bio-polymarker 1.3.2
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +7 -0
- data/.travis.yml +24 -0
- data/Gemfile +23 -0
- data/README.md +205 -0
- data/Rakefile +61 -0
- data/SECURITY.md +16 -0
- data/VERSION +1 -0
- data/bin/bfr.rb +128 -0
- data/bin/blast_triads.rb +166 -0
- data/bin/blast_triads_promoters.rb +192 -0
- data/bin/count_variations.rb +36 -0
- data/bin/filter_blat_by_target_coverage.rb +69 -0
- data/bin/filter_exonerate_by_identity.rb +38 -0
- data/bin/find_best_blat_hit.rb +33 -0
- data/bin/find_best_exonerate.rb +17 -0
- data/bin/get_longest_hsp_blastx_triads.rb +66 -0
- data/bin/hexaploid_primers.rb +168 -0
- data/bin/homokaryot_primers.rb +183 -0
- data/bin/mafft_triads.rb +120 -0
- data/bin/mafft_triads_promoters.rb +403 -0
- data/bin/map_markers_to_contigs.rb +66 -0
- data/bin/marker_to_vcf.rb +241 -0
- data/bin/markers_in_region.rb +42 -0
- data/bin/mask_triads.rb +169 -0
- data/bin/polymarker.rb +410 -0
- data/bin/polymarker_capillary.rb +443 -0
- data/bin/polymarker_deletions.rb +350 -0
- data/bin/snp_position_to_polymarker.rb +101 -0
- data/bin/snps_between_bams.rb +107 -0
- data/bin/tag_stats.rb +75 -0
- data/bin/vcfLineToTable.rb +56 -0
- data/bin/vcfToPolyMarker.rb +82 -0
- data/bio-polymarker.gemspec +227 -0
- data/conf/defaults.rb +1 -0
- data/conf/primer3_config/dangle.dh +128 -0
- data/conf/primer3_config/dangle.ds +128 -0
- data/conf/primer3_config/interpretations/dangle_i.dh +131 -0
- data/conf/primer3_config/interpretations/dangle_i.ds +131 -0
- data/conf/primer3_config/interpretations/loops_i.dh +34 -0
- data/conf/primer3_config/interpretations/loops_i.ds +31 -0
- data/conf/primer3_config/interpretations/stack_i.dh +257 -0
- data/conf/primer3_config/interpretations/stack_i.ds +256 -0
- data/conf/primer3_config/interpretations/stackmm_i_mm.dh +257 -0
- data/conf/primer3_config/interpretations/stackmm_i_mm.ds +256 -0
- data/conf/primer3_config/interpretations/tetraloop_i.dh +79 -0
- data/conf/primer3_config/interpretations/tetraloop_i.ds +81 -0
- data/conf/primer3_config/interpretations/triloop_i.dh +21 -0
- data/conf/primer3_config/interpretations/triloop_i.ds +18 -0
- data/conf/primer3_config/interpretations/tstack2_i.dh +256 -0
- data/conf/primer3_config/interpretations/tstack2_i.ds +256 -0
- data/conf/primer3_config/interpretations/tstack_i.dh +256 -0
- data/conf/primer3_config/interpretations/tstack_i.ds +256 -0
- data/conf/primer3_config/interpretations/tstack_tm_inf_i.dh +256 -0
- data/conf/primer3_config/interpretations/tstack_tm_inf_i.ds +256 -0
- data/conf/primer3_config/loops.dh +30 -0
- data/conf/primer3_config/loops.ds +30 -0
- data/conf/primer3_config/stack.dh +256 -0
- data/conf/primer3_config/stack.ds +256 -0
- data/conf/primer3_config/stackmm.dh +256 -0
- data/conf/primer3_config/stackmm.ds +256 -0
- data/conf/primer3_config/tetraloop.dh +77 -0
- data/conf/primer3_config/tetraloop.ds +77 -0
- data/conf/primer3_config/triloop.dh +16 -0
- data/conf/primer3_config/triloop.ds +16 -0
- data/conf/primer3_config/tstack.dh +256 -0
- data/conf/primer3_config/tstack2.dh +256 -0
- data/conf/primer3_config/tstack2.ds +256 -0
- data/conf/primer3_config/tstack_tm_inf.ds +256 -0
- data/lib/bio/BFRTools.rb +465 -0
- data/lib/bio/BIOExtensions.rb +153 -0
- data/lib/bio/PolyploidTools/ChromosomeArm.rb +63 -0
- data/lib/bio/PolyploidTools/ExonContainer.rb +245 -0
- data/lib/bio/PolyploidTools/Marker.rb +175 -0
- data/lib/bio/PolyploidTools/Mask.rb +116 -0
- data/lib/bio/PolyploidTools/NoSNPSequence.rb +292 -0
- data/lib/bio/PolyploidTools/PrimerRegion.rb +30 -0
- data/lib/bio/PolyploidTools/SNP.rb +804 -0
- data/lib/bio/PolyploidTools/SNPMutant.rb +86 -0
- data/lib/bio/PolyploidTools/SNPSequence.rb +55 -0
- data/lib/bio/db/blast.rb +114 -0
- data/lib/bio/db/exonerate.rb +333 -0
- data/lib/bio/db/primer3.rb +820 -0
- data/lib/bio-polymarker.rb +28 -0
- data/test/data/7B_amplicon_test.fa +12 -0
- data/test/data/7B_amplicon_test.fa.fai +1 -0
- data/test/data/7B_amplicon_test_reference.fa +110 -0
- data/test/data/7B_amplicon_test_reference.fa.fai +3 -0
- data/test/data/7B_marker_test.txt +1 -0
- data/test/data/BS00068396_51.fa +2 -0
- data/test/data/BS00068396_51_blast.tab +4 -0
- data/test/data/BS00068396_51_contigs.aln +1412 -0
- data/test/data/BS00068396_51_contigs.dnd +7 -0
- data/test/data/BS00068396_51_contigs.fa +8 -0
- data/test/data/BS00068396_51_contigs.fa.fai +4 -0
- data/test/data/BS00068396_51_contigs.fa.nhr +0 -0
- data/test/data/BS00068396_51_contigs.fa.nin +0 -0
- data/test/data/BS00068396_51_contigs.fa.nsq +0 -0
- data/test/data/BS00068396_51_contigs.nhr +0 -0
- data/test/data/BS00068396_51_contigs.nin +0 -0
- data/test/data/BS00068396_51_contigs.nsq +0 -0
- data/test/data/BS00068396_51_exonerate.tab +6 -0
- data/test/data/BS00068396_51_for_polymarker.txt +1 -0
- data/test/data/BS00068396_51_genes.txt +14 -0
- data/test/data/IWGSC_CSS_1AL_scaff_1455974.fa +112 -0
- data/test/data/IWGSC_CSS_1AL_scaff_1455974_aln_contigs.fa +2304 -0
- data/test/data/IWGSC_CSS_1AL_scaff_1455974_aln_contigs.fa.fai +11 -0
- data/test/data/LIB1716.bam +0 -0
- data/test/data/LIB1716.bam.bai +0 -0
- data/test/data/LIB1719.bam +0 -0
- data/test/data/LIB1719.bam.bai +0 -0
- data/test/data/LIB1721.bam +0 -0
- data/test/data/LIB1721.bam.bai +0 -0
- data/test/data/LIB1722.bam +0 -0
- data/test/data/LIB1722.bam.bai +0 -0
- data/test/data/PST130_7067.csv +1 -0
- data/test/data/PST130_7067.fa +2 -0
- data/test/data/PST130_7067.fa.fai +1 -0
- data/test/data/PST130_7067.fa.ndb +0 -0
- data/test/data/PST130_7067.fa.nhr +0 -0
- data/test/data/PST130_7067.fa.nin +0 -0
- data/test/data/PST130_7067.fa.not +0 -0
- data/test/data/PST130_7067.fa.nsq +0 -0
- data/test/data/PST130_7067.fa.ntf +0 -0
- data/test/data/PST130_7067.fa.nto +0 -0
- data/test/data/PST130_reverse_primer.csv +1 -0
- data/test/data/S22380157.fa +16 -0
- data/test/data/S22380157.fa.fai +1 -0
- data/test/data/S22380157.vcf +67 -0
- data/test/data/S58861868/LIB1716.bam +0 -0
- data/test/data/S58861868/LIB1716.sam +651 -0
- data/test/data/S58861868/LIB1719.bam +0 -0
- data/test/data/S58861868/LIB1719.sam +805 -0
- data/test/data/S58861868/LIB1721.bam +0 -0
- data/test/data/S58861868/LIB1721.sam +1790 -0
- data/test/data/S58861868/LIB1722.bam +0 -0
- data/test/data/S58861868/LIB1722.sam +1271 -0
- data/test/data/S58861868/S58861868.fa +16 -0
- data/test/data/S58861868/S58861868.fa.fai +1 -0
- data/test/data/S58861868/S58861868.vcf +76 -0
- data/test/data/S58861868/header.txt +9 -0
- data/test/data/S58861868/merged.bam +0 -0
- data/test/data/S58861868/merged_reheader.bam +0 -0
- data/test/data/S58861868/merged_reheader.bam.bai +0 -0
- data/test/data/Test3Aspecific.csv +2 -0
- data/test/data/Test3Aspecific_contigs.fa +6 -0
- data/test/data/bfr_out_test.csv +5 -0
- data/test/data/chr1A_C1145499T/chr1A_C1145499T.csv +1 -0
- data/test/data/chr1A_G540414846C/chr1A_G540414846C.csv +1 -0
- data/test/data/chr1A_G540414846C/chr1A_G540414846C.fa +2 -0
- data/test/data/chr1A_T517634750C/chr1A_T517634750C.csv +1 -0
- data/test/data/chr2D_C112180134A/chr2D_C112180134A.csv +1 -0
- data/test/data/chr4D_C14473543T/chr4D_C14473543T.csv +1 -0
- data/test/data/chr4D_C14473543T/chr4D_C14473543T.fa +2 -0
- data/test/data/headerMergeed.txt +9 -0
- data/test/data/headerS2238015 +1 -0
- data/test/data/mergedLibs.bam +0 -0
- data/test/data/mergedLibsReheader.bam +0 -0
- data/test/data/mergedLibsSorted.bam +0 -0
- data/test/data/mergedLibsSorted.bam.bai +0 -0
- data/test/data/patological_cases5D.csv +1 -0
- data/test/data/primer_3_input_header_test +5 -0
- data/test/data/short_primer_design_test.csv +10 -0
- data/test/data/some_tests/some_tests.csv +201 -0
- data/test/data/test_from_mutant.csv +3 -0
- data/test/data/test_iselect.csv +196 -0
- data/test/data/test_iselect_reference.fa +1868 -0
- data/test/data/test_iselect_reference.fa.fai +934 -0
- data/test/data/test_primer3_error.csv +4 -0
- data/test/data/test_primer3_error_contigs.fa +10 -0
- data/test/test_bfr.rb +135 -0
- data/test/test_blast.rb +47 -0
- data/test/test_exon_container.rb +17 -0
- data/test/test_exonearate.rb +48 -0
- data/test/test_integration.rb +76 -0
- data/test/test_snp_parsing.rb +121 -0
- data/test/test_wrong_selection.sh +5 -0
- metadata +356 -0
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TG_AT 105
|
229
|
+
TG_CA inf
|
230
|
+
TG_CC 80
|
231
|
+
TG_CG inf
|
232
|
+
TG_CT inf
|
233
|
+
TG_GA inf
|
234
|
+
TG_GC 90
|
235
|
+
TG_GG inf
|
236
|
+
TG_GT inf
|
237
|
+
TG_TA inf
|
238
|
+
TG_TC 169
|
239
|
+
TG_TG inf
|
240
|
+
TG_TT inf
|
241
|
+
TT_AA 0
|
242
|
+
TT_AC 12
|
243
|
+
TT_AG 98
|
244
|
+
TT_AT 89
|
245
|
+
TT_CA 17
|
246
|
+
TT_CC inf
|
247
|
+
TT_CG inf
|
248
|
+
TT_CT inf
|
249
|
+
TT_GA 87
|
250
|
+
TT_GC inf
|
251
|
+
TT_GG inf
|
252
|
+
TT_GT inf
|
253
|
+
TT_TA 65
|
254
|
+
TT_TC inf
|
255
|
+
TT_TG inf
|
256
|
+
TT_TT inf
|
@@ -0,0 +1,256 @@
|
|
1
|
+
AA_AA 0
|
2
|
+
AA_AC 0
|
3
|
+
AA_AG 0
|
4
|
+
AA_AT 25
|
5
|
+
AA_CA 0
|
6
|
+
AA_CC 0
|
7
|
+
AA_CG 0
|
8
|
+
AA_CT 27
|
9
|
+
AA_GA 0
|
10
|
+
AA_GC 0
|
11
|
+
AA_GG 0
|
12
|
+
AA_GT 24
|
13
|
+
AA_TA 31
|
14
|
+
AA_TC 16
|
15
|
+
AA_TG 19
|
16
|
+
AA_TT 0
|
17
|
+
AC_AA 0
|
18
|
+
AC_AC 0
|
19
|
+
AC_AG 80
|
20
|
+
AC_AT 0
|
21
|
+
AC_CA 0
|
22
|
+
AC_CC 0
|
23
|
+
AC_CG 32
|
24
|
+
AC_CT 0
|
25
|
+
AC_GA 0
|
26
|
+
AC_GC 0
|
27
|
+
AC_GG 46
|
28
|
+
AC_GT 0
|
29
|
+
AC_TA 18
|
30
|
+
AC_TC 1
|
31
|
+
AC_TG 0
|
32
|
+
AC_TT 9
|
33
|
+
AG_AA 0
|
34
|
+
AG_AC 43
|
35
|
+
AG_AG 0
|
36
|
+
AG_AT 0
|
37
|
+
AG_CA 0
|
38
|
+
AG_CC 27
|
39
|
+
AG_CG 0
|
40
|
+
AG_CT 0
|
41
|
+
AG_GA 0
|
42
|
+
AG_GC 60
|
43
|
+
AG_GG 0
|
44
|
+
AG_GT 0
|
45
|
+
AG_TA 25
|
46
|
+
AG_TC 0
|
47
|
+
AG_TG 11
|
48
|
+
AG_TT 32
|
49
|
+
AT_AA 31
|
50
|
+
AT_AC 0
|
51
|
+
AT_AG 0
|
52
|
+
AT_AT 0
|
53
|
+
AT_CA 18
|
54
|
+
AT_CC 0
|
55
|
+
AT_CG 0
|
56
|
+
AT_CT 0
|
57
|
+
AT_GA 25
|
58
|
+
AT_GC 0
|
59
|
+
AT_GG 0
|
60
|
+
AT_GT 0
|
61
|
+
AT_TA 0
|
62
|
+
AT_TC 23
|
63
|
+
AT_TG 35
|
64
|
+
AT_TT 24
|
65
|
+
CA_AA 0
|
66
|
+
CA_AC 0
|
67
|
+
CA_AG 0
|
68
|
+
CA_AT 23
|
69
|
+
CA_CA 0
|
70
|
+
CA_CC 0
|
71
|
+
CA_CG 0
|
72
|
+
CA_CT 7
|
73
|
+
CA_GA 43
|
74
|
+
CA_GC 26
|
75
|
+
CA_GG 39
|
76
|
+
CA_GT 0
|
77
|
+
CA_TA 0
|
78
|
+
CA_TC 0
|
79
|
+
CA_TG 0
|
80
|
+
CA_TT 7
|
81
|
+
CC_AA 0
|
82
|
+
CC_AC 0
|
83
|
+
CC_AG 50
|
84
|
+
CC_AT 0
|
85
|
+
CC_CA 0
|
86
|
+
CC_CC 0
|
87
|
+
CC_CG 39
|
88
|
+
CC_CT 0
|
89
|
+
CC_GA 27
|
90
|
+
CC_GC 21
|
91
|
+
CC_GG 0
|
92
|
+
CC_GT 32
|
93
|
+
CC_TA 0
|
94
|
+
CC_TC 0
|
95
|
+
CC_TG 30
|
96
|
+
CC_TT 0
|
97
|
+
CG_AA 0
|
98
|
+
CG_AC 26
|
99
|
+
CG_AG 0
|
100
|
+
CG_AT 0
|
101
|
+
CG_CA 0
|
102
|
+
CG_CC 21
|
103
|
+
CG_CG 0
|
104
|
+
CG_CT 0
|
105
|
+
CG_GA 60
|
106
|
+
CG_GC 0
|
107
|
+
CG_GG 38
|
108
|
+
CG_GT 38
|
109
|
+
CG_TA 0
|
110
|
+
CG_TC 39
|
111
|
+
CG_TG 0
|
112
|
+
CG_TT 0
|
113
|
+
CT_AA 16
|
114
|
+
CT_AC 0
|
115
|
+
CT_AG 0
|
116
|
+
CT_AT 0
|
117
|
+
CT_CA 1
|
118
|
+
CT_CC 0
|
119
|
+
CT_CG 0
|
120
|
+
CT_CT 0
|
121
|
+
CT_GA 0
|
122
|
+
CT_GC 39
|
123
|
+
CT_GG 66
|
124
|
+
CT_GT 61
|
125
|
+
CT_TA 23
|
126
|
+
CT_TC 0
|
127
|
+
CT_TG 0
|
128
|
+
CT_TT 0
|
129
|
+
GA_AA 0
|
130
|
+
GA_AC 0
|
131
|
+
GA_AG 0
|
132
|
+
GA_AT 20
|
133
|
+
GA_CA 80
|
134
|
+
GA_CC 50
|
135
|
+
GA_CG 43
|
136
|
+
GA_CT 0
|
137
|
+
GA_GA 0
|
138
|
+
GA_GC 0
|
139
|
+
GA_GG 0
|
140
|
+
GA_GT 11
|
141
|
+
GA_TA 0
|
142
|
+
GA_TC 0
|
143
|
+
GA_TG 0
|
144
|
+
GA_TT 36
|
145
|
+
GC_AA 0
|
146
|
+
GC_AC 0
|
147
|
+
GC_AG 43
|
148
|
+
GC_AT 0
|
149
|
+
GC_CA 32
|
150
|
+
GC_CC 39
|
151
|
+
GC_CG 0
|
152
|
+
GC_CT 49
|
153
|
+
GC_GA 0
|
154
|
+
GC_GC 0
|
155
|
+
GC_GG 7
|
156
|
+
GC_GT 0
|
157
|
+
GC_TA 0
|
158
|
+
GC_TC 0
|
159
|
+
GC_TG 59
|
160
|
+
GC_TT 0
|
161
|
+
GG_AA 0
|
162
|
+
GG_AC 39
|
163
|
+
GG_AG 0
|
164
|
+
GG_AT 0
|
165
|
+
GG_CA 46
|
166
|
+
GG_CC 0
|
167
|
+
GG_CG 7
|
168
|
+
GG_CT 57
|
169
|
+
GG_GA 0
|
170
|
+
GG_GC 38
|
171
|
+
GG_GG 0
|
172
|
+
GG_GT 0
|
173
|
+
GG_TA 0
|
174
|
+
GG_TC 66
|
175
|
+
GG_TG 0
|
176
|
+
GG_TT 0
|
177
|
+
GT_AA 19
|
178
|
+
GT_AC 0
|
179
|
+
GT_AG 0
|
180
|
+
GT_AT 0
|
181
|
+
GT_CA 0
|
182
|
+
GT_CC 30
|
183
|
+
GT_CG 59
|
184
|
+
GT_CT 74
|
185
|
+
GT_GA 11
|
186
|
+
GT_GC 0
|
187
|
+
GT_GG 0
|
188
|
+
GT_GT 0
|
189
|
+
GT_TA 35
|
190
|
+
GT_TC 0
|
191
|
+
GT_TG 0
|
192
|
+
GT_TT 0
|
193
|
+
TA_AA 25
|
194
|
+
TA_AC 23
|
195
|
+
TA_AG 20
|
196
|
+
TA_AT 72
|
197
|
+
TA_CA 0
|
198
|
+
TA_CC 0
|
199
|
+
TA_CG 0
|
200
|
+
TA_CT 25
|
201
|
+
TA_GA 0
|
202
|
+
TA_GC 0
|
203
|
+
TA_GG 0
|
204
|
+
TA_GT 39
|
205
|
+
TA_TA 0
|
206
|
+
TA_TC 0
|
207
|
+
TA_TG 0
|
208
|
+
TA_TT 32
|
209
|
+
TC_AA 27
|
210
|
+
TC_AC 7
|
211
|
+
TC_AG 0
|
212
|
+
TC_AT 25
|
213
|
+
TC_CA 0
|
214
|
+
TC_CC 0
|
215
|
+
TC_CG 49
|
216
|
+
TC_CT 0
|
217
|
+
TC_GA 0
|
218
|
+
TC_GC 0
|
219
|
+
TC_GG 57
|
220
|
+
TC_GT 0
|
221
|
+
TC_TA 0
|
222
|
+
TC_TC 0
|
223
|
+
TC_TG 74
|
224
|
+
TC_TT 0
|
225
|
+
TG_AA 24
|
226
|
+
TG_AC 0
|
227
|
+
TG_AG 11
|
228
|
+
TG_AT 39
|
229
|
+
TG_CA 0
|
230
|
+
TG_CC 32
|
231
|
+
TG_CG 0
|
232
|
+
TG_CT 0
|
233
|
+
TG_GA 0
|
234
|
+
TG_GC 38
|
235
|
+
TG_GG 0
|
236
|
+
TG_GT 0
|
237
|
+
TG_TA 0
|
238
|
+
TG_TC 61
|
239
|
+
TG_TG 0
|
240
|
+
TG_TT 0
|
241
|
+
TT_AA 0
|
242
|
+
TT_AC 7
|
243
|
+
TT_AG 36
|
244
|
+
TT_AT 32
|
245
|
+
TT_CA 9
|
246
|
+
TT_CC 0
|
247
|
+
TT_CG 0
|
248
|
+
TT_CT 0
|
249
|
+
TT_GA 32
|
250
|
+
TT_GC 0
|
251
|
+
TT_GG 0
|
252
|
+
TT_GT 0
|
253
|
+
TT_TA 24
|
254
|
+
TT_TC 0
|
255
|
+
TT_TG 0
|
256
|
+
TT_TT 0
|
@@ -0,0 +1,256 @@
|
|
1
|
+
AA_AA inf
|
2
|
+
AA_AC inf
|
3
|
+
AA_AG inf
|
4
|
+
AA_AT 63
|
5
|
+
AA_CA inf
|
6
|
+
AA_CC inf
|
7
|
+
AA_CG inf
|
8
|
+
AA_CT 70
|
9
|
+
AA_GA inf
|
10
|
+
AA_GC inf
|
11
|
+
AA_GG inf
|
12
|
+
AA_GT 58
|
13
|
+
AA_TA 78
|
14
|
+
AA_TC 40
|
15
|
+
AA_TG 44
|
16
|
+
AA_TT inf
|
17
|
+
AC_AA inf
|
18
|
+
AC_AC inf
|
19
|
+
AC_AG 225
|
20
|
+
AC_AT inf
|
21
|
+
AC_CA inf
|
22
|
+
AC_CC inf
|
23
|
+
AC_CG 71
|
24
|
+
AC_CT inf
|
25
|
+
AC_GA inf
|
26
|
+
AC_GC inf
|
27
|
+
AC_GG 114
|
28
|
+
AC_GT inf
|
29
|
+
AC_TA 38
|
30
|
+
AC_TC 5
|
31
|
+
AC_TG inf
|
32
|
+
AC_TT 17
|
33
|
+
AG_AA inf
|
34
|
+
AG_AC 107
|
35
|
+
AG_AG inf
|
36
|
+
AG_AT inf
|
37
|
+
AG_CA inf
|
38
|
+
AG_CC 60
|
39
|
+
AG_CG inf
|
40
|
+
AG_CT inf
|
41
|
+
AG_GA inf
|
42
|
+
AG_GC 155
|
43
|
+
AG_GG inf
|
44
|
+
AG_GT inf
|
45
|
+
AG_TA 59
|
46
|
+
AG_TC inf
|
47
|
+
AG_TG 21
|
48
|
+
AG_TT 87
|
49
|
+
AT_AA 78
|
50
|
+
AT_AC inf
|
51
|
+
AT_AG inf
|
52
|
+
AT_AT inf
|
53
|
+
AT_CA 38
|
54
|
+
AT_CC inf
|
55
|
+
AT_CG inf
|
56
|
+
AT_CT inf
|
57
|
+
AT_GA 59
|
58
|
+
AT_GC inf
|
59
|
+
AT_GG inf
|
60
|
+
AT_GT inf
|
61
|
+
AT_TA inf
|
62
|
+
AT_TC 63
|
63
|
+
AT_TG 94
|
64
|
+
AT_TT 65
|
65
|
+
CA_AA inf
|
66
|
+
CA_AC inf
|
67
|
+
CA_AG inf
|
68
|
+
CA_AT 59
|
69
|
+
CA_CA inf
|
70
|
+
CA_CC inf
|
71
|
+
CA_CG inf
|
72
|
+
CA_CT 13
|
73
|
+
CA_GA 107
|
74
|
+
CA_GC 59
|
75
|
+
CA_GG 96
|
76
|
+
CA_GT inf
|
77
|
+
CA_TA inf
|
78
|
+
CA_TC inf
|
79
|
+
CA_TG inf
|
80
|
+
CA_TT 12
|
81
|
+
CC_AA inf
|
82
|
+
CC_AC inf
|
83
|
+
CC_AG 138
|
84
|
+
CC_AT inf
|
85
|
+
CC_CA inf
|
86
|
+
CC_CC inf
|
87
|
+
CC_CG 106
|
88
|
+
CC_CT inf
|
89
|
+
CC_GA 60
|
90
|
+
CC_GC 51
|
91
|
+
CC_GG inf
|
92
|
+
CC_GT 80
|
93
|
+
CC_TA inf
|
94
|
+
CC_TC inf
|
95
|
+
CC_TG 78
|
96
|
+
CC_TT inf
|
97
|
+
CG_AA inf
|
98
|
+
CG_AC 59
|
99
|
+
CG_AG inf
|
100
|
+
CG_AT inf
|
101
|
+
CG_CA inf
|
102
|
+
CG_CC 51
|
103
|
+
CG_CG inf
|
104
|
+
CG_CT inf
|
105
|
+
CG_GA 155
|
106
|
+
CG_GC inf
|
107
|
+
CG_GG 95
|
108
|
+
CG_GT 90
|
109
|
+
CG_TA inf
|
110
|
+
CG_TC 106
|
111
|
+
CG_TG inf
|
112
|
+
CG_TT inf
|
113
|
+
CT_AA 40
|
114
|
+
CT_AC inf
|
115
|
+
CT_AG inf
|
116
|
+
CT_AT inf
|
117
|
+
CT_CA 5
|
118
|
+
CT_CC inf
|
119
|
+
CT_CG inf
|
120
|
+
CT_CT inf
|
121
|
+
CT_GA inf
|
122
|
+
CT_GC 106
|
123
|
+
CT_GG 187
|
124
|
+
CT_GT 169
|
125
|
+
CT_TA 63
|
126
|
+
CT_TC inf
|
127
|
+
CT_TG inf
|
128
|
+
CT_TT inf
|
129
|
+
GA_AA inf
|
130
|
+
GA_AC inf
|
131
|
+
GA_AG inf
|
132
|
+
GA_AT 47
|
133
|
+
GA_CA 225
|
134
|
+
GA_CC 138
|
135
|
+
GA_CG 111
|
136
|
+
GA_CT inf
|
137
|
+
GA_GA inf
|
138
|
+
GA_GC inf
|
139
|
+
GA_GG inf
|
140
|
+
GA_GT 27
|
141
|
+
GA_TA inf
|
142
|
+
GA_TC inf
|
143
|
+
GA_TG inf
|
144
|
+
GA_TT 98
|
145
|
+
GC_AA inf
|
146
|
+
GC_AC inf
|
147
|
+
GC_AG 111
|
148
|
+
GC_AT inf
|
149
|
+
GC_CA 71
|
150
|
+
GC_CC 106
|
151
|
+
GC_CG inf
|
152
|
+
GC_CT 135
|
153
|
+
GC_GA inf
|
154
|
+
GC_GC inf
|
155
|
+
GC_GG 192
|
156
|
+
GC_GT inf
|
157
|
+
GC_TA inf
|
158
|
+
GC_TC inf
|
159
|
+
GC_TG 161
|
160
|
+
GC_TT inf
|
161
|
+
GG_AA inf
|
162
|
+
GG_AC 96
|
163
|
+
GG_AG inf
|
164
|
+
GG_AT inf
|
165
|
+
GG_CA 114
|
166
|
+
GG_CC inf
|
167
|
+
GG_CG 192
|
168
|
+
GG_CT 159
|
169
|
+
GG_GA inf
|
170
|
+
GG_GC 95
|
171
|
+
GG_GG inf
|
172
|
+
GG_GT inf
|
173
|
+
GG_TA inf
|
174
|
+
GG_TC 187
|
175
|
+
GG_TG inf
|
176
|
+
GG_TT inf
|
177
|
+
GT_AA 44
|
178
|
+
GT_AC inf
|
179
|
+
GT_AG inf
|
180
|
+
GT_AT inf
|
181
|
+
GT_CA inf
|
182
|
+
GT_CC 78
|
183
|
+
GT_CG 161
|
184
|
+
GT_CT 212
|
185
|
+
GT_GA 21
|
186
|
+
GT_GC inf
|
187
|
+
GT_GG inf
|
188
|
+
GT_GT inf
|
189
|
+
GT_TA 94
|
190
|
+
GT_TC inf
|
191
|
+
GT_TG inf
|
192
|
+
GT_TT inf
|
193
|
+
TA_AA 63
|
194
|
+
TA_AC 59
|
195
|
+
TA_AG 47
|
196
|
+
TA_AT inf
|
197
|
+
TA_CA inf
|
198
|
+
TA_CC inf
|
199
|
+
TA_CG inf
|
200
|
+
TA_CT 63
|
201
|
+
TA_GA inf
|
202
|
+
TA_GC inf
|
203
|
+
TA_GG inf
|
204
|
+
TA_GT 105
|
205
|
+
TA_TA inf
|
206
|
+
TA_TC inf
|
207
|
+
TA_TG inf
|
208
|
+
TA_TT 89
|
209
|
+
TC_AA 70
|
210
|
+
TC_AC 13
|
211
|
+
TC_AG inf
|
212
|
+
TC_AT 63
|
213
|
+
TC_CA inf
|
214
|
+
TC_CC inf
|
215
|
+
TC_CG 135
|
216
|
+
TC_CT inf
|
217
|
+
TC_GA inf
|
218
|
+
TC_GC inf
|
219
|
+
TC_GG 159
|
220
|
+
TC_GT inf
|
221
|
+
TC_TA inf
|
222
|
+
TC_TC inf
|
223
|
+
TC_TG 212
|
224
|
+
TC_TT inf
|
225
|
+
TG_AA 58
|
226
|
+
TG_AC inf
|
227
|
+
TG_AG 27
|
228
|
+
TG_AT 105
|
229
|
+
TG_CA inf
|
230
|
+
TG_CC 80
|
231
|
+
TG_CG inf
|
232
|
+
TG_CT inf
|
233
|
+
TG_GA inf
|
234
|
+
TG_GC 90
|
235
|
+
TG_GG inf
|
236
|
+
TG_GT inf
|
237
|
+
TG_TA inf
|
238
|
+
TG_TC 169
|
239
|
+
TG_TG inf
|
240
|
+
TG_TT inf
|
241
|
+
TT_AA inf
|
242
|
+
TT_AC 12
|
243
|
+
TT_AG 98
|
244
|
+
TT_AT 89
|
245
|
+
TT_CA 17
|
246
|
+
TT_CC inf
|
247
|
+
TT_CG inf
|
248
|
+
TT_CT inf
|
249
|
+
TT_GA 87
|
250
|
+
TT_GC inf
|
251
|
+
TT_GG inf
|
252
|
+
TT_GT inf
|
253
|
+
TT_TA 65
|
254
|
+
TT_TC inf
|
255
|
+
TT_TG inf
|
256
|
+
TT_TT inf
|