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Viewing changes to test/primer_lib_amb_codes_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_lib_amb_codes_output
 
1
PRIMER_EXPLAIN_FLAG=1
 
2
PRIMER_NUM_RETURN=1
 
3
PRIMER_OPT_SIZE=20
 
4
PRIMER_PICK_INTERNAL_OLIGO=1
 
5
PRIMER_INTERNAL_OLIGO_SELF_END=8
 
6
PRIMER_INTERNAL_OLIGO_MAX_TM=100
 
7
PRIMER_INTERNAL_OLIGO_MIN_TM=0
 
8
PRIMER_MIN_SIZE=18
 
9
PRIMER_MAX_SIZE=25
 
10
PRIMER_OPT_TM=60.0
 
11
PRIMER_MIN_TM=0.0
 
12
PRIMER_MAX_TM=100.0
 
13
PRIMER_MIN_GC=0.0
 
14
PRIMER_MAX_GC=100.0
 
15
PRIMER_MAX_POLY_X=100
 
16
PRIMER_INTERNAL_OLIGO_MAX_POLY_X=100
 
17
PRIMER_SALT_CONC=50.0
 
18
PRIMER_DNA_CONC=50.0
 
19
PRIMER_NUM_NS_ACCEPTED=0
 
20
PRIMER_SELF_ANY=12
 
21
PRIMER_SELF_END=8
 
22
PRIMER_PRODUCT_SIZE_RANGE=75-500
 
23
PRIMER_MISPRIMING_LIBRARY=not_for_production.lib
 
24
MARKER_NAME=test_01
 
25
SEQUENCE=GCTTGCATGCCTGCAGGTCGACTCTAGAGGATCCCCCTACATTTTAGCATCAGTGAGTACAGCATGCTTACTGGAAGAGAGGGTCATGCAACAGATTAGGAGGTAAGTTTGCAAAGGCAGGCTAAGGAGGAGACGCACTGAATGCCATGGTAAGAACTCTGGACATAAAAATATTGGAAGTTGTTGAGCAAGTAAAAAAATGTTTGGAAGTGTTACTTTAGCAATGGCAAGAATGATAGTATGGAATAGATTGGCAGAATGAAGGCAAAATGATTAGACATATTGCATTAAGGTAAAAAATGATAACTGAAGAATTATGTGCCACACTTATTAATAAGAAAGAATATGTGAACCTTGCAGATGTTTCCCTCTAGTAG
 
26
PRIMER_COMMENT=Should succeed
 
27
PRIMER_LEFT_EXPLAIN=considered 2424, ok 2424
 
28
PRIMER_RIGHT_EXPLAIN=considered 2424, ok 2424
 
29
PRIMER_INTERNAL_OLIGO_EXPLAIN=considered 3555, GC content failed 92, ok 3463
 
30
PRIMER_PAIR_EXPLAIN=considered 94, unacceptable product size 90, ok 4
 
31
PRIMER_PAIR_PENALTY=0.3646
 
32
PRIMER_LEFT_PENALTY=0.346766
 
33
PRIMER_RIGHT_PENALTY=0.017846
 
34
PRIMER_INTERNAL_OLIGO_PENALTY=0.339231
 
35
PRIMER_LEFT_SEQUENCE=CGACTCTAGAGGATCCCCCT
 
36
PRIMER_RIGHT_SEQUENCE=TAGCCTGCCTTTGCAAACTT
 
37
PRIMER_INTERNAL_OLIGO_SEQUENCE=GGAAGAGAGGGTCATGCAAC
 
38
PRIMER_LEFT=18,20
 
39
PRIMER_RIGHT=123,20
 
40
PRIMER_INTERNAL_OLIGO=72,20
 
41
PRIMER_LEFT_TM=59.653
 
42
PRIMER_RIGHT_TM=60.018
 
43
PRIMER_INTERNAL_OLIGO_TM=59.661
 
44
PRIMER_LEFT_GC_PERCENT=60.000
 
45
PRIMER_RIGHT_GC_PERCENT=45.000
 
46
PRIMER_INTERNAL_OLIGO_GC_PERCENT=55.000
 
47
PRIMER_LEFT_SELF_ANY=8.00
 
48
PRIMER_RIGHT_SELF_ANY=8.00
 
49
PRIMER_INTERNAL_OLIGO_SELF_ANY=4.00
 
50
PRIMER_LEFT_SELF_END=4.00
 
51
PRIMER_RIGHT_SELF_END=3.00
 
52
PRIMER_INTERNAL_OLIGO_SELF_END=2.00
 
53
PRIMER_LEFT_MISPRIMING_SCORE=9.00, L1 Human L1 interspersed repetitive sequence - full length copy
 
54
PRIMER_RIGHT_MISPRIMING_SCORE=10.00, reverse L1 Human L1 interspersed repetitive sequence - full length copy
 
55
PRIMER_PAIR_MISPRIMING_SCORE=18.00, L1 Human L1 interspersed repetitive sequence - full length copy
 
56
PRIMER_LEFT_END_STABILITY=10.9000
 
57
PRIMER_RIGHT_END_STABILITY=6.7000
 
58
PRIMER_PAIR_COMPL_ANY=3.00
 
59
PRIMER_PAIR_COMPL_END=0.00
 
60
PRIMER_PRODUCT_SIZE=106
 
61
=
 
62
PRIMER_MISPRIMING_LIBRARY=not_for_production.lib
 
63
PRIMER_LIB_AMBIGUITY_CODES_CONSENSUS=0
 
64
MARKER_NAME=test_02
 
65
SEQUENCE=GCTTGCATGCCTGCAGGTCGACTCTAGAGGATCCCCCTACATTTTAGCATCAGTGAGTACAGCATGCTTACTGGAAGAGAGGGTCATGCAACAGATTAGGAGGTAAGTTTGCAAAGGCAGGCTAAGGAGGAGACGCACTGAATGCCATGGTAAGAACTCTGGACATAAAAATATTGGAAGTTGTTGAGCAAGTAAAAAAATGTTTGGAAGTGTTACTTTAGCAATGGCAAGAATGATAGTATGGAATAGATTGGCAGAATGAAGGCAAAATGATTAGACATATTGCATTAAGGTAAAAAATGATAACTGAAGAATTATGTGCCACACTTATTAATAAGAAAGAATATGTGAACCTTGCAGATGTTTCCCTCTAGTAG
 
66
PRIMER_COMMENT=Should still succeed
 
67
PRIMER_LEFT_EXPLAIN=considered 2424, ok 2424
 
68
PRIMER_RIGHT_EXPLAIN=considered 2424, ok 2424
 
69
PRIMER_INTERNAL_OLIGO_EXPLAIN=considered 3555, GC content failed 92, ok 3463
 
70
PRIMER_PAIR_EXPLAIN=considered 94, unacceptable product size 90, ok 4
 
71
PRIMER_PAIR_PENALTY=0.3646
 
72
PRIMER_LEFT_PENALTY=0.346766
 
73
PRIMER_RIGHT_PENALTY=0.017846
 
74
PRIMER_INTERNAL_OLIGO_PENALTY=0.339231
 
75
PRIMER_LEFT_SEQUENCE=CGACTCTAGAGGATCCCCCT
 
76
PRIMER_RIGHT_SEQUENCE=TAGCCTGCCTTTGCAAACTT
 
77
PRIMER_INTERNAL_OLIGO_SEQUENCE=GGAAGAGAGGGTCATGCAAC
 
78
PRIMER_LEFT=18,20
 
79
PRIMER_RIGHT=123,20
 
80
PRIMER_INTERNAL_OLIGO=72,20
 
81
PRIMER_LEFT_TM=59.653
 
82
PRIMER_RIGHT_TM=60.018
 
83
PRIMER_INTERNAL_OLIGO_TM=59.661
 
84
PRIMER_LEFT_GC_PERCENT=60.000
 
85
PRIMER_RIGHT_GC_PERCENT=45.000
 
86
PRIMER_INTERNAL_OLIGO_GC_PERCENT=55.000
 
87
PRIMER_LEFT_SELF_ANY=8.00
 
88
PRIMER_RIGHT_SELF_ANY=8.00
 
89
PRIMER_INTERNAL_OLIGO_SELF_ANY=4.00
 
90
PRIMER_LEFT_SELF_END=4.00
 
91
PRIMER_RIGHT_SELF_END=3.00
 
92
PRIMER_INTERNAL_OLIGO_SELF_END=2.00
 
93
PRIMER_LEFT_MISPRIMING_SCORE=9.00, L1 Human L1 interspersed repetitive sequence - full length copy
 
94
PRIMER_RIGHT_MISPRIMING_SCORE=10.00, reverse L1 Human L1 interspersed repetitive sequence - full length copy
 
95
PRIMER_PAIR_MISPRIMING_SCORE=18.00, L1 Human L1 interspersed repetitive sequence - full length copy
 
96
PRIMER_LEFT_END_STABILITY=10.9000
 
97
PRIMER_RIGHT_END_STABILITY=6.7000
 
98
PRIMER_PAIR_COMPL_ANY=3.00
 
99
PRIMER_PAIR_COMPL_END=0.00
 
100
PRIMER_PRODUCT_SIZE=106
 
101
=
 
102
MARKER_NAME=test_03
 
103
PRIMER_LIB_AMBIGUITY_CODES_CONSENSUS=1
 
104
PRIMER_MISPRIMING_LIBRARY=not_for_production_Ns.lib
 
105
SEQUENCE=GCTTGCATGCCTGCAGGTCGACTCTAGAGGATCCCCCTACATTTTAGCATCAGTGAGTACAGCATGCTTACTGGAAGAGAGGGTCATGCAACAGATTAGGAGGTAAGTTTGCAAAGGCAGGCTAAGGAGGAGACGCACTGAATGCCATGGTAAGAACTCTGGACATAAAAATATTGGAAGTTGTTGAGCAAGTAAAAAAATGTTTGGAAGTGTTACTTTAGCAATGGCAAGAATGATAGTATGGAATAGATTGGCAGAATGAAGGCAAAATGATTAGACATATTGCATTAAGGTAAAAAATGATAACTGAAGAATTATGTGCCACACTTATTAATAAGAAAGAATATGTGAACCTTGCAGATGTTTCCCTCTAGTAG
 
106
PRIMER_LEFT_INPUT=CGACTCTAGAGGATCCCCCT
 
107
PRIMER_RIGHT_INPUT=TAGCCTGCCTTTGCAAACTT
 
108
PRIMER_INTERNAL_OLIGO_INPUT=GGAAGAGAGGGTCATGCAAC
 
109
PRIMER_PICK_ANYWAY=1
 
110
PRIMER_COMMENT=Both primers should have high repeat similarity
 
111
PRIMER_WARNING=Left primer is unacceptable: High similarity to mispriming or mishyb library; Right primer is unacceptable: High similarity to mispriming or mishyb library
 
112
PRIMER_PAIR_EXPLAIN=considered 1, high mispriming library similarity 1, ok 0
 
113
=
 
114
MARKER_NAME=test_04
 
115
PRIMER_LIB_AMBIGUITY_CODES_CONSENSUS=0
 
116
PRIMER_MISPRIMING_LIBRARY=not_for_production_Ns.lib
 
117
SEQUENCE=GCTTGCATGCCTGCAGGTCGACTCTAGAGGATCCCCCTACATTTTAGCATCAGTGAGTACAGCATGCTTACTGGAAGAGAGGGTCATGCAACAGATTAGGAGGTAAGTTTGCAAAGGCAGGCTAAGGAGGAGACGCACTGAATGCCATGGTAAGAACTCTGGACATAAAAATATTGGAAGTTGTTGAGCAAGTAAAAAAATGTTTGGAAGTGTTACTTTAGCAATGGCAAGAATGATAGTATGGAATAGATTGGCAGAATGAAGGCAAAATGATTAGACATATTGCATTAAGGTAAAAAATGATAACTGAAGAATTATGTGCCACACTTATTAATAAGAAAGAATATGTGAACCTTGCAGATGTTTCCCTCTAGTAG
 
118
PRIMER_LEFT_INPUT=CGACTCTAGAGGATCCCCCT
 
119
PRIMER_RIGHT_INPUT=TAGCCTGCCTTTGCAAACTT
 
120
PRIMER_INTERNAL_OLIGO_INPUT=GGAAGAGAGGGTCATGCAAC
 
121
PRIMER_PICK_ANYWAY=1
 
122
PRIMER_COMMENT=Should succeed and both primers should have low repeat similarity
 
123
PRIMER_PAIR_EXPLAIN=considered 1, ok 1
 
124
PRIMER_PAIR_PENALTY=0.3646
 
125
PRIMER_LEFT_PENALTY=0.346766
 
126
PRIMER_RIGHT_PENALTY=0.017846
 
127
PRIMER_INTERNAL_OLIGO_PENALTY=0.339231
 
128
PRIMER_LEFT_SEQUENCE=CGACTCTAGAGGATCCCCCT
 
129
PRIMER_RIGHT_SEQUENCE=TAGCCTGCCTTTGCAAACTT
 
130
PRIMER_INTERNAL_OLIGO_SEQUENCE=GGAAGAGAGGGTCATGCAAC
 
131
PRIMER_LEFT=18,20
 
132
PRIMER_RIGHT=123,20
 
133
PRIMER_INTERNAL_OLIGO=72,20
 
134
PRIMER_LEFT_TM=59.653
 
135
PRIMER_RIGHT_TM=60.018
 
136
PRIMER_INTERNAL_OLIGO_TM=59.661
 
137
PRIMER_LEFT_GC_PERCENT=60.000
 
138
PRIMER_RIGHT_GC_PERCENT=45.000
 
139
PRIMER_INTERNAL_OLIGO_GC_PERCENT=55.000
 
140
PRIMER_LEFT_SELF_ANY=8.00
 
141
PRIMER_RIGHT_SELF_ANY=8.00
 
142
PRIMER_INTERNAL_OLIGO_SELF_ANY=4.00
 
143
PRIMER_LEFT_SELF_END=4.00
 
144
PRIMER_RIGHT_SELF_END=3.00
 
145
PRIMER_INTERNAL_OLIGO_SELF_END=2.00
 
146
PRIMER_LEFT_MISPRIMING_SCORE=9.00, L1 Human L1 interspersed repetitive sequence - full length copy
 
147
PRIMER_RIGHT_MISPRIMING_SCORE=10.00, reverse L1 Human L1 interspersed repetitive sequence - full length copy
 
148
PRIMER_PAIR_MISPRIMING_SCORE=18.00, L1 Human L1 interspersed repetitive sequence - full length copy
 
149
PRIMER_LEFT_END_STABILITY=10.9000
 
150
PRIMER_RIGHT_END_STABILITY=6.7000
 
151
PRIMER_PAIR_COMPL_ANY=3.00
 
152
PRIMER_PAIR_COMPL_END=0.00
 
153
PRIMER_PRODUCT_SIZE=106
 
154
=
 
155
MARKER_NAME=test_05
 
156
PRIMER_LIB_AMBIGUITY_CODES_CONSENSUS=1
 
157
PRIMER_MISPRIMING_LIBRARY=not_for_production_Ns.lib
 
158
SEQUENCE=GCTTGCATGCCTGCAGGTCGACTCTAGAGGATCCCCCTACATTTTAGCATCAGTGAGTACAGCATGCTTACTGGAAGAGAGGGTCATGCAACAGATTAGGAGGTAAGTTTGCAAAGGCAGGCTAAGGAGGAGACGCACTGAATGCCATGGTAAGAACTCTGGACATAAAAATATTGGAAGTTGTTGAGCAAGTAAAAAAATGTTTGGAAGTGTTACTTTAGCAATGGCAAGAATGATAGTATGGAATAGATTGGCAGAATGAAGGCAAAATGATTAGACATATTGCATTAAGGTAAAAAATGATAACTGAAGAATTATGTGCCACACTTATTAATAAGAAAGAATATGTGAACCTTGCAGATGTTTCCCTCTAGTAG
 
159
PRIMER_COMMENT=Both primers should have high repeat similarity, but the explain line for right primers will not indicate this because mispriming is calculated "lazily" -- only if there are good left primers.
 
160
PRIMER_LEFT_EXPLAIN=considered 2424, high end compl 27, high repeat similarity 2397, ok 0
 
161
PRIMER_RIGHT_EXPLAIN=considered 2424, ok 2424
 
162
PRIMER_INTERNAL_OLIGO_EXPLAIN=considered 3555, GC content failed 92, ok 3463
 
163
PRIMER_PAIR_EXPLAIN=considered 32248, unacceptable product size 32248, ok 0
 
164
=
 
165
MARKER_NAME=test_06
 
166
PRIMER_MISPRIMING_LIBRARY=not_for_production.lib
 
167
PRIMER_INTERNAL_OLIGO_MISHYB_LIBRARY=not_for_production_Ns.lib
 
168
SEQUENCE=GCTTGCATGCCTGCAGGTCGACTCTAGAGGATCCCCCTACATTTTAGCATCAGTGAGTACAGCATGCTTACTGGAAGAGAGGGTCATGCAACAGATTAGGAGGTAAGTTTGCAAAGGCAGGCTAAGGAGGAGACGCACTGAATGCCATGGTAAGAACTCTGGACATAAAAATATTGGAAGTTGTTGAGCAAGTAAAAAAATGTTTGGAAGTGTTACTTTAGCAATGGCAAGAATGATAGTATGGAATAGATTGGCAGAATGAAGGCAAAATGATTAGACATATTGCATTAAGGTAAAAAATGATAACTGAAGAATTATGTGCCACACTTATTAATAAGAAAGAATATGTGAACCTTGCAGATGTTTCCCTCTAGTAG
 
169
PRIMER_LEFT_INPUT=CGACTCTAGAGGATCCCCCT
 
170
PRIMER_RIGHT_INPUT=TAGCCTGCCTTTGCAAACTT
 
171
PRIMER_INTERNAL_OLIGO_INPUT=GGAAGAGAGGGTCATGCAAC
 
172
PRIMER_PICK_ANYWAY=1
 
173
PRIMER_COMMENT=Primers should be ok, but not internal oligo
 
174
PRIMER_WARNING=Hybridization probe is unacceptable: High similarity to mispriming or mishyb library
 
175
PRIMER_PAIR_EXPLAIN=considered 1, ok 1
 
176
PRIMER_PAIR_PENALTY=0.3646
 
177
PRIMER_LEFT_PENALTY=0.346766
 
178
PRIMER_RIGHT_PENALTY=0.017846
 
179
PRIMER_INTERNAL_OLIGO_PENALTY=0.339231
 
180
PRIMER_LEFT_SEQUENCE=CGACTCTAGAGGATCCCCCT
 
181
PRIMER_RIGHT_SEQUENCE=TAGCCTGCCTTTGCAAACTT
 
182
PRIMER_INTERNAL_OLIGO_SEQUENCE=GGAAGAGAGGGTCATGCAAC
 
183
PRIMER_LEFT=18,20
 
184
PRIMER_RIGHT=123,20
 
185
PRIMER_INTERNAL_OLIGO=72,20
 
186
PRIMER_LEFT_TM=59.653
 
187
PRIMER_RIGHT_TM=60.018
 
188
PRIMER_INTERNAL_OLIGO_TM=59.661
 
189
PRIMER_LEFT_GC_PERCENT=60.000
 
190
PRIMER_RIGHT_GC_PERCENT=45.000
 
191
PRIMER_INTERNAL_OLIGO_GC_PERCENT=55.000
 
192
PRIMER_LEFT_SELF_ANY=8.00
 
193
PRIMER_RIGHT_SELF_ANY=8.00
 
194
PRIMER_INTERNAL_OLIGO_SELF_ANY=4.00
 
195
PRIMER_LEFT_SELF_END=4.00
 
196
PRIMER_RIGHT_SELF_END=3.00
 
197
PRIMER_INTERNAL_OLIGO_SELF_END=2.00
 
198
PRIMER_LEFT_MISPRIMING_SCORE=9.00, L1 Human L1 interspersed repetitive sequence - full length copy
 
199
PRIMER_RIGHT_MISPRIMING_SCORE=10.00, reverse L1 Human L1 interspersed repetitive sequence - full length copy
 
200
PRIMER_PAIR_MISPRIMING_SCORE=18.00, L1 Human L1 interspersed repetitive sequence - full length copy
 
201
PRIMER_INTERNAL_OLIGO_MISHYB_SCORE=20.00, L1 Human L1 interspersed repetitive sequence - full length copy
 
202
PRIMER_LEFT_END_STABILITY=10.9000
 
203
PRIMER_RIGHT_END_STABILITY=6.7000
 
204
PRIMER_PAIR_COMPL_ANY=3.00
 
205
PRIMER_PAIR_COMPL_END=0.00
 
206
PRIMER_PRODUCT_SIZE=106
 
207
=
 
208
MARKER_NAME=test_07
 
209
PRIMER_MISPRIMING_LIBRARY=not_for_production.lib
 
210
PRIMER_INTERNAL_OLIGO_MISHYB_LIBRARY=not_for_production_Ns.lib
 
211
SEQUENCE=GCTTGCATGCCTGCAGGTCGACTCTAGAGGATCCCCCTACATTTTAGCATCAGTGAGTACAGCATGCTTACTGGAAGAGAGGGTCATGCAACAGATTAGGAGGTAAGTTTGCAAAGGCAGGCTAAGGAGGAGACGCACTGAATGCCATGGTAAGAACTCTGGACATAAAAATATTGGAAGTTGTTGAGCAAGTAAAAAAATGTTTGGAAGTGTTACTTTAGCAATGGCAAGAATGATAGTATGGAATAGATTGGCAGAATGAAGGCAAAATGATTAGACATATTGCATTAAGGTAAAAAATGATAACTGAAGAATTATGTGCCACACTTATTAATAAGAAAGAATATGTGAACCTTGCAGATGTTTCCCTCTAGTAG
 
212
PRIMER_PICK_ANYWAY=1
 
213
PRIMER_COMMENT=Primers should be ok, but not internal oligo
 
214
PRIMER_LEFT_EXPLAIN=considered 2424, high end compl 27, high repeat similarity 63, ok 2334
 
215
PRIMER_RIGHT_EXPLAIN=considered 2424, high end compl 52, high repeat similarity 72, ok 2300
 
216
PRIMER_INTERNAL_OLIGO_EXPLAIN=considered 3555, GC content failed 92, high end compl 75, high repeat similarity 3028, ok 360
 
217
PRIMER_PAIR_EXPLAIN=considered 5374476, unacceptable product size 2713327, high end compl 966, no internal oligo 2660183, ok 0
 
218
=
 
219
MARKER_NAME=test_08
 
220
PRIMER_LIB_AMBIGUITY_CODES_CONSENSUS=1
 
221
PRIMER_MISPRIMING_LIBRARY=not_for_production.lib
 
222
PRIMER_INTERNAL_OLIGO_MISHYB_LIBRARY=not_for_production_Ns.lib
 
223
SEQUENCE=GCTTGCATGCCTGCAGGTCGACTCTAGAGGATCCCCCTCTGATCATCTTCTGATCCAAGACCCGTGCTAGTCTACTGTATTCTACATGTACCCTTCTACAAGCTTTGAATTCCATAATCATCAGAGAATCCAGAAATTATTCATTATCACATAATAACAACACTCAAATATTTAAAGTTTTATGGTTGAATCTTTATGATTGAACCCATTCTATCAGGTGGTTATTTTATATCTAATAGAATTCATTTCAGGGTTACACAAAGGTCCGAATCTATCCATTTTACTGAG
 
224
PRIMER_COMMENT=Should fail because of high repeat similarity for all internal oligos
 
225
PRIMER_LEFT_EXPLAIN=considered 1712, high any compl 6, high end compl 24, high repeat similarity 26, ok 1656
 
226
PRIMER_RIGHT_EXPLAIN=considered 1712, high any compl 6, high end compl 25, high repeat similarity 28, ok 1653
 
227
PRIMER_INTERNAL_OLIGO_EXPLAIN=considered 2665, GC content failed 297, high any compl 15, high end compl 23, high repeat similarity 1970, ok 360
 
228
PRIMER_PAIR_EXPLAIN=considered 2737377, unacceptable product size 1340121, no internal oligo 1397256, ok 0
 
229
=
 
230
MARKER_NAME=test_09
 
231
PRIMER_LIB_AMBIGUITY_CODES_CONSENSUS=0
 
232
PRIMER_MISPRIMING_LIBRARY=not_for_production_Xs.lib
 
233
SEQUENCE=GCTTGCATGCCTGCAGGTCGACTCTAGAGGATCCCCCTACATTTTAGCATCAGTGAGTACAGCATGCTTACTGGAAGAGAGGGTCATGCAACAGATTAGGAGGTAAGTTTGCAAAGGCAGGCTAAGGAGGAGACGCACTGAATGCCATGGTAAGAACTCTGGACATAAAAATATTGGAAGTTGTTGAGCAAGTAAAAAAATGTTTGGAAGTGTTACTTTAGCAATGGCAAGAATGATAGTATGGAATAGATTGGCAGAATGAAGGCAAAATGATTAGACATATTGCATTAAGGTAAAAAATGATAACTGAAGAATTATGTGCCACACTTATTAATAAGAAAGAATATGTGAACCTTGCAGATGTTTCCCTCTAGTAG
 
234
PRIMER_COMMENT=Should succeed
 
235
PRIMER_WARNING=Unrecognized character (X) in mispriming library not_for_production_Xs.lib
 
236
PRIMER_LEFT_EXPLAIN=considered 2424, ok 2424
 
237
PRIMER_RIGHT_EXPLAIN=considered 2424, ok 2424
 
238
PRIMER_INTERNAL_OLIGO_EXPLAIN=considered 3555, GC content failed 92, ok 3463
 
239
PRIMER_PAIR_EXPLAIN=considered 94, unacceptable product size 90, ok 4
 
240
PRIMER_PAIR_PENALTY=0.3646
 
241
PRIMER_LEFT_PENALTY=0.346766
 
242
PRIMER_RIGHT_PENALTY=0.017846
 
243
PRIMER_INTERNAL_OLIGO_PENALTY=0.339231
 
244
PRIMER_LEFT_SEQUENCE=CGACTCTAGAGGATCCCCCT
 
245
PRIMER_RIGHT_SEQUENCE=TAGCCTGCCTTTGCAAACTT
 
246
PRIMER_INTERNAL_OLIGO_SEQUENCE=GGAAGAGAGGGTCATGCAAC
 
247
PRIMER_LEFT=18,20
 
248
PRIMER_RIGHT=123,20
 
249
PRIMER_INTERNAL_OLIGO=72,20
 
250
PRIMER_LEFT_TM=59.653
 
251
PRIMER_RIGHT_TM=60.018
 
252
PRIMER_INTERNAL_OLIGO_TM=59.661
 
253
PRIMER_LEFT_GC_PERCENT=60.000
 
254
PRIMER_RIGHT_GC_PERCENT=45.000
 
255
PRIMER_INTERNAL_OLIGO_GC_PERCENT=55.000
 
256
PRIMER_LEFT_SELF_ANY=8.00
 
257
PRIMER_RIGHT_SELF_ANY=8.00
 
258
PRIMER_INTERNAL_OLIGO_SELF_ANY=4.00
 
259
PRIMER_LEFT_SELF_END=4.00
 
260
PRIMER_RIGHT_SELF_END=3.00
 
261
PRIMER_INTERNAL_OLIGO_SELF_END=2.00
 
262
PRIMER_LEFT_MISPRIMING_SCORE=9.00, L1 Human L1 interspersed repetitive sequence - full length copy
 
263
PRIMER_RIGHT_MISPRIMING_SCORE=10.00, reverse L1 Human L1 interspersed repetitive sequence - full length copy
 
264
PRIMER_PAIR_MISPRIMING_SCORE=18.00, L1 Human L1 interspersed repetitive sequence - full length copy
 
265
PRIMER_INTERNAL_OLIGO_MISHYB_SCORE=11.00, L1 Human L1 interspersed repetitive sequence - full length copy
 
266
PRIMER_LEFT_END_STABILITY=10.9000
 
267
PRIMER_RIGHT_END_STABILITY=6.7000
 
268
PRIMER_PAIR_COMPL_ANY=3.00
 
269
PRIMER_PAIR_COMPL_END=0.00
 
270
PRIMER_PRODUCT_SIZE=106
 
271
=
 
272
MARKER_NAME=test_10
 
273
PRIMER_LIB_AMBIGUITY_CODES_CONSENSUS=1
 
274
PRIMER_MISPRIMING_LIBRARY=not_for_production_Xs.lib
 
275
SEQUENCE=GCTTGCATGCCTGCAGGTCGACTCTAGAGGATCCCCCTACATTTTAGCATCAGTGAGTACAGCATGCTTACTGGAAGAGAGGGTCATGCAACAGATTAGGAGGTAAGTTTGCAAAGGCAGGCTAAGGAGGAGACGCACTGAATGCCATGGTAAGAACTCTGGACATAAAAATATTGGAAGTTGTTGAGCAAGTAAAAAAATGTTTGGAAGTGTTACTTTAGCAATGGCAAGAATGATAGTATGGAATAGATTGGCAGAATGAAGGCAAAATGATTAGACATATTGCATTAAGGTAAAAAATGATAACTGAAGAATTATGTGCCACACTTATTAATAAGAAAGAATATGTGAACCTTGCAGATGTTTCCCTCTAGTAG
 
276
PRIMER_COMMENT=Should fail (Xs are treated as Ns).
 
277
PRIMER_WARNING=Unrecognized character (X) in mispriming library not_for_production_Xs.lib
 
278
PRIMER_LEFT_EXPLAIN=considered 2424, high end compl 27, high repeat similarity 2397, ok 0
 
279
PRIMER_RIGHT_EXPLAIN=considered 2424, ok 2424
 
280
PRIMER_INTERNAL_OLIGO_EXPLAIN=considered 3555, GC content failed 92, ok 3463
 
281
PRIMER_PAIR_EXPLAIN=considered 32248, unacceptable product size 32248, ok 0
 
282
=
 
283
MARKER_NAME=test_11
 
284
PRIMER_LIB_AMBIGUITY_CODES_CONSENSUS=1
 
285
PRIMER_MISPRIMING_LIBRARY=
 
286
PRIMER_INTERNAL_OLIGO_MISHYB_LIBRARY=not_for_production_Xs.lib
 
287
SEQUENCE=GCTTGCATGCCTGCAGGTCGACTCTAGAGGATCCCCCTACATTTTAGCATCAGTGAGTACAGCATGCTTACTGGAAGAGAGGGTCATGCAACAGATTAGGAGGTAAGTTTGCAAAGGCAGGCTAAGGAGGAGACGCACTGAATGCCATGGTAAGAACTCTGGACATAAAAATATTGGAAGTTGTTGAGCAAGTAAAAAAATGTTTGGAAGTGTTACTTTAGCAATGGCAAGAATGATAGTATGGAATAGATTGGCAGAATGAAGGCAAAATGATTAGACATATTGCATTAAGGTAAAAAATGATAACTGAAGAATTATGTGCCACACTTATTAATAAGAAAGAATATGTGAACCTTGCAGATGTTTCCCTCTAGTAG
 
288
PRIMER_COMMENT=Should fail (Xs are treated as Ns).
 
289
PRIMER_WARNING=Unrecognized character (X) in internal oligo mishyb library not_for_production_Xs.lib (for internal oligo)
 
290
PRIMER_LEFT_EXPLAIN=considered 2424, high end compl 27, ok 2397
 
291
PRIMER_RIGHT_EXPLAIN=considered 2424, high end compl 52, ok 2372
 
292
PRIMER_INTERNAL_OLIGO_EXPLAIN=considered 3555, GC content failed 92, high end compl 75, high repeat similarity 3028, ok 360
 
293
PRIMER_PAIR_EXPLAIN=considered 5691246, unacceptable product size 2862933, high end compl 994, no internal oligo 2827319, ok 0
 
294
=