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Viewing changes to test/primer_check_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_check_output
 
1
PRIMER_SEQUENCE_ID=00
 
2
PRIMER_MAX_POLY_X=0
 
3
PRIMER_INTERNAL_OLIGO_MAX_POLY_X=0
 
4
PRIMER_EXPLAIN_FLAG=1
 
5
PRIMER_PRODUCT_SIZE_RANGE=50-100
 
6
PRIMER_MIN_TM=0.0
 
7
PRIMER_MAX_TM=100.0
 
8
PRIMER_MIN_SIZE=25
 
9
PRIMER_MAX_SIZE=25
 
10
PRIMER_INTERNAL_OLIGO_MIN_SIZE=25
 
11
PRIMER_INTERNAL_OLIGO_MAX_SIZE=25
 
12
PRIMER_INTERNAL_OLIGO_OPT_SIZE=25
 
13
PRIMER_OPT_SIZE=25
 
14
PRIMER_MAX_GC=100
 
15
PRIMER_MIN_GC=0
 
16
PRIMER_SELF_END=100
 
17
PRIMER_SELF_ANY=100
 
18
PRIMER_INTERNAL_OLIGO_SELF_ANY=100
 
19
PRIMER_INTERNAL_OLIGO_SELF_END=100 
 
20
PRIMER_INTERNAL_OLIGO_MAX_TM=100
 
21
PRIMER_INTERNAL_OLIGO_MIN_TM=30
 
22
PRIMER_INTERNAL_OLIGO_MAX_GC=100
 
23
PRIMER_INTERNAL_OLIGO_MIN_GC=0
 
24
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNACGTACGTACGTTGCAGTCGACGCANNACTCACTGTCATTTCCAAACAATTCNN
 
25
PRIMER_LEFT_INPUT=CACGTCATCTCATCAAATTTGATTG
 
26
PRIMER_PICK_INTERNAL_OLIGO=1
 
27
PRIMER_LEFT_EXPLAIN=considered 1, ok 1
 
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 2, no internal oligo 1, 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=2,25
 
39
PRIMER_RIGHT=81,25
 
40
PRIMER_INTERNAL_OLIGO=30,25
 
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
PRIMER_SEQUENCE_ID=01
 
60
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNACGTACGTACGTTGCAGTCGACGCANNACTCACTGTCATTTCCAAACAATTCNN
 
61
PRIMER_LEFT_INPUT=CACGTCATCTCATCAAATTTGATTG
 
62
PRIMER_RIGHT_INPUT=GAATTGTTTGGAAATGACAGTGAGT
 
63
PRIMER_PICK_INTERNAL_OLIGO=1
 
64
PRIMER_LEFT_EXPLAIN=considered 1, ok 1
 
65
PRIMER_RIGHT_EXPLAIN=considered 1, ok 1
 
66
PRIMER_INTERNAL_OLIGO_EXPLAIN=considered 60, too many Ns 57, ok 3
 
67
PRIMER_PAIR_EXPLAIN=considered 1, ok 1
 
68
PRIMER_PAIR_PENALTY=3.3813
 
69
PRIMER_LEFT_PENALTY=2.731673
 
70
PRIMER_RIGHT_PENALTY=0.649600
 
71
PRIMER_INTERNAL_OLIGO_PENALTY=11.495378
 
72
PRIMER_LEFT_SEQUENCE=CACGTCATCTCATCAAATTTGATTG
 
73
PRIMER_RIGHT_SEQUENCE=GAATTGTTTGGAAATGACAGTGAGT
 
74
PRIMER_INTERNAL_OLIGO_SEQUENCE=ACGTACGTACGTTGCAGTCGACGCA
 
75
PRIMER_LEFT=2,25
 
76
PRIMER_RIGHT=81,25
 
77
PRIMER_INTERNAL_OLIGO=30,25
 
78
PRIMER_LEFT_TM=62.732
 
79
PRIMER_RIGHT_TM=60.650
 
80
PRIMER_INTERNAL_OLIGO_TM=71.495
 
81
PRIMER_LEFT_GC_PERCENT=36.000
 
82
PRIMER_RIGHT_GC_PERCENT=36.000
 
83
PRIMER_INTERNAL_OLIGO_GC_PERCENT=56.000
 
84
PRIMER_LEFT_SELF_ANY=12.00
 
85
PRIMER_RIGHT_SELF_ANY=4.00
 
86
PRIMER_INTERNAL_OLIGO_SELF_ANY=12.00
 
87
PRIMER_LEFT_SELF_END=10.00
 
88
PRIMER_RIGHT_SELF_END=3.00
 
89
PRIMER_INTERNAL_OLIGO_SELF_END=8.00
 
90
PRIMER_LEFT_END_STABILITY=6.9000
 
91
PRIMER_RIGHT_END_STABILITY=6.4000
 
92
PRIMER_PAIR_COMPL_ANY=7.00
 
93
PRIMER_PAIR_COMPL_END=1.00
 
94
PRIMER_PRODUCT_SIZE=80
 
95
=
 
96
PRIMER_SEQUENCE_ID=02
 
97
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNACGTACGTACGTTGCAGTCGACGCANNACTCACTGTCATTTCCAAACAATTCNN
 
98
PRIMER_LEFT_INPUT=CACGTCATCTCATCAAATTTGATTG
 
99
PRIMER_PICK_INTERNAL_OLIGO=0
 
100
PRIMER_LEFT_EXPLAIN=considered 1, ok 1
 
101
PRIMER_RIGHT_EXPLAIN=considered 35, too many Ns 33, ok 2
 
102
PRIMER_PAIR_EXPLAIN=considered 2, ok 2
 
103
PRIMER_PAIR_PENALTY=3.3813
 
104
PRIMER_LEFT_PENALTY=2.731673
 
105
PRIMER_RIGHT_PENALTY=0.649600
 
106
PRIMER_LEFT_SEQUENCE=CACGTCATCTCATCAAATTTGATTG
 
107
PRIMER_RIGHT_SEQUENCE=GAATTGTTTGGAAATGACAGTGAGT
 
108
PRIMER_LEFT=2,25
 
109
PRIMER_RIGHT=81,25
 
110
PRIMER_LEFT_TM=62.732
 
111
PRIMER_RIGHT_TM=60.650
 
112
PRIMER_LEFT_GC_PERCENT=36.000
 
113
PRIMER_RIGHT_GC_PERCENT=36.000
 
114
PRIMER_LEFT_SELF_ANY=12.00
 
115
PRIMER_RIGHT_SELF_ANY=4.00
 
116
PRIMER_LEFT_SELF_END=10.00
 
117
PRIMER_RIGHT_SELF_END=3.00
 
118
PRIMER_LEFT_END_STABILITY=6.9000
 
119
PRIMER_RIGHT_END_STABILITY=6.4000
 
120
PRIMER_PAIR_COMPL_ANY=7.00
 
121
PRIMER_PAIR_COMPL_END=1.00
 
122
PRIMER_PRODUCT_SIZE=80
 
123
PRIMER_PAIR_PENALTY_1=14.2271
 
124
PRIMER_LEFT_1_PENALTY=2.731673
 
125
PRIMER_RIGHT_1_PENALTY=11.495378
 
126
PRIMER_LEFT_1_SEQUENCE=CACGTCATCTCATCAAATTTGATTG
 
127
PRIMER_RIGHT_1_SEQUENCE=TGCGTCGACTGCAACGTACGTACGT
 
128
PRIMER_LEFT_1=2,25
 
129
PRIMER_RIGHT_1=54,25
 
130
PRIMER_LEFT_1_TM=62.732
 
131
PRIMER_RIGHT_1_TM=71.495
 
132
PRIMER_LEFT_1_GC_PERCENT=36.000
 
133
PRIMER_RIGHT_1_GC_PERCENT=56.000
 
134
PRIMER_LEFT_1_SELF_ANY=12.00
 
135
PRIMER_RIGHT_1_SELF_ANY=12.00
 
136
PRIMER_LEFT_1_SELF_END=10.00
 
137
PRIMER_RIGHT_1_SELF_END=12.00
 
138
PRIMER_LEFT_1_END_STABILITY=6.9000
 
139
PRIMER_RIGHT_1_END_STABILITY=7.1000
 
140
PRIMER_PAIR_1_COMPL_ANY=4.00
 
141
PRIMER_PAIR_1_COMPL_END=0.00
 
142
PRIMER_PRODUCT_SIZE_1=53
 
143
=
 
144
PRIMER_SEQUENCE_ID=03
 
145
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNACGTACGTACGTTGCAGTCGACGCANNACTCACTGTCATTTCCAAACAATTCNN
 
146
PRIMER_RIGHT_INPUT=GAATTGTTTGGAAATGACAGTGAGT
 
147
PRIMER_INTERNAL_OLIGO_INPUT=ACGTACGTACGTTGCAGTCGACGCA
 
148
PRIMER_PICK_INTERNAL_OLIGO=1
 
149
PRIMER_LEFT_EXPLAIN=considered 35, too many Ns 33, ok 2
 
150
PRIMER_RIGHT_EXPLAIN=considered 1, ok 1
 
151
PRIMER_INTERNAL_OLIGO_EXPLAIN=considered 1, ok 1
 
152
PRIMER_PAIR_EXPLAIN=considered 2, no internal oligo 1, ok 1
 
153
PRIMER_PAIR_PENALTY=3.3813
 
154
PRIMER_LEFT_PENALTY=2.731673
 
155
PRIMER_RIGHT_PENALTY=0.649600
 
156
PRIMER_INTERNAL_OLIGO_PENALTY=11.495378
 
157
PRIMER_LEFT_SEQUENCE=CACGTCATCTCATCAAATTTGATTG
 
158
PRIMER_RIGHT_SEQUENCE=GAATTGTTTGGAAATGACAGTGAGT
 
159
PRIMER_INTERNAL_OLIGO_SEQUENCE=ACGTACGTACGTTGCAGTCGACGCA
 
160
PRIMER_LEFT=2,25
 
161
PRIMER_RIGHT=81,25
 
162
PRIMER_INTERNAL_OLIGO=30,25
 
163
PRIMER_LEFT_TM=62.732
 
164
PRIMER_RIGHT_TM=60.650
 
165
PRIMER_INTERNAL_OLIGO_TM=71.495
 
166
PRIMER_LEFT_GC_PERCENT=36.000
 
167
PRIMER_RIGHT_GC_PERCENT=36.000
 
168
PRIMER_INTERNAL_OLIGO_GC_PERCENT=56.000
 
169
PRIMER_LEFT_SELF_ANY=12.00
 
170
PRIMER_RIGHT_SELF_ANY=4.00
 
171
PRIMER_INTERNAL_OLIGO_SELF_ANY=12.00
 
172
PRIMER_LEFT_SELF_END=10.00
 
173
PRIMER_RIGHT_SELF_END=3.00
 
174
PRIMER_INTERNAL_OLIGO_SELF_END=8.00
 
175
PRIMER_LEFT_END_STABILITY=6.9000
 
176
PRIMER_RIGHT_END_STABILITY=6.4000
 
177
PRIMER_PAIR_COMPL_ANY=7.00
 
178
PRIMER_PAIR_COMPL_END=1.00
 
179
PRIMER_PRODUCT_SIZE=80
 
180
=
 
181
PRIMER_SEQUENCE_ID=04
 
182
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNACGTACGTACGTTGCAGTCGACGCANNACTCACTGTCATTTCCAAACAATTCNN
 
183
PRIMER_INTERNAL_OLIGO_INPUT=ACGTACGTACGTTGCAGTCGACGCA
 
184
PRIMER_PICK_INTERNAL_OLIGO=1
 
185
PRIMER_LEFT_EXPLAIN=considered 35, too many Ns 33, ok 2
 
186
PRIMER_RIGHT_EXPLAIN=considered 35, too many Ns 33, ok 2
 
187
PRIMER_INTERNAL_OLIGO_EXPLAIN=considered 1, ok 1
 
188
PRIMER_PAIR_EXPLAIN=considered 4, unacceptable product size 1, no internal oligo 2, ok 1
 
189
PRIMER_PAIR_PENALTY=3.3813
 
190
PRIMER_LEFT_PENALTY=2.731673
 
191
PRIMER_RIGHT_PENALTY=0.649600
 
192
PRIMER_INTERNAL_OLIGO_PENALTY=11.495378
 
193
PRIMER_LEFT_SEQUENCE=CACGTCATCTCATCAAATTTGATTG
 
194
PRIMER_RIGHT_SEQUENCE=GAATTGTTTGGAAATGACAGTGAGT
 
195
PRIMER_INTERNAL_OLIGO_SEQUENCE=ACGTACGTACGTTGCAGTCGACGCA
 
196
PRIMER_LEFT=2,25
 
197
PRIMER_RIGHT=81,25
 
198
PRIMER_INTERNAL_OLIGO=30,25
 
199
PRIMER_LEFT_TM=62.732
 
200
PRIMER_RIGHT_TM=60.650
 
201
PRIMER_INTERNAL_OLIGO_TM=71.495
 
202
PRIMER_LEFT_GC_PERCENT=36.000
 
203
PRIMER_RIGHT_GC_PERCENT=36.000
 
204
PRIMER_INTERNAL_OLIGO_GC_PERCENT=56.000
 
205
PRIMER_LEFT_SELF_ANY=12.00
 
206
PRIMER_RIGHT_SELF_ANY=4.00
 
207
PRIMER_INTERNAL_OLIGO_SELF_ANY=12.00
 
208
PRIMER_LEFT_SELF_END=10.00
 
209
PRIMER_RIGHT_SELF_END=3.00
 
210
PRIMER_INTERNAL_OLIGO_SELF_END=8.00
 
211
PRIMER_LEFT_END_STABILITY=6.9000
 
212
PRIMER_RIGHT_END_STABILITY=6.4000
 
213
PRIMER_PAIR_COMPL_ANY=7.00
 
214
PRIMER_PAIR_COMPL_END=1.00
 
215
PRIMER_PRODUCT_SIZE=80
 
216
=
 
217
PRIMER_SEQUENCE_ID=05
 
218
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNACGTACGTACGTTGCAGTCGACGCANNACTCACTGTCATTTCCAAACAATTCNN
 
219
PRIMER_LEFT_INPUT=CACGTCATCTCATCAAATTTGATTG
 
220
PRIMER_INTERNAL_OLIGO_INPUT=ACGTACGTACGTTGCAGTCGACGCA
 
221
PRIMER_PICK_INTERNAL_OLIGO=1
 
222
PRIMER_LEFT_EXPLAIN=considered 1, ok 1
 
223
PRIMER_RIGHT_EXPLAIN=considered 35, too many Ns 33, ok 2
 
224
PRIMER_INTERNAL_OLIGO_EXPLAIN=considered 1, ok 1
 
225
PRIMER_PAIR_EXPLAIN=considered 2, no internal oligo 1, ok 1
 
226
PRIMER_PAIR_PENALTY=3.3813
 
227
PRIMER_LEFT_PENALTY=2.731673
 
228
PRIMER_RIGHT_PENALTY=0.649600
 
229
PRIMER_INTERNAL_OLIGO_PENALTY=11.495378
 
230
PRIMER_LEFT_SEQUENCE=CACGTCATCTCATCAAATTTGATTG
 
231
PRIMER_RIGHT_SEQUENCE=GAATTGTTTGGAAATGACAGTGAGT
 
232
PRIMER_INTERNAL_OLIGO_SEQUENCE=ACGTACGTACGTTGCAGTCGACGCA
 
233
PRIMER_LEFT=2,25
 
234
PRIMER_RIGHT=81,25
 
235
PRIMER_INTERNAL_OLIGO=30,25
 
236
PRIMER_LEFT_TM=62.732
 
237
PRIMER_RIGHT_TM=60.650
 
238
PRIMER_INTERNAL_OLIGO_TM=71.495
 
239
PRIMER_LEFT_GC_PERCENT=36.000
 
240
PRIMER_RIGHT_GC_PERCENT=36.000
 
241
PRIMER_INTERNAL_OLIGO_GC_PERCENT=56.000
 
242
PRIMER_LEFT_SELF_ANY=12.00
 
243
PRIMER_RIGHT_SELF_ANY=4.00
 
244
PRIMER_INTERNAL_OLIGO_SELF_ANY=12.00
 
245
PRIMER_LEFT_SELF_END=10.00
 
246
PRIMER_RIGHT_SELF_END=3.00
 
247
PRIMER_INTERNAL_OLIGO_SELF_END=8.00
 
248
PRIMER_LEFT_END_STABILITY=6.9000
 
249
PRIMER_RIGHT_END_STABILITY=6.4000
 
250
PRIMER_PAIR_COMPL_ANY=7.00
 
251
PRIMER_PAIR_COMPL_END=1.00
 
252
PRIMER_PRODUCT_SIZE=80
 
253
=
 
254
PRIMER_SEQUENCE_ID=06
 
255
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNACGTACGTACGTTGCAGTCGACGCANNACTCACTGTCATTTCCAAACAATTCNN
 
256
PRIMER_LEFT_INPUT=CACGTCATCTCATCAAATTTGATTG
 
257
PRIMER_RIGHT_INPUT=GAATTGTTTGGAAATGACAGTGAGT
 
258
PRIMER_INTERNAL_OLIGO_INPUT=ACGTACGTACGTTGCAGTCGACGCA
 
259
PRIMER_PICK_INTERNAL_OLIGO=1
 
260
PRIMER_LEFT_EXPLAIN=considered 1, ok 1
 
261
PRIMER_RIGHT_EXPLAIN=considered 1, ok 1
 
262
PRIMER_INTERNAL_OLIGO_EXPLAIN=considered 1, ok 1
 
263
PRIMER_PAIR_EXPLAIN=considered 1, ok 1
 
264
PRIMER_PAIR_PENALTY=3.3813
 
265
PRIMER_LEFT_PENALTY=2.731673
 
266
PRIMER_RIGHT_PENALTY=0.649600
 
267
PRIMER_INTERNAL_OLIGO_PENALTY=11.495378
 
268
PRIMER_LEFT_SEQUENCE=CACGTCATCTCATCAAATTTGATTG
 
269
PRIMER_RIGHT_SEQUENCE=GAATTGTTTGGAAATGACAGTGAGT
 
270
PRIMER_INTERNAL_OLIGO_SEQUENCE=ACGTACGTACGTTGCAGTCGACGCA
 
271
PRIMER_LEFT=2,25
 
272
PRIMER_RIGHT=81,25
 
273
PRIMER_INTERNAL_OLIGO=30,25
 
274
PRIMER_LEFT_TM=62.732
 
275
PRIMER_RIGHT_TM=60.650
 
276
PRIMER_INTERNAL_OLIGO_TM=71.495
 
277
PRIMER_LEFT_GC_PERCENT=36.000
 
278
PRIMER_RIGHT_GC_PERCENT=36.000
 
279
PRIMER_INTERNAL_OLIGO_GC_PERCENT=56.000
 
280
PRIMER_LEFT_SELF_ANY=12.00
 
281
PRIMER_RIGHT_SELF_ANY=4.00
 
282
PRIMER_INTERNAL_OLIGO_SELF_ANY=12.00
 
283
PRIMER_LEFT_SELF_END=10.00
 
284
PRIMER_RIGHT_SELF_END=3.00
 
285
PRIMER_INTERNAL_OLIGO_SELF_END=8.00
 
286
PRIMER_LEFT_END_STABILITY=6.9000
 
287
PRIMER_RIGHT_END_STABILITY=6.4000
 
288
PRIMER_PAIR_COMPL_ANY=7.00
 
289
PRIMER_PAIR_COMPL_END=1.00
 
290
PRIMER_PRODUCT_SIZE=80
 
291
=
 
292
PRIMER_SEQUENCE_ID=07
 
293
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNACGTACGTACGTTGCAGTCGACGCANNACTCACTGTCATTTCCAAACAATTCNN
 
294
PRIMER_RIGHT_INPUT=TGCGTCGACTGCAACGTACGTACGT
 
295
PRIMER_PICK_INTERNAL_OLIGO=0
 
296
PRIMER_LEFT_EXPLAIN=considered 35, too many Ns 33, ok 2
 
297
PRIMER_RIGHT_EXPLAIN=considered 1, ok 1
 
298
PRIMER_PAIR_EXPLAIN=considered 2, unacceptable product size 1, ok 1
 
299
PRIMER_PAIR_PENALTY=14.2271
 
300
PRIMER_LEFT_PENALTY=2.731673
 
301
PRIMER_RIGHT_PENALTY=11.495378
 
302
PRIMER_LEFT_SEQUENCE=CACGTCATCTCATCAAATTTGATTG
 
303
PRIMER_RIGHT_SEQUENCE=TGCGTCGACTGCAACGTACGTACGT
 
304
PRIMER_LEFT=2,25
 
305
PRIMER_RIGHT=54,25
 
306
PRIMER_LEFT_TM=62.732
 
307
PRIMER_RIGHT_TM=71.495
 
308
PRIMER_LEFT_GC_PERCENT=36.000
 
309
PRIMER_RIGHT_GC_PERCENT=56.000
 
310
PRIMER_LEFT_SELF_ANY=12.00
 
311
PRIMER_RIGHT_SELF_ANY=12.00
 
312
PRIMER_LEFT_SELF_END=10.00
 
313
PRIMER_RIGHT_SELF_END=12.00
 
314
PRIMER_LEFT_END_STABILITY=6.9000
 
315
PRIMER_RIGHT_END_STABILITY=7.1000
 
316
PRIMER_PAIR_COMPL_ANY=4.00
 
317
PRIMER_PAIR_COMPL_END=0.00
 
318
PRIMER_PRODUCT_SIZE=53
 
319
=
 
320
PRIMER_SEQUENCE_ID=08
 
321
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNACGTACGTACGTTGCAGTCGACGCANNACTCACTGTCATTTCCAAACAATTCNN
 
322
PRIMER_LEFT_INPUT=CACGTCATCTCATCAAATTTGATTG
 
323
PRIMER_RIGHT_INPUT=TGCGTCGACTGCAACGTACGTACGT
 
324
PRIMER_PICK_INTERNAL_OLIGO=0
 
325
PRIMER_LEFT_EXPLAIN=considered 1, ok 1
 
326
PRIMER_RIGHT_EXPLAIN=considered 1, ok 1
 
327
PRIMER_PAIR_EXPLAIN=considered 1, ok 1
 
328
PRIMER_PAIR_PENALTY=14.2271
 
329
PRIMER_LEFT_PENALTY=2.731673
 
330
PRIMER_RIGHT_PENALTY=11.495378
 
331
PRIMER_LEFT_SEQUENCE=CACGTCATCTCATCAAATTTGATTG
 
332
PRIMER_RIGHT_SEQUENCE=TGCGTCGACTGCAACGTACGTACGT
 
333
PRIMER_LEFT=2,25
 
334
PRIMER_RIGHT=54,25
 
335
PRIMER_LEFT_TM=62.732
 
336
PRIMER_RIGHT_TM=71.495
 
337
PRIMER_LEFT_GC_PERCENT=36.000
 
338
PRIMER_RIGHT_GC_PERCENT=56.000
 
339
PRIMER_LEFT_SELF_ANY=12.00
 
340
PRIMER_RIGHT_SELF_ANY=12.00
 
341
PRIMER_LEFT_SELF_END=10.00
 
342
PRIMER_RIGHT_SELF_END=12.00
 
343
PRIMER_LEFT_END_STABILITY=6.9000
 
344
PRIMER_RIGHT_END_STABILITY=7.1000
 
345
PRIMER_PAIR_COMPL_ANY=4.00
 
346
PRIMER_PAIR_COMPL_END=0.00
 
347
PRIMER_PRODUCT_SIZE=53
 
348
=
 
349
PRIMER_SEQUENCE_ID=09
 
350
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNACGTACGTACGTTGCAGTCGACGCANNACTCACTGTCATTTCCAAACAATTCNN
 
351
PRIMER_RIGHT_INPUT=TGCGTCGACTGCAACGTACGTACGT
 
352
PRIMER_INTERNAL_OLIGO_INPUT=ACGTACGTACGTTGCAGTCGACGCA
 
353
PRIMER_PICK_INTERNAL_OLIGO=1
 
354
PRIMER_LEFT_EXPLAIN=considered 35, too many Ns 33, ok 2
 
355
PRIMER_RIGHT_EXPLAIN=considered 1, ok 1
 
356
PRIMER_INTERNAL_OLIGO_EXPLAIN=considered 1, ok 1
 
357
PRIMER_PAIR_EXPLAIN=considered 2, unacceptable product size 1, no internal oligo 1, ok 0
 
358
=
 
359
PRIMER_SEQUENCE_ID=10
 
360
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNACGTACGTACGTTGCAGTCGACGCANNACTCACTGTCATTTCCAAACAATTCNN
 
361
PRIMER_LEFT_INPUT=CACGTCATCTCATCAAATTTGATTG
 
362
PRIMER_RIGHT_INPUT=TGCGTCGACTGCAACGTACGTACGT
 
363
PRIMER_INTERNAL_OLIGO_INPUT=ACGTACGTACGTTGCAGTCGACGCA
 
364
PRIMER_PICK_INTERNAL_OLIGO=1
 
365
PRIMER_LEFT_EXPLAIN=considered 1, ok 1
 
366
PRIMER_RIGHT_EXPLAIN=considered 1, ok 1
 
367
PRIMER_INTERNAL_OLIGO_EXPLAIN=considered 1, ok 1
 
368
PRIMER_PAIR_EXPLAIN=considered 1, no internal oligo 1, ok 0
 
369
=
 
370
PRIMER_SEQUENCE_ID=11
 
371
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNACGTACGTACGTTGCAGTCGACGCANNACTCACTGTCATTTCCAAACAATTCNN
 
372
PRIMER_LEFT_INPUT=CACGTCATCTCATCAATTTGATTG
 
373
PRIMER_RIGHT_INPUT=GAATTGTTTGGAAATGACAGTGAGT
 
374
PRIMER_PICK_INTERNAL_OLIGO=1
 
375
PRIMER_ERROR=Specified left primer too short; Specified left primer not in sequence
 
376
=
 
377
PRIMER_SEQUENCE_ID=12
 
378
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNACGTACGTACGTTGCAGTCGACGCANNACTCACTGTCATTTCCAAACAATTCNN
 
379
PRIMER_LEFT_INPUT=CACGTCATCTCATCAAATTTGATTG
 
380
PRIMER_RIGHT_INPUT=TGCGTCGACTGCAACGTACGTACGT
 
381
PRIMER_INTERNAL_OLIGO_INPUT=ACGTACGTACGTTGCAGTCGACGCA
 
382
PRIMER_PICK_INTERNAL_OLIGO=0
 
383
PRIMER_ERROR=Not specified to pick internal oligos but a specific internal oligo is provided
 
384
=
 
385
PRIMER_SEQUENCE_ID=13
 
386
SEQUENCE=nncacgtcaTCTCATCAAATTTGATTGNNNACGTACGTACGTTGCAGTCGACGCANNACTCACTGTCATTTCCAAACAATTCNN
 
387
PRIMER_LEFT_INPUT=cacgtcatctcatcaaatttgattg
 
388
PRIMER_RIGHT_INPUT=gaattgtttggaaatgacagtgagt
 
389
PRIMER_PICK_INTERNAL_OLIGO=1
 
390
PRIMER_LEFT_EXPLAIN=considered 1, ok 1
 
391
PRIMER_RIGHT_EXPLAIN=considered 1, ok 1
 
392
PRIMER_INTERNAL_OLIGO_EXPLAIN=considered 60, too many Ns 57, ok 3
 
393
PRIMER_PAIR_EXPLAIN=considered 1, ok 1
 
394
PRIMER_PAIR_PENALTY=3.3813
 
395
PRIMER_LEFT_PENALTY=2.731673
 
396
PRIMER_RIGHT_PENALTY=0.649600
 
397
PRIMER_INTERNAL_OLIGO_PENALTY=11.495378
 
398
PRIMER_LEFT_SEQUENCE=cacgtcaTCTCATCAAATTTGATTG
 
399
PRIMER_RIGHT_SEQUENCE=GAATTGTTTGGAAATGACAGTGAGT
 
400
PRIMER_INTERNAL_OLIGO_SEQUENCE=ACGTACGTACGTTGCAGTCGACGCA
 
401
PRIMER_LEFT=2,25
 
402
PRIMER_RIGHT=81,25
 
403
PRIMER_INTERNAL_OLIGO=30,25
 
404
PRIMER_LEFT_TM=62.732
 
405
PRIMER_RIGHT_TM=60.650
 
406
PRIMER_INTERNAL_OLIGO_TM=71.495
 
407
PRIMER_LEFT_GC_PERCENT=36.000
 
408
PRIMER_RIGHT_GC_PERCENT=36.000
 
409
PRIMER_INTERNAL_OLIGO_GC_PERCENT=56.000
 
410
PRIMER_LEFT_SELF_ANY=12.00
 
411
PRIMER_RIGHT_SELF_ANY=4.00
 
412
PRIMER_INTERNAL_OLIGO_SELF_ANY=12.00
 
413
PRIMER_LEFT_SELF_END=10.00
 
414
PRIMER_RIGHT_SELF_END=3.00
 
415
PRIMER_INTERNAL_OLIGO_SELF_END=8.00
 
416
PRIMER_LEFT_END_STABILITY=6.9000
 
417
PRIMER_RIGHT_END_STABILITY=6.4000
 
418
PRIMER_PAIR_COMPL_ANY=7.00
 
419
PRIMER_PAIR_COMPL_END=1.00
 
420
PRIMER_PRODUCT_SIZE=80
 
421
=
 
422
PRIMER_SEQUENCE_ID=14
 
423
SEQUENCE=NNCACGTCATCTCATCAAATTTGATTGNNNACGTACGTACGTTGCAGTCGACGCANNACTCACTGTCATTTCCAAACAATTCNN
 
424
PRIMER_LEFT_INPUT=CACGTCATctcatcaaattTGATTG
 
425
PRIMER_RIGHT_INPUT=gaattgtttggaAATGACAGTGAGT
 
426
PRIMER_PICK_INTERNAL_OLIGO=1
 
427
PRIMER_LEFT_EXPLAIN=considered 1, ok 1
 
428
PRIMER_RIGHT_EXPLAIN=considered 1, ok 1
 
429
PRIMER_INTERNAL_OLIGO_EXPLAIN=considered 60, too many Ns 57, ok 3
 
430
PRIMER_PAIR_EXPLAIN=considered 1, ok 1
 
431
PRIMER_PAIR_PENALTY=3.3813
 
432
PRIMER_LEFT_PENALTY=2.731673
 
433
PRIMER_RIGHT_PENALTY=0.649600
 
434
PRIMER_INTERNAL_OLIGO_PENALTY=11.495378
 
435
PRIMER_LEFT_SEQUENCE=CACGTCATCTCATCAAATTTGATTG
 
436
PRIMER_RIGHT_SEQUENCE=GAATTGTTTGGAAATGACAGTGAGT
 
437
PRIMER_INTERNAL_OLIGO_SEQUENCE=ACGTACGTACGTTGCAGTCGACGCA
 
438
PRIMER_LEFT=2,25
 
439
PRIMER_RIGHT=81,25
 
440
PRIMER_INTERNAL_OLIGO=30,25
 
441
PRIMER_LEFT_TM=62.732
 
442
PRIMER_RIGHT_TM=60.650
 
443
PRIMER_INTERNAL_OLIGO_TM=71.495
 
444
PRIMER_LEFT_GC_PERCENT=36.000
 
445
PRIMER_RIGHT_GC_PERCENT=36.000
 
446
PRIMER_INTERNAL_OLIGO_GC_PERCENT=56.000
 
447
PRIMER_LEFT_SELF_ANY=12.00
 
448
PRIMER_RIGHT_SELF_ANY=4.00
 
449
PRIMER_INTERNAL_OLIGO_SELF_ANY=12.00
 
450
PRIMER_LEFT_SELF_END=10.00
 
451
PRIMER_RIGHT_SELF_END=3.00
 
452
PRIMER_INTERNAL_OLIGO_SELF_END=8.00
 
453
PRIMER_LEFT_END_STABILITY=6.9000
 
454
PRIMER_RIGHT_END_STABILITY=6.4000
 
455
PRIMER_PAIR_COMPL_ANY=7.00
 
456
PRIMER_PAIR_COMPL_END=1.00
 
457
PRIMER_PRODUCT_SIZE=80
 
458
=