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  • 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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test/primer_must_use_output
 
1
PRIMER_SEQUENCE_ID=anyway_1
 
2
PRIMER_EXPLAIN_FLAG=1
 
3
PRIMER_SELF_ANY=12
 
4
PRIMER_MAX_POLY_X=100
 
5
PRIMER_INTERNAL_OLIGO_MAX_POLY_X=100
 
6
PRIMER_SELF_END=8
 
7
PRIMER_NUM_RETURN=1
 
8
PRIMER_PICK_ANYWAY=1
 
9
SEQUENCE=TCCTACAGCTGTGGGAAAATGatgcgtacgatccatgctagctagctactatcgattagctatcatctactatcatctactatctactacacatctactatcatctacacacacacacacactaggccgctatatcatctagcGCCGCCATGTACACACTG
 
10
TARGET=21,122
 
11
PRIMER_LEFT_EXPLAIN=considered 10, low tm 7, ok 3
 
12
PRIMER_RIGHT_EXPLAIN=considered 1, ok 1
 
13
PRIMER_PAIR_EXPLAIN=considered 1, ok 1
 
14
PRIMER_PAIR_PENALTY=3.4323
 
15
PRIMER_LEFT_PENALTY=1.117633
 
16
PRIMER_RIGHT_PENALTY=2.314641
 
17
PRIMER_LEFT_SEQUENCE=TCCTACAGCTGTGGGAAAATG
 
18
PRIMER_RIGHT_SEQUENCE=CAGTGTGTACATGGCGGC
 
19
PRIMER_LEFT=0,21
 
20
PRIMER_RIGHT=160,18
 
21
PRIMER_LEFT_TM=60.118
 
22
PRIMER_RIGHT_TM=59.685
 
23
PRIMER_LEFT_GC_PERCENT=47.619
 
24
PRIMER_RIGHT_GC_PERCENT=61.111
 
25
PRIMER_LEFT_SELF_ANY=12.00
 
26
PRIMER_RIGHT_SELF_ANY=6.00
 
27
PRIMER_LEFT_SELF_END=0.00
 
28
PRIMER_RIGHT_SELF_END=3.00
 
29
PRIMER_LEFT_END_STABILITY=7.2000
 
30
PRIMER_RIGHT_END_STABILITY=12.9000
 
31
PRIMER_PAIR_COMPL_ANY=4.00
 
32
PRIMER_PAIR_COMPL_END=1.00
 
33
PRIMER_PRODUCT_SIZE=161
 
34
=
 
35
PRIMER_SEQUENCE_ID=high_tm
 
36
PRIMER_SELF_ANY=12
 
37
PRIMER_MAX_POLY_X=100
 
38
PRIMER_INTERNAL_OLIGO_MAX_POLY_X=100
 
39
PRIMER_SELF_END=8
 
40
PRIMER_NUM_RETURN=1
 
41
SEQUENCE=TCCTACAGCTGTGGGAAAATGatgcgtacgatccatgctagctagctactatcgattagctatcatctactatcatctactatctactacacatctactatcatctacacacacacacacactaggccgctatatcatctagcGCCGCCATGTACACACTG
 
42
TARGET=21,122
 
43
PRIMER_LEFT_INPUT=TCCTACAGCTGTGGGAAAATG
 
44
PRIMER_MAX_TM=60
 
45
PRIMER_WARNING=Left primer is unacceptable: Tm too high
 
46
PRIMER_RIGHT_EXPLAIN=considered 1, ok 1
 
47
PRIMER_PAIR_EXPLAIN=considered 1, ok 1
 
48
PRIMER_PAIR_PENALTY=3.4323
 
49
PRIMER_LEFT_PENALTY=1.117633
 
50
PRIMER_RIGHT_PENALTY=2.314641
 
51
PRIMER_LEFT_SEQUENCE=TCCTACAGCTGTGGGAAAATG
 
52
PRIMER_RIGHT_SEQUENCE=CAGTGTGTACATGGCGGC
 
53
PRIMER_LEFT=0,21
 
54
PRIMER_RIGHT=160,18
 
55
PRIMER_LEFT_TM=60.118
 
56
PRIMER_RIGHT_TM=59.685
 
57
PRIMER_LEFT_GC_PERCENT=47.619
 
58
PRIMER_RIGHT_GC_PERCENT=61.111
 
59
PRIMER_LEFT_SELF_ANY=12.00
 
60
PRIMER_RIGHT_SELF_ANY=6.00
 
61
PRIMER_LEFT_SELF_END=0.00
 
62
PRIMER_RIGHT_SELF_END=3.00
 
63
PRIMER_LEFT_END_STABILITY=7.2000
 
64
PRIMER_RIGHT_END_STABILITY=12.9000
 
65
PRIMER_PAIR_COMPL_ANY=4.00
 
66
PRIMER_PAIR_COMPL_END=1.00
 
67
PRIMER_PRODUCT_SIZE=161
 
68
=
 
69
PRIMER_SEQUENCE_ID=high_tm_and_self_any
 
70
PRIMER_SELF_ANY=11
 
71
PRIMER_MAX_POLY_X=100
 
72
PRIMER_INTERNAL_OLIGO_MAX_POLY_X=100
 
73
PRIMER_SELF_END=8
 
74
PRIMER_NUM_RETURN=1
 
75
SEQUENCE=TCCTACAGCTGTGGGAAAATGatgcgtacgatccatgctagctagctactatcgattagctatcatctactatcatctactatctactacacatctactatcatctacacacacacacacactaggccgctatatcatctagcGCCGCCATGTACACACTG
 
76
TARGET=21,122
 
77
PRIMER_LEFT_INPUT=TCCTACAGCTGTGGGAAAATG
 
78
PRIMER_MAX_TM=60
 
79
PRIMER_WARNING=Left primer is unacceptable: Tm too high/High self complementarity
 
80
PRIMER_RIGHT_EXPLAIN=considered 1, ok 1
 
81
PRIMER_PAIR_EXPLAIN=considered 1, ok 1
 
82
PRIMER_PAIR_PENALTY=3.4323
 
83
PRIMER_LEFT_PENALTY=1.117633
 
84
PRIMER_RIGHT_PENALTY=2.314641
 
85
PRIMER_LEFT_SEQUENCE=TCCTACAGCTGTGGGAAAATG
 
86
PRIMER_RIGHT_SEQUENCE=CAGTGTGTACATGGCGGC
 
87
PRIMER_LEFT=0,21
 
88
PRIMER_RIGHT=160,18
 
89
PRIMER_LEFT_TM=60.118
 
90
PRIMER_RIGHT_TM=59.685
 
91
PRIMER_LEFT_GC_PERCENT=47.619
 
92
PRIMER_RIGHT_GC_PERCENT=61.111
 
93
PRIMER_LEFT_SELF_ANY=12.00
 
94
PRIMER_RIGHT_SELF_ANY=6.00
 
95
PRIMER_LEFT_SELF_END=0.00
 
96
PRIMER_RIGHT_SELF_END=3.00
 
97
PRIMER_LEFT_END_STABILITY=7.2000
 
98
PRIMER_RIGHT_END_STABILITY=12.9000
 
99
PRIMER_PAIR_COMPL_ANY=4.00
 
100
PRIMER_PAIR_COMPL_END=1.00
 
101
PRIMER_PRODUCT_SIZE=161
 
102
=
 
103
PRIMER_SEQUENCE_ID=high_tm_and_self_any_and_target
 
104
PRIMER_SELF_ANY=11
 
105
PRIMER_MAX_POLY_X=100
 
106
PRIMER_INTERNAL_OLIGO_MAX_POLY_X=100
 
107
PRIMER_SELF_END=8
 
108
PRIMER_NUM_RETURN=1
 
109
SEQUENCE=TCCTACAGCTGTGGGAAAATGatgcgtacgatccatgctagctagctactatcgattagctatcatctactatcatctactatctactacacatctactatcatctacacacacacacacactaggccgctatatcatctagcGCCGCCATGTACACACTG
 
110
TARGET=20,122
 
111
PRIMER_LEFT_INPUT=TCCTACAGCTGTGGGAAAATG
 
112
PRIMER_MAX_TM=60
 
113
PRIMER_WARNING=Left primer is unacceptable: Overlaps Target/Tm too high/High self complementarity
 
114
PRIMER_RIGHT_EXPLAIN=considered 3, high tm 2, ok 1
 
115
PRIMER_PAIR_EXPLAIN=considered 1, ok 1
 
116
PRIMER_PAIR_PENALTY=3.4323
 
117
PRIMER_LEFT_PENALTY=1.117633
 
118
PRIMER_RIGHT_PENALTY=2.314641
 
119
PRIMER_LEFT_SEQUENCE=TCCTACAGCTGTGGGAAAATG
 
120
PRIMER_RIGHT_SEQUENCE=CAGTGTGTACATGGCGGC
 
121
PRIMER_LEFT=0,21
 
122
PRIMER_RIGHT=160,18
 
123
PRIMER_LEFT_TM=60.118
 
124
PRIMER_RIGHT_TM=59.685
 
125
PRIMER_LEFT_GC_PERCENT=47.619
 
126
PRIMER_RIGHT_GC_PERCENT=61.111
 
127
PRIMER_LEFT_SELF_ANY=12.00
 
128
PRIMER_RIGHT_SELF_ANY=6.00
 
129
PRIMER_LEFT_SELF_END=0.00
 
130
PRIMER_RIGHT_SELF_END=3.00
 
131
PRIMER_LEFT_END_STABILITY=7.2000
 
132
PRIMER_RIGHT_END_STABILITY=12.9000
 
133
PRIMER_PAIR_COMPL_ANY=4.00
 
134
PRIMER_PAIR_COMPL_END=1.00
 
135
PRIMER_PRODUCT_SIZE=161
 
136
=
 
137
PRIMER_SEQUENCE_ID=high_tm_and_self_any_and_excl_region
 
138
PRIMER_SELF_ANY=11
 
139
PRIMER_MAX_POLY_X=100
 
140
PRIMER_INTERNAL_OLIGO_MAX_POLY_X=100
 
141
PRIMER_SELF_END=8
 
142
EXCLUDED_REGION=20,1
 
143
PRIMER_NUM_RETURN=1
 
144
SEQUENCE=TCCTACAGCTGTGGGAAAATGatgcgtacgatccatgctagctagctactatcgattagctatcatctactatcatctactatctactacacatctactatcatctacacacacacacacactaggccgctatatcatctagcGCCGCCATGTACACACTG
 
145
TARGET=21,122
 
146
PRIMER_LEFT_INPUT=TCCTACAGCTGTGGGAAAATG
 
147
PRIMER_MAX_TM=60
 
148
PRIMER_WARNING=Left primer is unacceptable: Overlaps Excluded Region/Tm too high/High self complementarity
 
149
PRIMER_RIGHT_EXPLAIN=considered 1, ok 1
 
150
PRIMER_PAIR_EXPLAIN=considered 1, ok 1
 
151
PRIMER_PAIR_PENALTY=3.4323
 
152
PRIMER_LEFT_PENALTY=1.117633
 
153
PRIMER_RIGHT_PENALTY=2.314641
 
154
PRIMER_LEFT_SEQUENCE=TCCTACAGCTGTGGGAAAATG
 
155
PRIMER_RIGHT_SEQUENCE=CAGTGTGTACATGGCGGC
 
156
PRIMER_LEFT=0,21
 
157
PRIMER_RIGHT=160,18
 
158
PRIMER_LEFT_TM=60.118
 
159
PRIMER_RIGHT_TM=59.685
 
160
PRIMER_LEFT_GC_PERCENT=47.619
 
161
PRIMER_RIGHT_GC_PERCENT=61.111
 
162
PRIMER_LEFT_SELF_ANY=12.00
 
163
PRIMER_RIGHT_SELF_ANY=6.00
 
164
PRIMER_LEFT_SELF_END=0.00
 
165
PRIMER_RIGHT_SELF_END=3.00
 
166
PRIMER_LEFT_END_STABILITY=7.2000
 
167
PRIMER_RIGHT_END_STABILITY=12.9000
 
168
PRIMER_PAIR_COMPL_ANY=4.00
 
169
PRIMER_PAIR_COMPL_END=1.00
 
170
PRIMER_PRODUCT_SIZE=161
 
171
=
 
172
PRIMER_SEQUENCE_ID=high_tm_and_self_any_and_incl_region
 
173
PRIMER_SELF_ANY=11
 
174
PRIMER_MAX_POLY_X=100
 
175
PRIMER_INTERNAL_OLIGO_MAX_POLY_X=100
 
176
PRIMER_SELF_END=8
 
177
INCLUDED_REGION=1,160
 
178
PRIMER_NUM_RETURN=1
 
179
SEQUENCE=TCCTACAGCTGTGGGAAAATGatgcgtacgatccatgctagctagctactatcgattagctatcatctactatcatctactatctactacacatctactatcatctacacacacacacacactaggccgctatatcatctagcGCCGCCATGTACACACTG
 
180
TARGET=21,122
 
181
PRIMER_LEFT_INPUT=TCCTACAGCTGTGGGAAAATG
 
182
PRIMER_MAX_TM=60
 
183
PRIMER_ERROR=Specified left primer not in Included Region
 
184
=
 
185
PRIMER_SEQUENCE_ID=left_high_tm_and_self_any_and_right
 
186
PRIMER_SELF_ANY=11
 
187
PRIMER_MAX_POLY_X=100
 
188
PRIMER_INTERNAL_OLIGO_MAX_POLY_X=100
 
189
PRIMER_SELF_END=8
 
190
PRIMER_NUM_RETURN=1
 
191
SEQUENCE=TCCTACAGCTGTGGGAAAATGatgcgtacgatccatgctagctagctactatcgattagctatcatctactatcatctactatctactacacatctactatcatctacacacacacacacactaggccgctatatcatctagcGCCGCCATGTACACACTG
 
192
TARGET=21,122
 
193
PRIMER_LEFT_INPUT=TCCTACAGCTGTGGGAAAATG
 
194
PRIMER_RIGHT_INPUT=CAGTGTGTACATGGCGGC
 
195
PRIMER_MAX_TM=60
 
196
PRIMER_WARNING=Left primer is unacceptable: Tm too high/High self complementarity
 
197
PRIMER_PAIR_EXPLAIN=considered 1, ok 1
 
198
PRIMER_PAIR_PENALTY=3.4323
 
199
PRIMER_LEFT_PENALTY=1.117633
 
200
PRIMER_RIGHT_PENALTY=2.314641
 
201
PRIMER_LEFT_SEQUENCE=TCCTACAGCTGTGGGAAAATG
 
202
PRIMER_RIGHT_SEQUENCE=CAGTGTGTACATGGCGGC
 
203
PRIMER_LEFT=0,21
 
204
PRIMER_RIGHT=160,18
 
205
PRIMER_LEFT_TM=60.118
 
206
PRIMER_RIGHT_TM=59.685
 
207
PRIMER_LEFT_GC_PERCENT=47.619
 
208
PRIMER_RIGHT_GC_PERCENT=61.111
 
209
PRIMER_LEFT_SELF_ANY=12.00
 
210
PRIMER_RIGHT_SELF_ANY=6.00
 
211
PRIMER_LEFT_SELF_END=0.00
 
212
PRIMER_RIGHT_SELF_END=3.00
 
213
PRIMER_LEFT_END_STABILITY=7.2000
 
214
PRIMER_RIGHT_END_STABILITY=12.9000
 
215
PRIMER_PAIR_COMPL_ANY=4.00
 
216
PRIMER_PAIR_COMPL_END=1.00
 
217
PRIMER_PRODUCT_SIZE=161
 
218
=
 
219
PRIMER_SEQUENCE_ID=left_high_tm_and_self_any_and_right_bad_gc
 
220
PRIMER_SELF_ANY=11
 
221
PRIMER_MAX_POLY_X=100
 
222
PRIMER_INTERNAL_OLIGO_MAX_POLY_X=100
 
223
PRIMER_SELF_END=8
 
224
PRIMER_NUM_RETURN=1
 
225
SEQUENCE=TCCTACAGCTGTGGGAAAATGatgcgtacgatccatgctagctagctactatcgattagctatcatctactatcatctactatctactacacatctactatcatctacacacacacacacactaggccgctatatcatctagcGCCGCCATGTACACACTG
 
226
TARGET=21,122
 
227
PRIMER_LEFT_INPUT=TCCTACAGCTGTGGGAAAATG
 
228
PRIMER_RIGHT_INPUT=CAGTGTGTACATGGCGGC
 
229
PRIMER_MAX_TM=60
 
230
PRIMER_MAX_GC=60
 
231
PRIMER_WARNING=Left primer is unacceptable: Tm too high/High self complementarity; Right primer is unacceptable: Unacceptable GC content
 
232
PRIMER_PAIR_EXPLAIN=considered 1, ok 1
 
233
PRIMER_PAIR_PENALTY=3.4323
 
234
PRIMER_LEFT_PENALTY=1.117633
 
235
PRIMER_RIGHT_PENALTY=2.314641
 
236
PRIMER_LEFT_SEQUENCE=TCCTACAGCTGTGGGAAAATG
 
237
PRIMER_RIGHT_SEQUENCE=CAGTGTGTACATGGCGGC
 
238
PRIMER_LEFT=0,21
 
239
PRIMER_RIGHT=160,18
 
240
PRIMER_LEFT_TM=60.118
 
241
PRIMER_RIGHT_TM=59.685
 
242
PRIMER_LEFT_GC_PERCENT=47.619
 
243
PRIMER_RIGHT_GC_PERCENT=61.111
 
244
PRIMER_LEFT_SELF_ANY=12.00
 
245
PRIMER_RIGHT_SELF_ANY=6.00
 
246
PRIMER_LEFT_SELF_END=0.00
 
247
PRIMER_RIGHT_SELF_END=3.00
 
248
PRIMER_LEFT_END_STABILITY=7.2000
 
249
PRIMER_RIGHT_END_STABILITY=12.9000
 
250
PRIMER_PAIR_COMPL_ANY=4.00
 
251
PRIMER_PAIR_COMPL_END=1.00
 
252
PRIMER_PRODUCT_SIZE=161
 
253
=
 
254
PRIMER_SEQUENCE_ID=left_high_tm_and_self_any_and_right_bad_gc_and_target
 
255
PRIMER_SELF_ANY=11
 
256
PRIMER_MAX_POLY_X=100
 
257
PRIMER_INTERNAL_OLIGO_MAX_POLY_X=100
 
258
PRIMER_SELF_END=8
 
259
PRIMER_NUM_RETURN=1
 
260
SEQUENCE=TCCTACAGCTGTGGGAAAATGatgcgtacgatccatgctagctagctactatcgattagctatcatctactatcatctactatctactacacatctactatcatctacacacacacacacactaggccgctatatcatctagcGCCGCCATGTACACACTG
 
261
TARGET=21,122 143,1
 
262
PRIMER_LEFT_INPUT=TCCTACAGCTGTGGGAAAATG
 
263
PRIMER_RIGHT_INPUT=CAGTGTGTACATGGCGGC
 
264
PRIMER_MAX_TM=60
 
265
PRIMER_MAX_GC=60
 
266
PRIMER_WARNING=Left primer is unacceptable: Tm too high/High self complementarity; Right primer is unacceptable: Overlaps Target/Unacceptable GC content
 
267
PRIMER_PAIR_EXPLAIN=considered 1, ok 1
 
268
PRIMER_PAIR_PENALTY=3.4323
 
269
PRIMER_LEFT_PENALTY=1.117633
 
270
PRIMER_RIGHT_PENALTY=2.314641
 
271
PRIMER_LEFT_SEQUENCE=TCCTACAGCTGTGGGAAAATG
 
272
PRIMER_RIGHT_SEQUENCE=CAGTGTGTACATGGCGGC
 
273
PRIMER_LEFT=0,21
 
274
PRIMER_RIGHT=160,18
 
275
PRIMER_LEFT_TM=60.118
 
276
PRIMER_RIGHT_TM=59.685
 
277
PRIMER_LEFT_GC_PERCENT=47.619
 
278
PRIMER_RIGHT_GC_PERCENT=61.111
 
279
PRIMER_LEFT_SELF_ANY=12.00
 
280
PRIMER_RIGHT_SELF_ANY=6.00
 
281
PRIMER_LEFT_SELF_END=0.00
 
282
PRIMER_RIGHT_SELF_END=3.00
 
283
PRIMER_LEFT_END_STABILITY=7.2000
 
284
PRIMER_RIGHT_END_STABILITY=12.9000
 
285
PRIMER_PAIR_COMPL_ANY=4.00
 
286
PRIMER_PAIR_COMPL_END=1.00
 
287
PRIMER_PRODUCT_SIZE=161
 
288
=
 
289
PRIMER_SEQUENCE_ID=internal_too_short
 
290
PRIMER_PICK_INTERNAL_OLIGO=1
 
291
PRIMER_SELF_ANY=11
 
292
PRIMER_MAX_POLY_X=100
 
293
PRIMER_INTERNAL_OLIGO_MAX_POLY_X=100
 
294
PRIMER_SELF_END=8
 
295
PRIMER_NUM_RETURN=1
 
296
SEQUENCE=TCCTACAGCTGTGGGAAAATGatgcgtacgatccatgctagctagctactatcgattagctatcatctactatcatctactatctactacacatctactatcatctacacacacacacacactaggccgctatatcatctagcGCCGCCATGTACACACTG
 
297
TARGET=21,122 143,1
 
298
PRIMER_LEFT_INPUT=TCCTACAGCTGTGGGAAAATG
 
299
PRIMER_RIGHT_INPUT=CAGTGTGTACATGGCGGC
 
300
PRIMER_INTERNAL_OLIGO_INPUT=gcgtacgatccat
 
301
PRIMER_MAX_TM=60
 
302
PRIMER_MAX_GC=60
 
303
PRIMER_ERROR=Specified internal oligo too short
 
304
=
 
305
PRIMER_SEQUENCE_ID=internal_ok
 
306
PRIMER_PICK_INTERNAL_OLIGO=1
 
307
PRIMER_SELF_ANY=11
 
308
PRIMER_MAX_POLY_X=100
 
309
PRIMER_INTERNAL_OLIGO_MAX_POLY_X=100
 
310
PRIMER_SELF_END=8
 
311
PRIMER_NUM_RETURN=1
 
312
SEQUENCE=TCCTACAGCTGTGGGAAAATGatgcgtacgatccatgctagctagctactatcgattagctatcatctactatcatctactatctactacacatctactatcatctacacacacacacacactaggccgctatatcatctagcGCCGCCATGTACACACTG
 
313
TARGET=21,122 143,1
 
314
PRIMER_LEFT_INPUT=TCCTACAGCTGTGGGAAAATG
 
315
PRIMER_RIGHT_INPUT=CAGTGTGTACATGGCGGC
 
316
PRIMER_INTERNAL_OLIGO_INPUT=gcgtacgatccatgctagc
 
317
PRIMER_MAX_TM=60
 
318
PRIMER_MAX_GC=60
 
319
PRIMER_WARNING=Left primer is unacceptable: Tm too high/High self complementarity; Right primer is unacceptable: Overlaps Target/Unacceptable GC content
 
320
PRIMER_PAIR_EXPLAIN=considered 1, ok 1
 
321
PRIMER_PAIR_PENALTY=3.4323
 
322
PRIMER_LEFT_PENALTY=1.117633
 
323
PRIMER_RIGHT_PENALTY=2.314641
 
324
PRIMER_INTERNAL_OLIGO_PENALTY=1.580164
 
325
PRIMER_LEFT_SEQUENCE=TCCTACAGCTGTGGGAAAATG
 
326
PRIMER_RIGHT_SEQUENCE=CAGTGTGTACATGGCGGC
 
327
PRIMER_INTERNAL_OLIGO_SEQUENCE=gcgtacgatccatgctagc
 
328
PRIMER_LEFT=0,21
 
329
PRIMER_RIGHT=160,18
 
330
PRIMER_INTERNAL_OLIGO=23,19
 
331
PRIMER_LEFT_TM=60.118
 
332
PRIMER_RIGHT_TM=59.685
 
333
PRIMER_INTERNAL_OLIGO_TM=59.420
 
334
PRIMER_LEFT_GC_PERCENT=47.619
 
335
PRIMER_RIGHT_GC_PERCENT=61.111
 
336
PRIMER_INTERNAL_OLIGO_GC_PERCENT=57.895
 
337
PRIMER_LEFT_SELF_ANY=12.00
 
338
PRIMER_RIGHT_SELF_ANY=6.00
 
339
PRIMER_INTERNAL_OLIGO_SELF_ANY=6.00
 
340
PRIMER_LEFT_SELF_END=0.00
 
341
PRIMER_RIGHT_SELF_END=3.00
 
342
PRIMER_INTERNAL_OLIGO_SELF_END=6.00
 
343
PRIMER_LEFT_END_STABILITY=7.2000
 
344
PRIMER_RIGHT_END_STABILITY=12.9000
 
345
PRIMER_PAIR_COMPL_ANY=4.00
 
346
PRIMER_PAIR_COMPL_END=1.00
 
347
PRIMER_PRODUCT_SIZE=161
 
348
=
 
349
PRIMER_SEQUENCE_ID=internal_too_cold
 
350
PRIMER_PICK_INTERNAL_OLIGO=1
 
351
PRIMER_SELF_ANY=11
 
352
PRIMER_MAX_POLY_X=100
 
353
PRIMER_INTERNAL_OLIGO_MAX_POLY_X=100
 
354
PRIMER_SELF_END=8
 
355
PRIMER_NUM_RETURN=1
 
356
SEQUENCE=TCCTACAGCTGTGGGAAAATGatgcgtacgatccatgctagctagctactatcgattagctatcatctactatcatctactatctactacacatctactatcatctacacacacacacacactaggccgctatatcatctagcGCCGCCATGTACACACTG
 
357
TARGET=21,122 143,1
 
358
PRIMER_LEFT_INPUT=TCCTACAGCTGTGGGAAAATG
 
359
PRIMER_RIGHT_INPUT=CAGTGTGTACATGGCGGC
 
360
PRIMER_INTERNAL_OLIGO_INPUT=gcgtacgatccatgctagc
 
361
PRIMER_INTERNAL_OLIGO_MIN_TM=60
 
362
PRIMER_MAX_TM=60
 
363
PRIMER_MAX_GC=60
 
364
PRIMER_WARNING=Left primer is unacceptable: Tm too high/High self complementarity; Right primer is unacceptable: Overlaps Target/Unacceptable GC content; Hybridization probe is unacceptable: Tm too low
 
365
PRIMER_PAIR_EXPLAIN=considered 1, ok 1
 
366
PRIMER_PAIR_PENALTY=3.4323
 
367
PRIMER_LEFT_PENALTY=1.117633
 
368
PRIMER_RIGHT_PENALTY=2.314641
 
369
PRIMER_INTERNAL_OLIGO_PENALTY=1.580164
 
370
PRIMER_LEFT_SEQUENCE=TCCTACAGCTGTGGGAAAATG
 
371
PRIMER_RIGHT_SEQUENCE=CAGTGTGTACATGGCGGC
 
372
PRIMER_INTERNAL_OLIGO_SEQUENCE=gcgtacgatccatgctagc
 
373
PRIMER_LEFT=0,21
 
374
PRIMER_RIGHT=160,18
 
375
PRIMER_INTERNAL_OLIGO=23,19
 
376
PRIMER_LEFT_TM=60.118
 
377
PRIMER_RIGHT_TM=59.685
 
378
PRIMER_INTERNAL_OLIGO_TM=59.420
 
379
PRIMER_LEFT_GC_PERCENT=47.619
 
380
PRIMER_RIGHT_GC_PERCENT=61.111
 
381
PRIMER_INTERNAL_OLIGO_GC_PERCENT=57.895
 
382
PRIMER_LEFT_SELF_ANY=12.00
 
383
PRIMER_RIGHT_SELF_ANY=6.00
 
384
PRIMER_INTERNAL_OLIGO_SELF_ANY=6.00
 
385
PRIMER_LEFT_SELF_END=0.00
 
386
PRIMER_RIGHT_SELF_END=3.00
 
387
PRIMER_INTERNAL_OLIGO_SELF_END=6.00
 
388
PRIMER_LEFT_END_STABILITY=7.2000
 
389
PRIMER_RIGHT_END_STABILITY=12.9000
 
390
PRIMER_PAIR_COMPL_ANY=4.00
 
391
PRIMER_PAIR_COMPL_END=1.00
 
392
PRIMER_PRODUCT_SIZE=161
 
393
=
 
394
PRIMER_SEQUENCE_ID=internal_too_cold2
 
395
PRIMER_PICK_INTERNAL_OLIGO=1
 
396
PRIMER_SELF_ANY=11
 
397
PRIMER_MAX_POLY_X=100
 
398
PRIMER_INTERNAL_OLIGO_MAX_POLY_X=100
 
399
PRIMER_SELF_END=12
 
400
PRIMER_NUM_RETURN=1
 
401
SEQUENCE=TCCTACAGCTGTGGGAAAATGatgcgtacgatccatgctagctagctactatcgattagctatcatctactatcatctactatctactacacatctactatcatctacacacacacacacactaggccgctatatcatctagcGCCGCCATGTACACACTG
 
402
TARGET=21,122
 
403
PRIMER_LEFT_INPUT=CCTACAGCTGTGGGAAAATG
 
404
PRIMER_INTERNAL_OLIGO_INPUT=gcgtacgatccatgctagc
 
405
PRIMER_INTERNAL_OLIGO_MIN_TM=60
 
406
PRIMER_MAX_TM=100
 
407
PRIMER_MAX_GC=100
 
408
PRIMER_WARNING=Hybridization probe is unacceptable: Tm too low
 
409
PRIMER_RIGHT_EXPLAIN=considered 1, ok 1
 
410
PRIMER_PAIR_EXPLAIN=considered 1, ok 1
 
411
PRIMER_PAIR_PENALTY=4.0864
 
412
PRIMER_LEFT_PENALTY=1.771733
 
413
PRIMER_RIGHT_PENALTY=2.314641
 
414
PRIMER_INTERNAL_OLIGO_PENALTY=1.580164
 
415
PRIMER_LEFT_SEQUENCE=CCTACAGCTGTGGGAAAATG
 
416
PRIMER_RIGHT_SEQUENCE=CAGTGTGTACATGGCGGC
 
417
PRIMER_INTERNAL_OLIGO_SEQUENCE=gcgtacgatccatgctagc
 
418
PRIMER_LEFT=1,20
 
419
PRIMER_RIGHT=160,18
 
420
PRIMER_INTERNAL_OLIGO=23,19
 
421
PRIMER_LEFT_TM=58.228
 
422
PRIMER_RIGHT_TM=59.685
 
423
PRIMER_INTERNAL_OLIGO_TM=59.420
 
424
PRIMER_LEFT_GC_PERCENT=50.000
 
425
PRIMER_RIGHT_GC_PERCENT=61.111
 
426
PRIMER_INTERNAL_OLIGO_GC_PERCENT=57.895
 
427
PRIMER_LEFT_SELF_ANY=10.00
 
428
PRIMER_RIGHT_SELF_ANY=6.00
 
429
PRIMER_INTERNAL_OLIGO_SELF_ANY=6.00
 
430
PRIMER_LEFT_SELF_END=0.00
 
431
PRIMER_RIGHT_SELF_END=3.00
 
432
PRIMER_INTERNAL_OLIGO_SELF_END=6.00
 
433
PRIMER_LEFT_END_STABILITY=7.2000
 
434
PRIMER_RIGHT_END_STABILITY=12.9000
 
435
PRIMER_PAIR_COMPL_ANY=4.00
 
436
PRIMER_PAIR_COMPL_END=1.00
 
437
PRIMER_PRODUCT_SIZE=160
 
438
=
 
439
PRIMER_SEQUENCE_ID=mispriming
 
440
PRIMER_PICK_INTERNAL_OLIGO=1
 
441
PRIMER_SELF_ANY=11
 
442
PRIMER_MAX_POLY_X=100
 
443
PRIMER_INTERNAL_OLIGO_MAX_POLY_X=100
 
444
PRIMER_SELF_END=12
 
445
PRIMER_NUM_RETURN=1
 
446
SEQUENCE=TCCTACAGCTGTGGGAAAATGatgcgtacgatccatgctagctagctactatcgattagctatcatctactatcatctactatctactacacatctactatcatctacacacacacacacactaggccgctatatcatctagcGCCGCCATGTACACACTG
 
447
TARGET=21,122
 
448
PRIMER_LEFT_INPUT=CCTACAGCTGTGGGAAAATG
 
449
PRIMER_INTERNAL_OLIGO_INPUT=gcgtacgatccatgctagc
 
450
PRIMER_INTERNAL_OLIGO_MIN_TM=60
 
451
PRIMER_MAX_TM=100
 
452
PRIMER_MAX_GC=100
 
453
PRIMER_MISPRIMING_LIBRARY=not_for_production.lib
 
454
PRIMER_MAX_MISPRIMING=8
 
455
PRIMER_WARNING=Left primer is unacceptable: High similarity to mispriming or mishyb library; Hybridization probe is unacceptable: Tm too low
 
456
PRIMER_RIGHT_EXPLAIN=considered 1, ok 1
 
457
PRIMER_PAIR_EXPLAIN=considered 1, ok 1
 
458
PRIMER_PAIR_PENALTY=4.0864
 
459
PRIMER_LEFT_PENALTY=1.771733
 
460
PRIMER_RIGHT_PENALTY=2.314641
 
461
PRIMER_INTERNAL_OLIGO_PENALTY=1.580164
 
462
PRIMER_LEFT_SEQUENCE=CCTACAGCTGTGGGAAAATG
 
463
PRIMER_RIGHT_SEQUENCE=CAGTGTGTACATGGCGGC
 
464
PRIMER_INTERNAL_OLIGO_SEQUENCE=gcgtacgatccatgctagc
 
465
PRIMER_LEFT=1,20
 
466
PRIMER_RIGHT=160,18
 
467
PRIMER_INTERNAL_OLIGO=23,19
 
468
PRIMER_LEFT_TM=58.228
 
469
PRIMER_RIGHT_TM=59.685
 
470
PRIMER_INTERNAL_OLIGO_TM=59.420
 
471
PRIMER_LEFT_GC_PERCENT=50.000
 
472
PRIMER_RIGHT_GC_PERCENT=61.111
 
473
PRIMER_INTERNAL_OLIGO_GC_PERCENT=57.895
 
474
PRIMER_LEFT_SELF_ANY=10.00
 
475
PRIMER_RIGHT_SELF_ANY=6.00
 
476
PRIMER_INTERNAL_OLIGO_SELF_ANY=6.00
 
477
PRIMER_LEFT_SELF_END=0.00
 
478
PRIMER_RIGHT_SELF_END=3.00
 
479
PRIMER_INTERNAL_OLIGO_SELF_END=6.00
 
480
PRIMER_LEFT_MISPRIMING_SCORE=9.00, L1 Human L1 interspersed repetitive sequence - full length copy
 
481
PRIMER_RIGHT_MISPRIMING_SCORE=8.00, L1 Human L1 interspersed repetitive sequence - full length copy
 
482
PRIMER_PAIR_MISPRIMING_SCORE=17.00, L1 Human L1 interspersed repetitive sequence - full length copy
 
483
PRIMER_LEFT_END_STABILITY=7.2000
 
484
PRIMER_RIGHT_END_STABILITY=12.9000
 
485
PRIMER_PAIR_COMPL_ANY=4.00
 
486
PRIMER_PAIR_COMPL_END=1.00
 
487
PRIMER_PRODUCT_SIZE=160
 
488
=