUCT_SIZE_RANGE=50-100
 
62
PRIMER_MIN_SIZE=25
 
63
PRIMER_MAX_SIZE=25
 
64
PRIMER_OPT_SIZE=25
 
65
INCLUDED_REGION=3,55
 
66
COMMENT=should fail
 
67
=
 
68
PRIMER_SEQUENCE_ID=boundary_test_09
 
69
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
 
70
PRIMER_PRODUCT_SIZE_RANGE=50-100
 
71
INCLUDED_REGION=2,54
 
72
COMMENT=should fail
 
73
=
 
74
PRIMER_SEQUENCE_ID=boundary_test_10
 
75
SEQUENCE=NNCACGTCATCTNATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
 
76
PRIMER_PRODUCT_SIZE_RANGE=55-55
 
77
PRIMER_MIN_TM=0.0
 
78
PRIMER_MAX_TM=100.0
 
79
PRIMER_MIN_SIZE=25
 
80
PRIMER_MAX_SIZE=25
 
81
PRIMER_OPT_SIZE=25
 
82
PRIMER_MAX_GC=100
 
83
PRIMER_MIN_GC=0
 
84
PRIMER_SELF_END=100
 
85
PRIMER_SELF_ANY=100
 
86
COMMENT=should fail
 
87
=
 
88
PRIMER_SEQUENCE_ID=boundary_test_11
 
89
PRIMER_NUM_NS_ACCEPTED=1
 
90
SEQUENCE=NNCACGTCATCTNATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
 
91
=
 
92
PRIMER_SEQUENCE_ID=boundary_test_11
 
93
PRIMER_NUM_NS_ACCEPTED=1
 
94
SEQUENCE=NNCACGTCATCNNATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
 
95
=
 
96
PRIMER_SEQUENCE_ID=boundary_test_12
 
97
PRIMER_NUM_NS_ACCEPTED=2
 
98
SEQUENCE=NNCACGTCATCNNATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
 
99
=
 
100
PRIMER_SEQUENCE_ID=boundary_test_13
 
101
PRIMER_NUM_NS_ACCEPTED=0
 
102
PRIMER_MIN_GC=0
 
103
SEQUENCE=NNAAAAAAAAAAAAAAAAAAAAAAAAANNNNNACTCACTGTCATTTCCAAACAATTCNN
 
104
=
 
105
PRIMER_SEQUENCE_ID=boundary_test_14
 
106
PRIMER_NUM_NS_ACCEPTED=0
 
107
PRIMER_MIN_GC=.0001
 
108
SEQUENCE=NNAAAAAAAAAAAAAAAAAAAAAAAAANNNNNACTCACTGTCATTTCCAAACAATTCNN
 
109
=
 
110
PRIMER_SEQUENCE_ID=boundary_test_15
 
111
PRIMER_NUM_NS_ACCEPTED=0
 
112
PRIMER_MIN_GC=20
 
113
PRIMER_MAX_GC=100
 
114
SEQUENCE=NNGGGGGGGGGGGGGGGGGGGGGGGGGNNNNNACTCACTGTCATTTCCAAACAATTCNN
 
115
=
 
116
PRIMER_SEQUENCE_ID=boundary_test_16
 
117
PRIMER_NUM_NS_ACCEPTED=0
 
118
PRIMER_MIN_GC=0
 
119
PRIMER_MAX_GC=.0001
 
120
SEQUENCE=NNGGGGGGGGGGGGGGGGGGGGGGGGGNNNNNACTCACTGTCATTTCCAAACAATTCNN
 
121
=
 
122
PRIMER_SEQUENCE_ID=boundary_test_17
 
123
PRIMER_NUM_NS_ACCEPTED=0
 
124
PRIMER_MIN_GC=0
 
125
PRIMER_MAX_GC=100
 
126
INCLUDED_REGION=2,55
 
127
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
 
128
=
 
129
PRIMER_SEQUENCE_ID=boundary_test_18
 
130
PRIMER_NUM_NS_ACCEPTED=0
 
131
PRIMER_MIN_GC=0
 
132
PRIMER_MAX_GC=100
 
133
INCLUDED_REGION=3,55
 
134
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
 
135
=
 
136
PRIMER_SEQUENCE_ID=boundary_test_19
 
137
PRIMER_NUM_NS_ACCEPTED=0
 
138
PRIMER_MIN_GC=0
 
139
PRIMER_MAX_GC=100
 
140
INCLUDED_REGION=2,54
 
141
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
 
142
=
 
143
PRIMER_SEQUENCE_ID=boundary_test_20
 
144
PRIMER_NUM_NS_ACCEPTED=0
 
145
PRIMER_MIN_GC=0
 
146
PRIMER_MAX_GC=100
 
147
PRIMER_PRODUCT_SIZE_RANGE=54-55
 
148
INCLUDED_REGION=2,54
 
149
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
 
150
=
 
151
PRIMER_SEQUENCE_ID=boundary_test_21
 
152
PRIMER_NUM_NS_ACCEPTED=0
 
153
PRIMER_MIN_GC=0
 
154
PRIMER_MAX_GC=100
 
155
TARGET=27,5,X
 
156
PRIMER_PRODUCT_SIZE_RANGE=55-55
 
157
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
 
158
=
 
159
PRIMER_SELF_END=100
 
160
PRIMER_SELF_ANY=100
 
161
PRIMER_MIN_SIZE=25
 
162
PRIMER_MAX_SIZE=25
 
163
PRIMER_OPT_SIZE=25
 
164
PRIMER_MIN_GC=0
 
165
PRIMER_MAX_GC=100
 
166
PRIMER_SEQUENCE_ID=boundary_test_22
 
167
PRIMER_NUM_NS_ACCEPTED=0
 
168
PRIMER_MIN_GC=0
 
169
PRIMER_MAX_GC=100
 
170
TARGET=26,6,X
 
171
PRIMER_PRODUCT_SIZE_RANGE=55-55
 
172
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
 
173
COMMENT=should fail
 
174
=
 
175
PRIMER_SEQUENCE_ID=boundary_test_23
 
176
PRIMER_NUM_NS_ACCEPTED=0
 
177
PRIMER_MIN_GC=0
 
178
PRIMER_MAX_GC=100
 
179
TARGET=27,6,X
 
180
PRIMER_PRODUCT_SIZE_RANGE=55-55
 
181
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
 
182
COMMENT=should fail
 
183
=
 
184
PRIMER_SEQUENCE_ID=boundary_test_24
 
185
PRIMER_NUM_NS_ACCEPTED=0
 
186
PRIMER_MIN_GC=0
 
187
PRIMER_MAX_GC=100
 
188
TARGET=28,5,X
 
189
PRIMER_PRODUCT_SIZE_RANGE=55-55
 
190
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
 
191
COMMENT=should fail
 
192
=
 
193
PRIMER_SEQUENCE_ID=boundary_test_25
 
194
PRIMER_NUM_NS_ACCEPTED=0
 
195
PRIMER_MIN_GC=0
 
196
PRIMER_MAX_GC=100
 
197
TARGET=27,1,X,
 
198
TARGET=28,4,X
 
199
PRIMER_PRODUCT_SIZE_RANGE=55-55
 
200
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
 
201
=
 
202
PRIMER_SEQUENCE_ID=boundary_test_26
 
203
PRIMER_SELF_END=100
 
204
PRIMER_SELF_ANY=100
 
205
PRIMER_MIN_SIZE=25
 
206
PRIMER_MAX_SIZE=25
 
207
PRIMER_OPT_SIZE=25
 
208
PRIMER_MIN_GC=0
 
209
PRIMER_MAX_GC=100
 
210
PRIMER_NUM_NS_ACCEPTED=0
 
211
PRIMER_MIN_GC=0
 
212
PRIMER_MAX_GC=100
 
213
TARGET=26,1,X
 
214
TARGET=27,5,X
 
215
PRIMER_PRODUCT_SIZE_RANGE=55-55
 
216
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
 
217
COMMENT=should fail
 
218
=
 
219
PRIMER_SEQUENCE_ID=boundary_test_27
 
220
PRIMER_NUM_NS_ACCEPTED=0
 
221
PRIMER_MIN_GC=0
 
222
PRIMER_MAX_GC=100
 
223
TARGET=27,1,X
 
224
TARGET=28,5,X
 
225
PRIMER_PRODUCT_SIZE_RANGE=55-55
 
226
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
 
227
COMMENT=should fail
 
228
=
 
229
PRIMER_SEQUENCE_ID=boundary_test_28
 
230
PRIMER_NUM_NS_ACCEPTED=0
 
231
PRIMER_MIN_GC=0
 
232
PRIMER_MAX_GC=100
 
233
TARGET=28,1,X
 
234
TARGET=29,4,X
 
235
PRIMER_PRODUCT_SIZE_RANGE=55-55
 
236
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
 
237
COMMENT=should fail
 
238
=
 
239
PRIMER_SEQUENCE_ID=boundary_test_29
 
240
PRIMER_NUM_NS_ACCEPTED=0
 
241
PRIMER_MIN_GC=0
 
242
PRIMER_MAX_GC=100
 
243
TARGET=28,1,X
 
244
PRIMER_PRODUCT_SIZE_RANGE=55-55
 
245
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
 
246
=
 
247
PRIMER_SEQUENCE_ID=boundary_test_30
 
248
PRIMER_NUM_NS_ACCEPTED=0
 
249
PRIMER_MIN_GC=0
 
250
PRIMER_MAX_GC=100
 
251
TARGET=28,0,X
 
252
PRIMER_PRODUCT_SIZE_RANGE=55-55
 
253
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
 
254
=
 
255
PRIMER_SEQUENCE_ID=boundary_test_31
 
256
PRIMER_NUM_NS_ACCEPTED=0
 
257
PRIMER_MIN_GC=0
 
258
PRIMER_MAX_GC=100
 
259
TARGET=0,1,X
 
260
PRIMER_PRODUCT_SIZE_RANGE=55-55
 
261
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
 
262
COMMENT=should fail
 
263
=
 
264
PRIMER_SEQUENCE_ID=boundary_test_32
 
265
PRIMER_NUM_NS_ACCEPTED=0
 
266
PRIMER_MIN_GC=0
 
267
PRIMER_MAX_GC=100
 
268
EXCLUDED_REGION=27,5
 
269
PRIMER_PRODUCT_SIZE_RANGE=55-55
 
270
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
 
271
=
 
272
PRIMER_SEQUENCE_ID=boundary_test_33
 
273
PRIMER_SELF_END=100
 
274
PRIMER_SELF_ANY=100
 
275
PRIMER_MIN_SIZE=25
 
276
PRIMER_MAX_SIZE=25
 
277
PRIMER_OPT_SIZE=25
 
278
PRIMER_MIN_GC=0
 
279
PRIMER_MAX_GC=100
 
280
PRIMER_NUM_NS_ACCEPTED=0
 
281
PRIMER_MIN_GC=0
 
282
PRIMER_MAX_GC=100
 
283
EXCLUDED_REGION=26,6
 
284
PRIMER_PRODUCT_SIZE_RANGE=55-55
 
285
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
 
286
COMMENT=should fail
 
287
=
 
288
PRIMER_SEQUENCE_ID=boundary_test_34
 
289
PRIMER_NUM_NS_ACCEPTED=0
 
290
PRIMER_MIN_GC=0
 
291
PRIMER_MAX_GC=100
 
292
EXCLUDED_REGION=27,6
 
293
PRIMER_PRODUCT_SIZE_RANGE=55-55
 
294
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
 
295
COMMENT=should fail
 
296
=
 
297
PRIMER_SEQUENCE_ID=boundary_test_35
 
298
PRIMER_NUM_NS_ACCEPTED=0
 
299
PRIMER_MIN_GC=0
 
300
PRIMER_MAX_GC=100
 
301
EXCLUDED_REGION=28,5
 
302
PRIMER_PRODUCT_SIZE_RANGE=55-55
 
303
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
 
304
COMMENT=should fail
 
305
=
 
306
PRIMER_SEQUENCE_ID=boundary_test_36
 
307
PRIMER_NUM_NS_ACCEPTED=0
 
308
PRIMER_MIN_GC=0
 
309
PRIMER_MAX_GC=100
 
310
EXCLUDED_REGION=27,1
 
311
EXCLUDED_REGION=28,4
 
312
PRIMER_PRODUCT_SIZE_RANGE=55-55
 
313
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
 
314
=
 
315
PRIMER_SEQUENCE_ID=boundary_test_37
 
316
PRIMER_SELF_END=100
 
317
PRIMER_SELF_ANY=100
 
318
PRIMER_MIN_SIZE=25
 
319
PRIMER_MAX_SIZE=25
 
320
PRIMER_OPT_SIZE=25
 
321
PRIMER_MIN_GC=0
 
322
PRIMER_MAX_GC=100
 
323
PRIMER_NUM_NS_ACCEPTED=0
 
324
PRIMER_MIN_GC=0
 
325
PRIMER_MAX_GC=100
 
326
EXCLUDED_REGION=26,1
 
327
EXCLUDED_REGION=27,5
 
328
PRIMER_PRODUCT_SIZE_RANGE=55-55
 
329
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
 
330
COMMENT=should fail
 
331
=
 
332
PRIMER_SEQUENCE_ID=boundary_test_37
 
333
PRIMER_NUM_NS_ACCEPTED=0
 
334
PRIMER_MIN_GC=0
 
335
PRIMER_MAX_GC=100
 
336
EXCLUDED_REGION=27,1
 
337
EXCLUDED_REGION=28,5
 
338
PRIMER_PRODUCT_SIZE_RANGE=55-55
 
339
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
 
340
COMMENT=should fail
 
341
=
 
342
PRIMER_SEQUENCE_ID=boundary_test_38
 
343
PRIMER_NUM_NS_ACCEPTED=0
 
344
PRIMER_MIN_GC=0
 
345
PRIMER_MAX_GC=100
 
346
EXCLUDED_REGION=28,1
 
347
EXCLUDED_REGION=29,4
 
348
PRIMER_PRODUCT_SIZE_RANGE=55-55
 
349
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
 
350
COMMENT=should fail
 
351
=
 
352
PRIMER_SEQUENCE_ID=boundary_test_39
 
353
PRIMER_NUM_NS_ACCEPTED=0
 
354
PRIMER_MIN_GC=0
 
355
PRIMER_MAX_GC=100
 
356
EXCLUDED_REGION=28,1
 
357
PRIMER_PRODUCT_SIZE_RANGE=55-55
 
358
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
 
359
=
 
360
PRIMER_SEQUENCE_ID=boundary_test_40
 
361
PRIMER_NUM_NS_ACCEPTED=0
 
362
PRIMER_MIN_GC=0
 
363
PRIMER_MAX_GC=100
 
364
EXCLUDED_REGION=28,0
 
365
PRIMER_PRODUCT_SIZE_RANGE=55-55
 
366
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
 
367
=
 
368
PRIMER_SEQUENCE_ID=boundary_test_41
 
369
PRIMER_NUM_NS_ACCEPTED=0
 
370
PRIMER_MIN_GC=0
 
371
PRIMER_MAX_GC=100
 
372
EXCLUDED_REGION=10,0
 
373
PRIMER_PRODUCT_SIZE_RANGE=55-55
 
374
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
 
375
=
 
376
PRIMER_SEQUENCE_ID=boundary_test_42
 
377
PRIMER_NUM_NS_ACCEPTED=0
 
378
PRIMER_MIN_GC=0
 
379
PRIMER_MAX_GC=100
 
380
EXCLUDED_REGION=28,1
 
381
PRIMER_PRODUCT_SIZE_RANGE=55-55
 
382
PRIMER_MAX_SIZE=25
 
383
PRIMER_MIN_SIZE=25
 
384
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
 
385
COMMENT="should succeed"
 
386
=
 
387
PRIMER_SEQUENCE_ID=boundary_test_43
 
388
PRIMER_NUM_NS_ACCEPTED=0
 
389
PRIMER_MIN_GC=0
 
390
PRIMER_MAX_GC=100
 
391
EXCLUDED_REGION=28,1
 
392
PRIMER_PRODUCT_SIZE_RANGE="55-55"
 
393
PRIMER_MAX_SIZE=25
 
394
PRIMER_MIN_SIZE=25
 
395
PRIMER_SELF_END=9.99
 
396
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
 
397
COMMENT="should fail (because one primer has end compl == 10.00)"
 
398
=
 
399
PRIMER_SEQUENCE_ID=boundary_test_44
 
400
PRIMER_NUM_NS_ACCEPTED=0
 
401
PRIMER_MIN_GC=0
 
402
PRIMER_MAX_GC=100
 
403
EXCLUDED_REGION=28,1
 
404
PRIMER_PRODUCT_SIZE_RANGE="55-55"
 
405
PRIMER_MAX_SIZE=25
 
406
PRIMER_MIN_SIZE=25
 
407
PRIMER_SELF_END=10.01
 
408
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
 
409
COMMENT=should succeed
 
410
=
 
411
PRIMER_SEQUENCE_ID=boundary_test_45
 
412
PRIMER_NUM_NS_ACCEPTED=0
 
413
PRIMER_MIN_GC=0
 
414
PRIMER_MAX_GC=100
 
415
EXCLUDED_REGION=28,1
 
416
PRIMER_PRODUCT_SIZE_RANGE="55-55"
 
417
PRIMER_MAX_SIZE=25
 
418
PRIMER_MIN_SIZE=25
 
419
PRIMER_SELF_END=100
 
420
PRIMER_SELF_ANY=12.01
 
421
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
 
422
COMMENT=should succeed
 
423
=
 
424
PRIMER_SEQUENCE_ID=boundary_test_46
 
425
PRIMER_NUM_NS_ACCEPTED=0
 
426
PRIMER_MIN_GC=0
 
427
PRIMER_MAX_GC=100
 
428
EXCLUDED_REGION=28,1
 
429
PRIMER_PRODUCT_SIZE_RANGE="55-55"
 
430
PRIMER_MAX_SIZE=25
 
431
PRIMER_MIN_SIZE=25
 
432
PRIMER_SELF_END=100
 
433
PRIMER_SELF_ANY=11.99
 
434
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
 
435
COMMENT="should fail (because self any for one primer is 12.00"
 
436
=
 
437
PRIMER_SEQUENCE_ID=boundary_test_47
 
438
PRIMER_GC_CLAMP=0
 
439
PRIMER_NUM_NS_ACCEPTED=0
 
440
PRIMER_MIN_GC=0
 
441
PRIMER_MAX_GC=100
 
442
EXCLUDED_REGION=28,1
 
443
PRIMER_PRODUCT_SIZE_RANGE="55-55"
 
444
PRIMER_MAX_SIZE=25
 
445
PRIMER_MIN_SIZE=25
 
446
PRIMER_SELF_END=100
 
447
PRIMER_SELF_ANY=100
 
448
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
 
449
COMMENT="should succeed"
 
450
=
 
451
PRIMER_SEQUENCE_ID=boundary_test_48
 
452
PRIMER_GC_CLAMP=1
 
453
PRIMER_NUM_NS_ACCEPTED=0
 
454
PRIMER_MIN_GC=0
 
455
PRIMER_MAX_GC=100
 
456
EXCLUDED_REGION=28,1
 
457
PRIMER_PRODUCT_SIZE_RANGE="55-55"
 
458
PRIMER_MAX_SIZE=25
 
459
PRIMER_MIN_SIZE=25
 
460
PRIMER_SELF_END=100
 
461
PRIMER_SELF_ANY=100
 
462
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
 
463
COMMENT="should fail (because of GC clamp)"
 
464
=
 
465
PRIMER_SEQUENCE_ID=boundary_test_49
 
466
PRIMER_GC_CLAMP=1
 
467
PRIMER_NUM_NS_ACCEPTED=0
 
468
PRIMER_MIN_GC=0
 
469
PRIMER_MAX_GC=100
 
470
EXCLUDED_REGION=28,1
 
471
PRIMER_PRODUCT_SIZE_RANGE="55-55"
 
472
PRIMER_MAX_SIZE=25
 
473
PRIMER_MIN_SIZE=25
 
474
PRIMER_SELF_END=100
 
475
PRIMER_SELF_ANY=100
 
476
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNCCTCACTGTCATTTCCAAACAATTCNN
 
477
COMMENT="should succeed"
 
478
=
 
479
PRIMER_SEQUENCE_ID=boundary_test_50
 
480
PRIMER_GC_CLAMP=2
 
481
PRIMER_NUM_NS_ACCEPTED=0
 
482
PRIMER_MIN_GC=0
 
483
PRIMER_MAX_GC=100
 
484
EXCLUDED_REGION=28,1
 
485
PRIMER_PRODUCT_SIZE_RANGE="55-55"
 
486
PRIMER_MAX_SIZE=25
 
487
PRIMER_MIN_SIZE=25
 
488
PRIMER_SELF_END=100
 
489
PRIMER_SELF_ANY=100
 
490
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNCCTCACTGTCATTTCCAAACAATTCNN
 
491
COMMENT="should fail (because of GC clamp)"
 
492
=
 
493
PRIMER_SEQUENCE_ID=boundary_test_51
 
494
PRIMER_MAX_DIFF_TM=100
 
495
PRIMER_GC_CLAMP=0
 
496
PRIMER_NUM_NS_ACCEPTED=0
 
497
PRIMER_MIN_GC=0
 
498
PRIMER_MAX_GC=100
 
499
EXCLUDED_REGION=28,1
 
500
PRIMER_PRODUCT_SIZE_RANGE="55-55"
 
501
PRIMER_MAX_SIZE=25
 
502
PRIMER_MIN_SIZE=25
 
503
PRIMER_SELF_END=100
 
504
PRIMER_SELF_ANY=100
 
505
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNCCTCACTGTCATTTCCAAACAATTCNN
 
506
COMMENT="should succeed"
 
507
=
 
508
PRIMER_SEQUENCE_ID=boundary_test_52
 
509
PRIMER_MAX_DIFF_TM=0.29
 
510
PRIMER_GC_CLAMP=0
 
511
PRIMER_NUM_NS_ACCEPTED=0
 
512
PRIMER_MIN_GC=0
 
513
PRIMER_MAX_GC=100
 
514
EXCLUDED_REGION=28,1
 
515
PRIMER_PRODUCT_SIZE_RANGE="55-55"
 
516
PRIMER_MAX_SIZE=25
 
517
PRIMER_MIN_SIZE=25
 
518
PRIMER_SELF_END=100
 
519
PRIMER_SELF_ANY=100
 
520
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNCCTCACTGTCATTTCCAAACAATTCNN
 
521
COMMENT="should succeed"
 
522
=
 
523
PRIMER_SEQUENCE_ID=boundary_test_53
 
524
PRIMER_MAX_DIFF_TM=0.28
 
525
PRIMER_GC_CLAMP=0
 
526
PRIMER_NUM_NS_ACCEPTED=0
 
527
PRIMER_MIN_GC=0
 
528
PRIMER_MAX_GC=100
 
529
EXCLUDED_REGION=28,1
 
530
PRIMER_PRODUCT_SIZE_RANGE="55-55"
 
531
PRIMER_MAX_SIZE=25
 
532
PRIMER_MIN_SIZE=25
 
533
PRIMER_SELF_END=100
 
534
PRIMER_SELF_ANY=100
 
535
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNCCTCACTGTCATTTCCAAACAATTCNN
 
536
COMMENT="should fail (due to max diff tm)"
 
537
=
 
538
PRIMER_SEQUENCE_ID=boundary_test_54
 
539
PRIMER_LIBERAL_BASE=1
 
540
PRIMER_MAX_DIFF_TM=0.29
 
541
PRIMER_GC_CLAMP=0
 
542
PRIMER_NUM_NS_ACCEPTED=0
 
543
PRIMER_MIN_GC=0
 
544
PRIMER_MAX_GC=100
 
545
EXCLUDED_REGION=28,1
 
546
PRIMER_PRODUCT_SIZE_RANGE="55-55"
 
547
PRIMER_MAX_SIZE=25
 
548
PRIMER_MIN_SIZE=25
 
549
PRIMER_SELF_END=100
 
550
PRIMER_SELF_ANY=100
 
551
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNKNNCCTCACTGTCATTTCCAAACAATTCNN
 
552
COMMENT="should succeed"
 
553
=
 
554
PRIMER_SEQUENCE_ID=boundary_test_55
 
555
PRIMER_LIBERAL_BASE=0
 
556
PRIMER_MAX_DIFF_TM=0.29
 
557
PRIMER_GC_CLAMP=0
 
558
PRIMER_NUM_NS_ACCEPTED=0
 
559
PRIMER_MIN_GC=0
 
560
PRIMER_MAX_GC=100
 
561
EXCLUDED_REGION=28,1
 
562
PRIMER_PRODUCT_SIZE_RANGE="55-55"
 
563
PRIMER_MAX_SIZE=25
 
564
PRIMER_MIN_SIZE=25
 
565
PRIMER_SELF_END=100
 
566
PRIMER_SELF_ANY=100
 
567
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNKNNCCTCACTGTCATTTCCAAACAATTCNN
 
568
COMMENT="should generate error"
 
569
=
 
570
PRIMER_SEQUENCE_ID=poly_x_1
 
571
SEQUENCE=AAAAAATTTTTTGGGGGGCCCCCCAAAAAAGGGGGGTTTTTTCCCCCCAAAAAAGGGGGGTTTTTTCCCCCCAAAAAAGGGGGGCCCCCCTTTTTTGGGGGGAAAAAACCCCCCTTTTTTGGGGGGAAAAAACCCCCCTTTTTTAAAAAAGGGGGGCCCCCCAAAAAAGGGGGGTTTTTTTCCCCCC
 
572
PRIMER_MAX_POLY_X=5
 
573
PRIMER_INTERNAL_OLIGO_MAX_POLY_X=6
 
574
PRIMER_PRODUCT_SIZE_RANGE=50-300
 
575
PRIMER_PICK_INTERNAL_OLIGO=1
 
576
PRIMER_MAX_DIFF_TM=100
 
577
PRIMER_SELF_ANY=100
 
578
PRIMER_SELF_END=100
 
579
=
 
580
PRIMER_SEQUENCE_ID=poly_x_2
 
581
PRIMER_INTERNAL_OLIGO_MIN_TM=0
 
582
PRIMER_INTERNAL_OLIGO_MAX_TM=100
 
583
SEQUENCE=AAAAATTTTTCCCCCGGGGGAAAAACCCCCTTTTTGGGGGAAAAATTTTTCCCCCGGGGGAAAAACCCCCTTTTTGGGGGAAAAACCCCCTTTTTGGGGGAAAAACCCCCTTTTTGGGGGAAAAATTTTTCCCCCGGGGGAAAAACCCCCTTTTTGGGGGAAAAACCCCCTTTTTGGGGG
 
584
=
 
585
PRIMER_SEQUENCE_ID=poly_x_3
 
586
SEQUENCE=AAAAAACCCCCCTTTTTTGGGGGGAAAAAACCCCCCTTTTTTGGGGGGAAAAAACCCCCCTTTTTTGGGGGGAAAAAAACCCCCCTTTTTTGGGGGGAAAAAACCCCCCCTTTTTTGGGGGGAAAAAACCCCCCTTTTTTGGGGGGAAAAAAACCCCCCTTTTTTGGGGGGAAAAAACCCCCCTTTTTTTGGGGGGGGGGGGGG
 
587
PRIMER_MAX_POLY_X=6
 
588
PRIMER_INTERNAL_OLIGO_MAX_POLY_X=5
 
589
=
 
590
PRIMER_SEQUENCE_ID=boundary_test_59
 
591
PRIMER_PICK_INTERNAL_OLIGO=0
 
592
PRIMER_MIN_SIZE=25
 
593
PRIMER_NUM_NS_ACCEPTED=0
 
594
PRIMER_MIN_GC=0
 
595
PRIMER_MAX_GC=100
 
596
EXCLUDED_REGION=27,0
 
597
PRIMER_PRODUCT_SIZE_RANGE="55-55"
 
598
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
 
599
COMMENT=ok (excluded region is between G and N and end of left primer).
 
600
=
 
601
PRIMER_SEQUENCE_ID=boundary_test_60
 
602
PRIMER_PICK_INTERNAL_OLIGO=0
 
603
PRIMER_MIN_SIZE=25
 
604
PRIMER_NUM_NS_ACCEPTED=0
 
605
PRIMER_MIN_GC=0
 
606
PRIMER_MAX_GC=100
 
607
EXCLUDED_REGION=26,0
 
608
PRIMER_PRODUCT_SIZE_RANGE="55-55"
 
609
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
 
610
COMMENT=should fail (excluded region is between T and G at end of left primer).
 
611
=
 
612
PRIMER_SEQUENCE_ID=boundary_test_61
 
613
PRIMER_PICK_INTERNAL_OLIGO=0
 
614
PRIMER_MIN_SIZE=25
 
615
PRIMER_NUM_NS_ACCEPTED=0
 
616
PRIMER_MIN_GC=0
 
617
PRIMER_MAX_GC=100
 
618
EXCLUDED_REGION=26,-1
 
619
PRIMER_PRODUCT_SIZE_RANGE="55-55"
 
620
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
 
621
COMMENT=should fail (negative excluded region size).
 
622
=
 
623
PRIMER_SEQUENCE_ID=boundary_test_62
 
624
PRIMER_PICK_INTERNAL_OLIGO=0
 
625
PRIMER_MIN_SIZE=25
 
626
PRIMER_NUM_NS_ACCEPTED=0
 
627
PRIMER_MIN_GC=0
 
628
PRIMER_MAX_GC=100
 
629
INCLUDED_REGION=2,55
 
630
EXCLUDED_REGION=1,1
 
631
PRIMER_PRODUCT_SIZE_RANGE=55-55
 
632
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
 
633
COMMENT=should succeed with PRIMER_WARNING EXCLUDED_REGION outside of INCLUDED REGION
 
634
=
 
635
PRIMER_SEQUENCE_ID=boundary_test_63
 
636
PRIMER_PICK_INTERNAL_OLIGO=0
 
637
PRIMER_MIN_SIZE=25
 
638
PRIMER_NUM_NS_ACCEPTED=0
 
639
PRIMER_MIN_GC=0
 
640
PRIMER_MAX_GC=100
 
641
INCLUDED_REGION=2,55
 
642
EXCLUDED_REGION=2,1
 
643
PRIMER_PRODUCT_SIZE_RANGE=55-55
 
644
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
 
645
COMMENT=should fail with no legal primers
 
646
=
 
647
PRIMER_SEQUENCE_ID=boundary_test_64
 
648
PRIMER_PICK_INTERNAL_OLIGO=0
 
649
PRIMER_MIN_SIZE=25
 
650
PRIMER_NUM_NS_ACCEPTED=0
 
651
PRIMER_MIN_GC=0
 
652
PRIMER_MAX_GC=100
 
653
INCLUDED_REGION=2,55
 
654
EXCLUDED_REGION=59,1
 
655
PRIMER_PRODUCT_SIZE_RANGE=55-55
 
656
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
 
657
COMMENT=should fail with EXCLUDED_REGION outside of sequence
 
658
=
 
659
PRIMER_SEQUENCE_ID=boundary_test_65
 
660
PRIMER_PICK_INTERNAL_OLIGO=0
 
661
PRIMER_MIN_SIZE=25
 
662
PRIMER_NUM_NS_ACCEPTED=0
 
663
PRIMER_MIN_GC=0
 
664
PRIMER_MAX_GC=100
 
665
INCLUDED_REGION=2,55
 
666
EXCLUDED_REGION=58,1
 
667
PRIMER_PRODUCT_SIZE_RANGE=55-55
 
668
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
 
669
COMMENT=should succeed with PRIMER_WARNING EXCLUDED_REGION outside of INCLUDED_REGION
 
670
=
 
671
PRIMER_SEQUENCE_ID=boundary_test_66
 
672
PRIMER_PICK_INTERNAL_OLIGO=0
 
673
PRIMER_MIN_SIZE=25
 
674
PRIMER_NUM_NS_ACCEPTED=0
 
675
PRIMER_MIN_GC=0
 
676
PRIMER_MAX_GC=100
 
677
INCLUDED_REGION=2,55
 
678
EXCLUDED_REGION=56,1
 
679
PRIMER_PRODUCT_SIZE_RANGE=55-55
 
680
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
 
681
COMMENT=should fail with no legal primers
 
682
=
 
683
PRIMER_SEQUENCE_ID=boundary_test_67
 
684
PRIMER_PICK_INTERNAL_OLIGO=0
 
685
PRIMER_MIN_SIZE=25
 
686
PRIMER_NUM_NS_ACCEPTED=0
 
687
PRIMER_MIN_GC=0
 
688
PRIMER_MAX_GC=100
 
689
INCLUDED_REGION=2,55
 
690
EXCLUDED_REGION=56,2
 
691
PRIMER_PRODUCT_SIZE_RANGE=50-55
 
692
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
 
693
COMMENT=should fail to pick primers and warn EXCLUDED_REGION outside of INCLUDED_REGION
 
694
=
 
695
PRIMER_SEQUENCE_ID=boundary_test_68
 
696
PRIMER_PICK_INTERNAL_OLIGO=0
 
697
PRIMER_MIN_SIZE=25
 
698
PRIMER_NUM_NS_ACCEPTED=0
 
699
PRIMER_MIN_GC=0
 
700
PRIMER_MAX_GC=100
 
701
TARGET=27,0
 
702
PRIMER_PRODUCT_SIZE_RANGE=55-55
 
703
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
 
704
COMMENT=ok (TARGET is between G and N and end of left primer).
 
705
=
 
706
PRIMER_SEQUENCE_ID=boundary_test_69
 
707
PRIMER_PICK_INTERNAL_OLIGO=0
 
708
PRIMER_MIN_SIZE=25
 
709
PRIMER_NUM_NS_ACCEPTED=0
 
710
PRIMER_MIN_GC=0
 
711
PRIMER_MAX_GC=100
 
712
TARGET=26,0
 
713
PRIMER_PRODUCT_SIZE_RANGE="55-55"
 
714
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
 
715
COMMENT=should fail (TARGET is between T and G at end of left primer).
 
716
=
 
717
PRIMER_SEQUENCE_ID=boundary_test_70
 
718
PRIMER_PICK_INTERNAL_OLIGO=0
 
719
PRIMER_MIN_SIZE=25
 
720
PRIMER_NUM_NS_ACCEPTED=0
 
721
PRIMER_MIN_GC=0
 
722
PRIMER_MAX_GC=100
 
723
TARGET=26,-1
 
724
PRIMER_PRODUCT_SIZE_RANGE="55-55"
 
725
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
 
726
COMMENT=should fail (negative TARGET size).
 
727
=
 
728
PRIMER_SEQUENCE_ID=boundary_test_71
 
729
PRIMER_PICK_INTERNAL_OLIGO=0
 
730
PRIMER_MIN_SIZE=25
 
731
PRIMER_NUM_NS_ACCEPTED=0
 
732
PRIMER_MIN_GC=0
 
733
PRIMER_MAX_GC=100
 
734
INCLUDED_REGION=2,55
 
735
TARGET=1,1
 
736
PRIMER_PRODUCT_SIZE_RANGE=55-55
 
737
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
 
738
COMMENT=should fail to find legal primers, and warn TARGET outside of INCLUDED REGION
 
739
=
 
740
PRIMER_SEQUENCE_ID=boundary_test_72
 
741
PRIMER_PICK_INTERNAL_OLIGO=0
 
742
PRIMER_MIN_SIZE=25
 
743
PRIMER_NUM_NS_ACCEPTED=0
 
744
PRIMER_MIN_GC=0
 
745
PRIMER_MAX_GC=100
 
746
INCLUDED_REGION=2,55
 
747
TARGET=2,1
 
748
PRIMER_PRODUCT_SIZE_RANGE=55-55
 
749
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
 
750
COMMENT=should fail with no legal primers
 
751
=
 
752
PRIMER_SEQUENCE_ID=boundary_test_73
 
753
PRIMER_PICK_INTERNAL_OLIGO=0
 
754
PRIMER_MIN_SIZE=25
 
755
PRIMER_NUM_NS_ACCEPTED=0
 
756
PRIMER_MIN_GC=0
 
757
PRIMER_MAX_GC=100
 
758
INCLUDED_REGION=2,55
 
759
TARGET=59,1
 
760
PRIMER_PRODUCT_SIZE_RANGE=55-55
 
761
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
 
762
COMMENT=should fail with TARGET outside of sequence
 
763
=
 
764
PRIMER_SEQUENCE_ID=boundary_test_74
 
765
PRIMER_PICK_INTERNAL_OLIGO=0
 
766
PRIMER_MIN_SIZE=25
 
767
PRIMER_NUM_NS_ACCEPTED=0
 
768
PRIMER_MIN_GC=0
 
769
PRIMER_MAX_GC=100
 
770
INCLUDED_REGION=2,55
 
771
TARGET=58,1
 
772
PRIMER_PRODUCT_SIZE_RANGE=55-55
 
773
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
 
774
COMMENT=should fail to find primers (none spans target), and warn TARGET outside of INCLUDED_REGION
 
775
=
 
776
PRIMER_SEQUENCE_ID=boundary_test_75
 
777
PRIMER_PICK_INTERNAL_OLIGO=0
 
778
PRIMER_MIN_SIZE=25
 
779
PRIMER_NUM_NS_ACCEPTED=0
 
780
PRIMER_MIN_GC=0
 
781
PRIMER_MAX_GC=100
 
782
INCLUDED_REGION=2,55
 
783
TARGET=56,1
 
784
PRIMER_PRODUCT_SIZE_RANGE=55-55
 
785
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
 
786
COMMENT=should fail with no legal primers
 
787
=
 
788
PRIMER_SEQUENCE_ID=boundary_test_76
 
789
PRIMER_PICK_INTERNAL_OLIGO=0
 
790
PRIMER_MIN_SIZE=25
 
791
PRIMER_NUM_NS_ACCEPTED=0
 
792
PRIMER_MIN_GC=0
 
793
PRIMER_MAX_GC=100
 
794
INCLUDED_REGION=2,55
 
795
TARGET=56,2
 
796
PRIMER_PRODUCT_SIZE_RANGE=50-55
 
797
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
 
798
COMMENT=should fail to pick primers, and warn TARGET outside of INCLUDED_REGION
 
799
=
 
800
PRIMER_SEQUENCE_ID=boundary_test_77
 
801
PRIMER_PICK_INTERNAL_OLIGO=0
 
802
PRIMER_MIN_SIZE=25
 
803
PRIMER_NUM_NS_ACCEPTED=0
 
804
PRIMER_MIN_GC=0
 
805
PRIMER_MAX_GC=100
 
806
INCLUDED_REGION=2,55
 
807
TARGET=27,1
 
808
PRIMER_PRODUCT_SIZE_RANGE=50-55
 
809
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
 
810
COMMENT=should succeed (target is at TTG^NNN)
 
811
=
 
812
PRIMER_SEQUENCE_ID=boundary_test_78
 
813
PRIMER_PICK_INTERNAL_OLIGO=0
 
814
PRIMER_MIN_SIZE=25
 
815
PRIMER_NUM_NS_ACCEPTED=0
 
816
PRIMER_MIN_GC=0
 
817
PRIMER_MAX_GC=100
 
818
INCLUDED_REGION=2,55
 
819
TARGET=27,5
 
820
PRIMER_PRODUCT_SIZE_RANGE=50-55
 
821
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
 
822
COMMENT=should succeed (target is the middle run of N)
 
823
=
 
824
PRIMER_SEQUENCE_ID=boundary_test_79
 
825
PRIMER_PICK_INTERNAL_OLIGO=0
 
826
PRIMER_MIN_SIZE=25
 
827
PRIMER_NUM_NS_ACCEPTED=0
 
828
PRIMER_MIN_GC=0
 
829
PRIMER_MAX_GC=100
 
830
INCLUDED_REGION=2,55
 
831
TARGET=27,0
 
832
PRIMER_PRODUCT_SIZE_RANGE=50-55
 
833
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
 
834
COMMENT=should succeed
 
835
=
 
836
PRIMER_SEQUENCE_ID=boundary_test_80
 
837
PRIMER_PICK_INTERNAL_OLIGO=0
 
838
PRIMER_MIN_SIZE=25
 
839
PRIMER_NUM_NS_ACCEPTED=0
 
840
PRIMER_MIN_GC=0
 
841
PRIMER_MAX_GC=100
 
842
INCLUDED_REGION=2,55
 
843
TARGET=31,1
 
844
PRIMER_PRODUCT_SIZE_RANGE=50-55
 
845
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
 
846
COMMENT=should succeed
 
847
=
 
848
PRIMER_SEQUENCE_ID=boundary_test_81
 
849
PRIMER_PICK_INTERNAL_OLIGO=0
 
850
PRIMER_MIN_SIZE=25
 
851
PRIMER_NUM_NS_ACCEPTED=0
 
852
PRIMER_MIN_GC=0
 
853
PRIMER_MAX_GC=100
 
854
INCLUDED_REGION=2,55
 
855
TARGET=32,0
 
856
PRIMER_PRODUCT_SIZE_RANGE=50-55
 
857
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
 
858
COMMENT=should succeed
 
859
=
 
860
PRIMER_SEQUENCE_ID=boundary_test_82
 
861
PRIMER_PICK_INTERNAL_OLIGO=0
 
862
PRIMER_MIN_SIZE=25
 
863
PRIMER_NUM_NS_ACCEPTED=0
 
864
PRIMER_MIN_GC=0
 
865
PRIMER_MAX_GC=100
 
866
INCLUDED_REGION=0,59
 
867
TARGET=32,0 0,1 58,1
 
868
PRIMER_PRODUCT_SIZE_RANGE=50-55
 
869
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
 
870
COMMENT=should succeed
 
871
=
 
872
PRIMER_SEQUENCE_ID=boundary_test_83
 
873
PRIMER_PICK_INTERNAL_OLIGO=0
 
874
PRIMER_MIN_SIZE=25
 
875
PRIMER_NUM_NS_ACCEPTED=0
 
876
PRIMER_MIN_GC=0
 
877
PRIMER_MAX_GC=100
 
878
INCLUDED_REGION=0,59
 
879
TARGET=0,1 58,1
 
880
PRIMER_PRODUCT_SIZE_RANGE=50-55
 
881
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
 
882
COMMENT=should fail (no target)
 
883
=
 
884
PRIMER_SEQUENCE_ID=boundary_test_84
 
885
PRIMER_PICK_INTERNAL_OLIGO=0
 
886
PRIMER_MIN_SIZE=25
 
887
PRIMER_NUM_NS_ACCEPTED=0
 
888
PRIMER_MIN_GC=0
 
889
PRIMER_MAX_GC=100
 
890
INCLUDED_REGION=0,59
 
891
TARGET=0,1 32,0
 
892
PRIMER_PRODUCT_SIZE_RANGE=50-55
 
893
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
 
894
COMMENT=should succeed
 
895
=
 
896
PRIMER_SEQUENCE_ID=boundary_test_85
 
897
PRIMER_PICK_INTERNAL_OLIGO=0
 
898
PRIMER_MIN_SIZE=25
 
899
PRIMER_NUM_NS_ACCEPTED=0
 
900
PRIMER_MIN_GC=0
 
901
PRIMER_MAX_GC=100
 
902
INCLUDED_REGION=0,59
 
903
TARGET=32,0 58,1
 
904
PRIMER_PRODUCT_SIZE_RANGE=50-55
 
905
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
 
906
COMMENT=should succeed
 
907
=
 
908
PRIMER_SEQUENCE_ID=boundary_test_86
 
909
PRIMER_PICK_INTERNAL_OLIGO=0
 
910
PRIMER_MIN_SIZE=35
 
911
PRIMER_MAX_SIZE=35
 
912
PRIMER_OPT_SIZE=35
 
913
PRIMER_NUM_NS_ACCEPTED=0
 
914
PRIMER_MIN_GC=0
 
915
PRIMER_MAX_GC=100
 
916
PRIMER_PRODUCT_SIZE_RANGE=75-75
 
917
SEQUENCE=NNCACGTCATCTATATATATATCATCAAATTTGATTGNNNNNACTCATATATATATACTGTCATTTCCAAACAATTCNN
 
918
COMMENT=should succeed (testing hard limit MAX_PRIMER_LENGTH)
 
919
=
 
920
PRIMER_SEQUENCE_ID=boundary_test_71
 
921
PRIMER_PICK_INTERNAL_OLIGO=0
 
922
PRIMER_MIN_SIZE=25
 
923
PRIMER_MAX_SIZE=25
 
924
PRIMER_OPT_SIZE=25
 
925
PRIMER_NUM_NS_ACCEPTED=0
 
926
PRIMER_MIN_GC=0
 
927
PRIMER_MAX_GC=100
 
928
INCLUDED_REGION=2,55
 
929
TARGET=1,1 27,1
 
930
PRIMER_PRODUCT_SIZE_RANGE=55-55
 
931
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
 
932
COMMENT=should warn TARGET outside of INCLUDED REGION
 
933
=
 
934
PRIMER_SEQUENCE_ID=boundary_test_72
 
935
PRIMER_PICK_INTERNAL_OLIGO=0
 
936
PRIMER_MIN_SIZE=25
 
937
PRIMER_MAX_SIZE=25
 
938
PRIMER_OPT_SIZE=25
 
939
PRIMER_NUM_NS_ACCEPTED=0
 
940
PRIMER_MIN_GC=0
 
941
PRIMER_MAX_GC=100
 
942
INCLUDED_REGION=2,56
 
943
PRIMER_PRODUCT_SIZE_RANGE=54-54 55-55 56-56
 
944
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
 
945
COMMENT=should succed with exactly one pair
 
946
=
 
947
PRIMER_SEQUENCE_ID=boundary_test_73
 
948
PRIMER_PICK_INTERNAL_OLIGO=0
 
949
PRIMER_MIN_SIZE=25
 
950
PRIMER_MAX_SIZE=25
 
951
PRIMER_OPT_SIZE=25
 
952
PRIMER_NUM_NS_ACCEPTED=0
 
953
PRIMER_MIN_GC=0
 
954
PRIMER_MAX_GC=100
 
955
INCLUDED_REGION=2,56
 
956
PRIMER_PRODUCT_SIZE_RANGE=54-54 56-56
 
957
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
 
958
COMMENT=should fail (no primers with acceptable product size)
 
959
=
 
960
PRIMER_SEQUENCE_ID=boundary_test_74
 
961
PRIMER_PICK_INTERNAL_OLIGO=0
 
962
PRIMER_MIN_SIZE=25
 
963
PRIMER_MAX_SIZE=25
 
964
PRIMER_OPT_SIZE=25
 
965
PRIMER_NUM_NS_ACCEPTED=0
 
966
PRIMER_MIN_GC=0
 
967
PRIMER_MAX_GC=100
 
968
INCLUDED_REGION=2,56
 
969
PRIMER_PRODUCT_SIZE_RANGE=54-55 55-56
 
970
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
 
971
COMMENT=should succeed with exactly one primer pair
 
972
=
 
973
PRIMER_SEQUENCE_ID=boundary_test_75
 
974
PRIMER_PICK_INTERNAL_OLIGO=0
 
975
PRIMER_MIN_SIZE=25
 
976
PRIMER_MAX_SIZE=25
 
977
PRIMER_OPT_SIZE=25
 
978
PRIMER_NUM_NS_ACCEPTED=0
 
979
PRIMER_MIN_GC=0
 
980
PRIMER_MAX_GC=100
 
981
INCLUDED_REGION=2,55
 
982
PRIMER_PRODUCT_SIZE_RANGE=54-54 55-55
 
983
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
 
984
COMMENT=should succeed with exactly one primer pair
 
985
=
 
986
PRIMER_SEQUENCE_ID=boundary_test_76
 
987
PRIMER_PICK_INTERNAL_OLIGO=0
 
988
PRIMER_MIN_SIZE=25
 
989
PRIMER_MAX_SIZE=25
 
990
PRIMER_OPT_SIZE=25
 
991
PRIMER_NUM_NS_ACCEPTED=0
 
992
PRIMER_MIN_GC=0
 
993
PRIMER_MAX_GC=100
 
994
INCLUDED_REGION=2,56
 
995
PRIMER_PRODUCT_SIZE_RANGE=55-55 56-56
 
996
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
 
997
COMMENT=should succeed with exactly one primer pair
 
998
=
 
999
PRIMER_SEQUENCE_ID=boundary_test_77
 
1000
PRIMER_PICK_INTERNAL_OLIGO=0
 
1001
PRIMER_MIN_SIZE=25
 
1002
PRIMER_MAX_SIZE=25
 
1003
PRIMER_OPT_SIZE=25
 
1004
PRIMER_NUM_NS_ACCEPTED=0
 
1005
PRIMER_MIN_GC=0
 
1006
PRIMER_MAX_GC=100
 
1007
INCLUDED_REGION=2,82
 
1008
PRIMER_PRODUCT_SIZE_RANGE=55-55 82-82
 
1009
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNNACTCACTGTCATTTCCAAACAATTCNN
 
1010
COMMENT=should succeed with exactly 2 primer pairs, biggest product second
 
1011
=
 
1012
PRIMER_SEQUENCE_ID=boundary_test_78
 
1013
PRIMER_PICK_INTERNAL_OLIGO=0
 
1014
PRIMER_MIN_SIZE=25
 
1015
PRIMER_MAX_SIZE=25
 
1016
PRIMER_OPT_SIZE=25
 
1017
PRIMER_NUM_NS_ACCEPTED=0
 
1018
PRIMER_MIN_GC=0
 
1019
PRIMER_MAX_GC=100
 
1020
INCLUDED_REGION=2,82
 
1021
PRIMER_PRODUCT_SIZE_RANGE=82-82 55-55
 
1022
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNNACTCACTGTCATTTCCAAACAATTCNN
 
1023
COMMENT=should succeed with exactly 2 primer pairs, biggest product first
 
1024
=
 
1025
PRIMER_SEQUENCE_ID=boundary_test_79
 
1026
PRIMER_PICK_INTERNAL_OLIGO=0
 
1027
PRIMER_MIN_SIZE=25
 
1028
PRIMER_MAX_SIZE=25
 
1029
PRIMER_OPT_SIZE=25
 
1030
PRIMER_NUM_NS_ACCEPTED=0
 
1031
PRIMER_MIN_GC=0
 
1032
PRIMER_MAX_GC=100
 
1033
INCLUDED_REGION=2,82
 
1034
PRIMER_PRODUCT_SIZE_RANGE=55-55 55-82
 
1035
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNNACTCACTGTCATTTCCAAACAATTCNN
 
1036
COMMENT=should succeed with exactly 2 primer pairs, biggest product second
 
1037
=
 
1038
PRIMER_SEQUENCE_ID=boundary_test_80
 
1039
PRIMER_PICK_INTERNAL_OLIGO=0
 
1040
PRIMER_MIN_SIZE=25
 
1041
PRIMER_MAX_SIZE=25
 
1042
PRIMER_OPT_SIZE=25
 
1043
PRIMER_NUM_NS_ACCEPTED=0
 
1044
PRIMER_MIN_GC=0
 
1045
PRIMER_MAX_GC=100
 
1046
INCLUDED_REGION=2,82
 
1047
PRIMER_PRODUCT_SIZE_RANGE=82-82 55-82
 
1048
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNNACTCACTGTCATTTCCAAACAATTCNN
 
1049
COMMENT=should succeed with exactly 2 primer pairs, biggest product first
 
1050
=
 
1051
PRIMER_SEQUENCE_ID=boundary_test_81
 
1052
PRIMER_PICK_INTERNAL_OLIGO=0
 
1053
PRIMER_MIN_SIZE=25
 
1054
PRIMER_MAX_SIZE=25
 
1055
PRIMER_OPT_SIZE=25
 
1056
PRIMER_NUM_NS_ACCEPTED=0
 
1057
PRIMER_MIN_GC=0
 
1058
PRIMER_MAX_GC=100
 
1059
INCLUDED_REGION=2,55
 
1060
PRIMER_PRODUCT_SIZE_RANGE=55-55
 
1061
PRIMER_SELF_ANY=11
 
1062
SEQUENCE=NNAATGTGATTGCATCAAATGTGATTGNNNNNAATGTGATTGTCATTTCCACAATTCNN
 
1063
COMMENT=should succeed (testing pairwise complementarity checking)
 
1064
=
 
1065
PRIMER_SEQUENCE_ID=boundary_test_82
 
1066
PRIMER_PICK_INTERNAL_OLIGO=0
 
1067
PRIMER_MIN_SIZE=25
 
1068
PRIMER_MAX_SIZE=25
 
1069
PRIMER_OPT_SIZE=25
 
1070
PRIMER_NUM_NS_ACCEPTED=0
 
1071
PRIMER_MIN_GC=0
 
1072
PRIMER_MAX_GC=100
 
1073
INCLUDED_REGION=2,55
 
1074
PRIMER_PRODUCT_SIZE_RANGE=55-55
 
1075
PRIMER_SELF_ANY=10.99
 
1076
SEQUENCE=NNAATGTGATTGCATCAAATGTGATTGNNNNNAATGTGATTGTCATTTCCACAATTCNN
 
1077
COMMENT=should fail (self any for pairs)
 
1078
=
 
1079
PRIMER_SEQUENCE_ID=boundary_test_83
 
1080
PRIMER_PICK_INTERNAL_OLIGO=0
 
1081
PRIMER_MIN_SIZE=25
 
1082
PRIMER_MAX_SIZE=25
 
1083
PRIMER_OPT_SIZE=25
 
1084
PRIMER_NUM_NS_ACCEPTED=0
 
1085
PRIMER_MIN_GC=0
 
1086
PRIMER_MAX_GC=100
 
1087
INCLUDED_REGION=2,55
 
1088
PRIMER_PRODUCT_SIZE_RANGE=55-55
 
1089
PRIMER_SELF_ANY=11
 
1090
PRIMER_SELF_END=10
 
1091
SEQUENCE=NNAATGTGATTGCATCAAATGTGATTGNNNNNAATGTGATTGTCATTTCCACAATTCNN
 
1092
COMMENT=should succeed (testing pairwise complementarity checking)
 
1093
=
 
1094
PRIMER_SEQUENCE_ID=boundary_test_84
 
1095
PRIMER_PICK_INTERNAL_OLIGO=0
 
1096
PRIMER_MIN_SIZE=25
 
1097
PRIMER_MAX_SIZE=25
 
1098
PRIMER_OPT_SIZE=25
 
1099
PRIMER_NUM_NS_ACCEPTED=0
 
1100
PRIMER_MIN_GC=0
 
1101
PRIMER_MAX_GC=100
 
1102
INCLUDED_REGION=2,55
 
1103
PRIMER_PRODUCT_SIZE_RANGE=55-55
 
1104
PRIMER_SELF_ANY=11
 
1105
PRIMER_SELF_END=9.99
 
1106
SEQUENCE=NNAATGTGATTGCATCAAATGTGATTGNNNNNAATGTGATTGTCATTTCCACAATTCNN
 
1107
COMMENT=should fail (self end for pairs)
 
1108
=
 
1109
PRIMER_SEQUENCE_ID=boundary_test_85
 
1110
PRIMER_PICK_INTERNAL_OLIGO=0
 
1111
PRIMER_MIN_SIZE=25
 
1112
PRIMER_MAX_SIZE=25
 
1113
PRIMER_OPT_SIZE=25
 
1114
PRIMER_NUM_NS_ACCEPTED=0
 
1115
PRIMER_MIN_GC=0
 
1116
PRIMER_MAX_GC=100
 
1117
INCLUDED_REGION=2,55
 
1118
PRIMER_PRODUCT_SIZE_RANGE=55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 55-55 
 
1119
PRIMER_SELF_ANY=11
 
1120
PRIMER_SELF_END=10
 
1121
SEQUENCE=NNAATGTGATTGCATCAAATGTGATTGNNNNNAATGTGATTGTCATTTCCACAATTCNN
 
1122
COMMENT=should succeed (testing number of product size ranges)
 
1123
=
 
1124
PRIMER_SEQUENCE_ID=boundary_test_86
 
1125
PRIMER_PICK_INTERNAL_OLIGO=0
 
1126
PRIMER_MIN_SIZE=25
 
1127
PRIMER_MAX_SIZE=25
 
1128
PRIMER_OPT_SIZE=25
 
1129
PRIMER_NUM_NS_ACCEPTED=0
 
1130
PRIMER_MIN_GC=0
 
1131
PRIMER_MAX_GC=100
 
1132
INCLUDED_REGION=2,55
 
1133
PRIMER_PRODUCT_SIZE_RANGE=55-55
 
1134
TARGET=27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1
 
1135
PRIMER_SELF_ANY=11
 
1136
PRIMER_SELF_END=10
 
1137
SEQUENCE=NNAATGTGATTGCATCAAATGTGATTGNNNNNAATGTGATTGTCATTTCCACAATTCNN
 
1138
COMMENT=should succeed (testing number of targets)
 
1139
=
 
1140
PRIMER_SEQUENCE_ID=boundary_test_87
 
1141
PRIMER_PICK_INTERNAL_OLIGO=0
 
1142
PRIMER_MIN_SIZE=25
 
1143
PRIMER_MAX_SIZE=25
 
1144
PRIMER_OPT_SIZE=25
 
1145
PRIMER_NUM_NS_ACCEPTED=0
 
1146
PRIMER_MIN_GC=0
 
1147
PRIMER_MAX_GC=100
 
1148
INCLUDED_REGION=2,55
 
1149
PRIMER_PRODUCT_SIZE_RANGE=55-55
 
1150
TARGET=27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1
 
1151
PRIMER_SELF_ANY=11
 
1152
PRIMER_SELF_END=10
 
1153
SEQUENCE=NNAATGTGATTGCATCAAATGTGATTGNNNNNAATGTGATTGTCATTTCCACAATTCNN
 
1154
COMMENT=should fail (testing number of targets)
 
1155
=
 
1156
PRIMER_SEQUENCE_ID=boundary_test_88
 
1157
PRIMER_PICK_INTERNAL_OLIGO=0
 
1158
PRIMER_MIN_SIZE=25
 
1159
PRIMER_MAX_SIZE=25
 
1160
PRIMER_OPT_SIZE=25
 
1161
PRIMER_NUM_NS_ACCEPTED=0
 
1162
PRIMER_MIN_GC=0
 
1163
PRIMER_MAX_GC=100
 
1164
INCLUDED_REGION=2,55
 
1165
PRIMER_PRODUCT_SIZE_RANGE=55-55
 
1166
EXCLUDED_REGION=27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1
 
1167
PRIMER_SELF_ANY=11
 
1168
PRIMER_SELF_END=10
 
1169
SEQUENCE=NNAATGTGATTGCATCAAATGTGATTGNNNNNAATGTGATTGTCATTTCCACAATTCNN
 
1170
COMMENT=should succeed (testing number of excluded regions)
 
1171
=
 
1172
PRIMER_SEQUENCE_ID=boundary_test_89
 
1173
PRIMER_PICK_INTERNAL_OLIGO=0
 
1174
PRIMER_MIN_SIZE=25
 
1175
PRIMER_MAX_SIZE=25
 
1176
PRIMER_OPT_SIZE=25
 
1177
PRIMER_NUM_NS_ACCEPTED=0
 
1178
PRIMER_MIN_GC=0
 
1179
PRIMER_MAX_GC=100
 
1180
INCLUDED_REGION=2,55
 
1181
PRIMER_PRODUCT_SIZE_RANGE=55-55
 
1182
EXCLUDED_REGION=27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1 27,1
 
1183
PRIMER_SELF_ANY=11
 
1184
PRIMER_SELF_END=10
 
1185
SEQUENCE=NNAATGTGATTGCATCAAATGTGATTGNNNNNAATGTGATTGTCATTTCCACAATTCNN
 
1186
COMMENT=should fail (testing number of excluded regions)
 
1187
=
 
1188
PRIMER_SEQUENCE_ID=boundary_test_90
 
1189
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
 
1190
PRIMER_EXPLAIN_FLAG=1
 
1191
PRIMER_MAX_POLY_X=0
 
1192
PRIMER_INTERNAL_OLIGO_MAX_POLY_X=0
 
1193
PRIMER_PRODUCT_SIZE_RANGE=50-100
 
1194
PRIMER_MIN_TM=0.0
 
1195
PRIMER_MAX_TM=100.0
 
1196
PRIMER_MIN_SIZE=25
 
1197
PRIMER_MAX_SIZE=25
 
1198
PRIMER_OPT_SIZE=25
 
1199
PRIMER_MAX_GC=100
 
1200
PRIMER_MIN_GC=0
 
1201
PRIMER_SELF_END=100
 
1202
PRIMER_SELF_ANY=100
 
1203
PRIMER_MAX_END_STABILITY=6.9
 
1204
PRIMER_COMMENT=should succeed
 
1205
=
 
1206
PRIMER_SEQUENCE_ID=boundary_test_91
 
1207
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCNN
 
1208
PRIMER_EXPLAIN_FLAG=1
 
1209
PRIMER_MAX_POLY_X=0
 
1210
PRIMER_INTERNAL_OLIGO_MAX_POLY_X=0
 
1211
PRIMER_PRODUCT_SIZE_RANGE=50-100
 
1212
PRIMER_MIN_TM=0.0
 
1213
PRIMER_MAX_TM=100.0
 
1214
PRIMER_MIN_SIZE=25
 
1215
PRIMER_MAX_SIZE=25
 
1216
PRIMER_OPT_SIZE=25
 
1217
PRIMER_MAX_GC=100
 
1218
PRIMER_MIN_GC=0
 
1219
PRIMER_SELF_END=100
 
1220
PRIMER_SELF_ANY=100
 
1221
PRIMER_MAX_END_STABILITY=6.8999
 
1222
PRIMER_COMMENT=should fail
 
1223
=
 
1224
PRIMER_SEQUENCE_ID=boundary_test_92
 
1225
PRIMER_NUM_NS_ACCEPTED=0
 
1226
PRIMER_MIN_GC=0
 
1227
PRIMER_MAX_GC=100
 
1228
TARGET=27,1
 
1229
PRIMER_MAX_END_STABILITY=100
 
1230
PRIMER_PRODUCT_SIZE_RANGE=55-55
 
1231
PRIMER_OUTSIDE_PENALTY=100
 
1232
SEQUENCE=ATCACGTCATCTCATCAAATTTGATTGNNNNNACTCACTGTCATTTCCAAACAATTCGG
 
1233
=
 
1234
PRIMER_SEQUENCE_ID=boundary_test_93
 
1235
PRIMER_NUM_NS_ACCEPTED=0
 
1236
PRIMER_MIN_GC=0
 
1237
PRIMER_MAX_GC=100
 
1238
TARGET=27,1
 
1239
PRIMER_MAX_END_STABILITY=100
 
1240
PRIMER_PRODUCT_SIZE_RANGE=55-55
 
1241
PRIMER_OUTSIDE_PENALTY=100
 
1242
SEQUENCE=ATCACGTCATCTCATCAAATTTGATNGNCGATACTCACTGTCATTTCCAAACAATTCGG
 
1243
=
 
1244
PRIMER_SEQUENCE_ID=boundary_test_94
 
1245
PRIMER_NUM_NS_ACCEPTED=0
 
1246
PRIMER_MIN_GC=0
 
1247
PRIMER_MAX_GC=100
 
1248
PRIMER_MAX_END_STABILITY=100
 
1249
PRIMER_PRODUCT_SIZE_RANGE=55-55
 
1250
PRIMER_OUTSIDE_PENALTY=100
 
1251
SEQUENCE=ATCACGTCATCTCATCAAATTTGATNGNCGATACTCACTGTCATTTCCAAACAATTCGG
 
1252
=
 
1253
PRIMER_SEQUENCE_ID=boundary_test_95
 
1254
PRIMER_NUM_NS_ACCEPTED=0
 
1255
PRIMER_MIN_GC=0
 
1256
PRIMER_MAX_GC=100
 
1257
TARGET=27,10
 
1258
PRIMER_MAX_END_STABILITY=100
 
1259
PRIMER_PRODUCT_SIZE_RANGE=55-55
 
1260
PRIMER_OUTSIDE_PENALTY=0
 
1261
PRIMER_INSIDE_PENALTY=1000
 
1262
SEQUENCE=ATCACGTCATCTCATCAAATTTGATTGATCGTACTCACTGTCATTTCCAAACAATNCGG
 
1263
=
 
1264
PRIMER_SEQUENCE_ID=boundary_test_96
 
1265
PRIMER_NUM_NS_ACCEPTED=0
 
1266
PRIMER_MIN_GC=0
 
1267
PRIMER_MAX_GC=100
 
1268
TARGET=27,10
 
1269
PRIMER_MAX_END_STABILITY=100
 
1270
PRIMER_PRODUCT_SIZE_RANGE=55-55
 
1271
PRIMER_OUTSIDE_PENALTY=0
 
1272
PRIMER_INSIDE_PENALTY=1000
 
1273
SEQUENCE=ATCNCATCATCTCATCAAATTTGATTGATCGTACTCACTGTCATTTCCAAACAATACGG
 
1274
=
 
1275
PRIMER_SEQUENCE_ID=boundary_test_97
 
1276
PRIMER_NUM_NS_ACCEPTED=0
 
1277
PRIMER_MIN_GC=0
 
1278
PRIMER_MAX_GC=100
 
1279
PRIMER_MAX_END_STABILITY=100
 
1280
PRIMER_PRODUCT_SIZE_RANGE=55-55
 
1281
PRIMER_OUTSIDE_PENALTY=0
 
1282
PRIMER_INSIDE_PENALTY=1000
 
1283
SEQUENCE=ATCNCATCATCTCATCAAATTTGATTGATCGTACTCACTGTCATTTCCAAACAATACGG
 
1284
=
 
1285
PRIMER_SEQUENCE_ID=test_098
 
1286
SEQUENCE=ATCNCATCATCTCATCAAATTTGATTGATTTTACTCACTGTCATTTCCAAACAATACGG
 
1287
PRIMER_INSIDE_PENALTY=-1.0
 
1288
PRIMER_PRODUCT_MAX_TM=62.4120
 
1289
PRIMER_COMMENT=Should succeed.
 
1290
=
 
1291
PRIMER_SEQUENCE_ID=test_099
 
1292
SEQUENCE=ATCNCATCATCTCATCAAATTTGATTGATCGTACTCACTGTCATTTCCAAACAATACGG
 
1293
PRIMER_PRODUCT_MAX_TM=62.4119
 
1294
PRIMER_COMMENT=Should fail.
 
1295
=
 
1296
PRIMER_SEQUENCE_ID=test_100
 
1297
SEQUENCE=ATCNCATCATCTCATCAAATTTGATTGATCGTACTCACTGTCATTTCCAAACAATACGG
 
1298
PRIMER_PRODUCT_MAX_TM=1000000
 
1299
PRIMER_COMMENT=Make sure that product tm output gets turned off again.
 
1300
=
 
1301
PRIMER_SEQUENCE_ID=test_101
 
1302
SEQUENCE=ATCNCATCATCTCATCAAATTTGATTGATCGTACTCACTGTCATTTCCAAACAATACGG
 
1303
PRIMER_PRODUCT_MIN_TM=62.4119
 
1304
PRIMER_COMMENT=Should succeed.
 
1305
=
 
1306
PRIMER_SEQUENCE_ID=test_102
 
1307
SEQUENCE=ATCNCATCATCTCATCAAATTTGATTGATCGTACTCACTGTCATTTCCAAACAATACGG
 
1308
PRIMER_PRODUCT_MIN_TM=63.9030
 
1309
PRIMER_COMMENT=Should fail.
 
1310
=
 
1311
PRIMER_SEQUENCE_ID=test_103
 
1312
SEQUENCE=ATCNCATCATCTCATCAAATTTGATTGATCGTACTCACTGTCATTTCCAAACAATACGG
 
1313
PRIMER_PRODUCT_MIN_TM=-1000000
 
1314
PRIMER_COMMENT=Make sure that product tm output gets turned off again.
 
1315
=