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.
Files changed (177) hide show
  1. checksums.yaml +7 -0
  2. data/.travis.yml +24 -0
  3. data/Gemfile +23 -0
  4. data/README.md +205 -0
  5. data/Rakefile +61 -0
  6. data/SECURITY.md +16 -0
  7. data/VERSION +1 -0
  8. data/bin/bfr.rb +128 -0
  9. data/bin/blast_triads.rb +166 -0
  10. data/bin/blast_triads_promoters.rb +192 -0
  11. data/bin/count_variations.rb +36 -0
  12. data/bin/filter_blat_by_target_coverage.rb +69 -0
  13. data/bin/filter_exonerate_by_identity.rb +38 -0
  14. data/bin/find_best_blat_hit.rb +33 -0
  15. data/bin/find_best_exonerate.rb +17 -0
  16. data/bin/get_longest_hsp_blastx_triads.rb +66 -0
  17. data/bin/hexaploid_primers.rb +168 -0
  18. data/bin/homokaryot_primers.rb +183 -0
  19. data/bin/mafft_triads.rb +120 -0
  20. data/bin/mafft_triads_promoters.rb +403 -0
  21. data/bin/map_markers_to_contigs.rb +66 -0
  22. data/bin/marker_to_vcf.rb +241 -0
  23. data/bin/markers_in_region.rb +42 -0
  24. data/bin/mask_triads.rb +169 -0
  25. data/bin/polymarker.rb +410 -0
  26. data/bin/polymarker_capillary.rb +443 -0
  27. data/bin/polymarker_deletions.rb +350 -0
  28. data/bin/snp_position_to_polymarker.rb +101 -0
  29. data/bin/snps_between_bams.rb +107 -0
  30. data/bin/tag_stats.rb +75 -0
  31. data/bin/vcfLineToTable.rb +56 -0
  32. data/bin/vcfToPolyMarker.rb +82 -0
  33. data/bio-polymarker.gemspec +227 -0
  34. data/conf/defaults.rb +1 -0
  35. data/conf/primer3_config/dangle.dh +128 -0
  36. data/conf/primer3_config/dangle.ds +128 -0
  37. data/conf/primer3_config/interpretations/dangle_i.dh +131 -0
  38. data/conf/primer3_config/interpretations/dangle_i.ds +131 -0
  39. data/conf/primer3_config/interpretations/loops_i.dh +34 -0
  40. data/conf/primer3_config/interpretations/loops_i.ds +31 -0
  41. data/conf/primer3_config/interpretations/stack_i.dh +257 -0
  42. data/conf/primer3_config/interpretations/stack_i.ds +256 -0
  43. data/conf/primer3_config/interpretations/stackmm_i_mm.dh +257 -0
  44. data/conf/primer3_config/interpretations/stackmm_i_mm.ds +256 -0
  45. data/conf/primer3_config/interpretations/tetraloop_i.dh +79 -0
  46. data/conf/primer3_config/interpretations/tetraloop_i.ds +81 -0
  47. data/conf/primer3_config/interpretations/triloop_i.dh +21 -0
  48. data/conf/primer3_config/interpretations/triloop_i.ds +18 -0
  49. data/conf/primer3_config/interpretations/tstack2_i.dh +256 -0
  50. data/conf/primer3_config/interpretations/tstack2_i.ds +256 -0
  51. data/conf/primer3_config/interpretations/tstack_i.dh +256 -0
  52. data/conf/primer3_config/interpretations/tstack_i.ds +256 -0
  53. data/conf/primer3_config/interpretations/tstack_tm_inf_i.dh +256 -0
  54. data/conf/primer3_config/interpretations/tstack_tm_inf_i.ds +256 -0
  55. data/conf/primer3_config/loops.dh +30 -0
  56. data/conf/primer3_config/loops.ds +30 -0
  57. data/conf/primer3_config/stack.dh +256 -0
  58. data/conf/primer3_config/stack.ds +256 -0
  59. data/conf/primer3_config/stackmm.dh +256 -0
  60. data/conf/primer3_config/stackmm.ds +256 -0
  61. data/conf/primer3_config/tetraloop.dh +77 -0
  62. data/conf/primer3_config/tetraloop.ds +77 -0
  63. data/conf/primer3_config/triloop.dh +16 -0
  64. data/conf/primer3_config/triloop.ds +16 -0
  65. data/conf/primer3_config/tstack.dh +256 -0
  66. data/conf/primer3_config/tstack2.dh +256 -0
  67. data/conf/primer3_config/tstack2.ds +256 -0
  68. data/conf/primer3_config/tstack_tm_inf.ds +256 -0
  69. data/lib/bio/BFRTools.rb +465 -0
  70. data/lib/bio/BIOExtensions.rb +153 -0
  71. data/lib/bio/PolyploidTools/ChromosomeArm.rb +63 -0
  72. data/lib/bio/PolyploidTools/ExonContainer.rb +245 -0
  73. data/lib/bio/PolyploidTools/Marker.rb +175 -0
  74. data/lib/bio/PolyploidTools/Mask.rb +116 -0
  75. data/lib/bio/PolyploidTools/NoSNPSequence.rb +292 -0
  76. data/lib/bio/PolyploidTools/PrimerRegion.rb +30 -0
  77. data/lib/bio/PolyploidTools/SNP.rb +804 -0
  78. data/lib/bio/PolyploidTools/SNPMutant.rb +86 -0
  79. data/lib/bio/PolyploidTools/SNPSequence.rb +55 -0
  80. data/lib/bio/db/blast.rb +114 -0
  81. data/lib/bio/db/exonerate.rb +333 -0
  82. data/lib/bio/db/primer3.rb +820 -0
  83. data/lib/bio-polymarker.rb +28 -0
  84. data/test/data/7B_amplicon_test.fa +12 -0
  85. data/test/data/7B_amplicon_test.fa.fai +1 -0
  86. data/test/data/7B_amplicon_test_reference.fa +110 -0
  87. data/test/data/7B_amplicon_test_reference.fa.fai +3 -0
  88. data/test/data/7B_marker_test.txt +1 -0
  89. data/test/data/BS00068396_51.fa +2 -0
  90. data/test/data/BS00068396_51_blast.tab +4 -0
  91. data/test/data/BS00068396_51_contigs.aln +1412 -0
  92. data/test/data/BS00068396_51_contigs.dnd +7 -0
  93. data/test/data/BS00068396_51_contigs.fa +8 -0
  94. data/test/data/BS00068396_51_contigs.fa.fai +4 -0
  95. data/test/data/BS00068396_51_contigs.fa.nhr +0 -0
  96. data/test/data/BS00068396_51_contigs.fa.nin +0 -0
  97. data/test/data/BS00068396_51_contigs.fa.nsq +0 -0
  98. data/test/data/BS00068396_51_contigs.nhr +0 -0
  99. data/test/data/BS00068396_51_contigs.nin +0 -0
  100. data/test/data/BS00068396_51_contigs.nsq +0 -0
  101. data/test/data/BS00068396_51_exonerate.tab +6 -0
  102. data/test/data/BS00068396_51_for_polymarker.txt +1 -0
  103. data/test/data/BS00068396_51_genes.txt +14 -0
  104. data/test/data/IWGSC_CSS_1AL_scaff_1455974.fa +112 -0
  105. data/test/data/IWGSC_CSS_1AL_scaff_1455974_aln_contigs.fa +2304 -0
  106. data/test/data/IWGSC_CSS_1AL_scaff_1455974_aln_contigs.fa.fai +11 -0
  107. data/test/data/LIB1716.bam +0 -0
  108. data/test/data/LIB1716.bam.bai +0 -0
  109. data/test/data/LIB1719.bam +0 -0
  110. data/test/data/LIB1719.bam.bai +0 -0
  111. data/test/data/LIB1721.bam +0 -0
  112. data/test/data/LIB1721.bam.bai +0 -0
  113. data/test/data/LIB1722.bam +0 -0
  114. data/test/data/LIB1722.bam.bai +0 -0
  115. data/test/data/PST130_7067.csv +1 -0
  116. data/test/data/PST130_7067.fa +2 -0
  117. data/test/data/PST130_7067.fa.fai +1 -0
  118. data/test/data/PST130_7067.fa.ndb +0 -0
  119. data/test/data/PST130_7067.fa.nhr +0 -0
  120. data/test/data/PST130_7067.fa.nin +0 -0
  121. data/test/data/PST130_7067.fa.not +0 -0
  122. data/test/data/PST130_7067.fa.nsq +0 -0
  123. data/test/data/PST130_7067.fa.ntf +0 -0
  124. data/test/data/PST130_7067.fa.nto +0 -0
  125. data/test/data/PST130_reverse_primer.csv +1 -0
  126. data/test/data/S22380157.fa +16 -0
  127. data/test/data/S22380157.fa.fai +1 -0
  128. data/test/data/S22380157.vcf +67 -0
  129. data/test/data/S58861868/LIB1716.bam +0 -0
  130. data/test/data/S58861868/LIB1716.sam +651 -0
  131. data/test/data/S58861868/LIB1719.bam +0 -0
  132. data/test/data/S58861868/LIB1719.sam +805 -0
  133. data/test/data/S58861868/LIB1721.bam +0 -0
  134. data/test/data/S58861868/LIB1721.sam +1790 -0
  135. data/test/data/S58861868/LIB1722.bam +0 -0
  136. data/test/data/S58861868/LIB1722.sam +1271 -0
  137. data/test/data/S58861868/S58861868.fa +16 -0
  138. data/test/data/S58861868/S58861868.fa.fai +1 -0
  139. data/test/data/S58861868/S58861868.vcf +76 -0
  140. data/test/data/S58861868/header.txt +9 -0
  141. data/test/data/S58861868/merged.bam +0 -0
  142. data/test/data/S58861868/merged_reheader.bam +0 -0
  143. data/test/data/S58861868/merged_reheader.bam.bai +0 -0
  144. data/test/data/Test3Aspecific.csv +2 -0
  145. data/test/data/Test3Aspecific_contigs.fa +6 -0
  146. data/test/data/bfr_out_test.csv +5 -0
  147. data/test/data/chr1A_C1145499T/chr1A_C1145499T.csv +1 -0
  148. data/test/data/chr1A_G540414846C/chr1A_G540414846C.csv +1 -0
  149. data/test/data/chr1A_G540414846C/chr1A_G540414846C.fa +2 -0
  150. data/test/data/chr1A_T517634750C/chr1A_T517634750C.csv +1 -0
  151. data/test/data/chr2D_C112180134A/chr2D_C112180134A.csv +1 -0
  152. data/test/data/chr4D_C14473543T/chr4D_C14473543T.csv +1 -0
  153. data/test/data/chr4D_C14473543T/chr4D_C14473543T.fa +2 -0
  154. data/test/data/headerMergeed.txt +9 -0
  155. data/test/data/headerS2238015 +1 -0
  156. data/test/data/mergedLibs.bam +0 -0
  157. data/test/data/mergedLibsReheader.bam +0 -0
  158. data/test/data/mergedLibsSorted.bam +0 -0
  159. data/test/data/mergedLibsSorted.bam.bai +0 -0
  160. data/test/data/patological_cases5D.csv +1 -0
  161. data/test/data/primer_3_input_header_test +5 -0
  162. data/test/data/short_primer_design_test.csv +10 -0
  163. data/test/data/some_tests/some_tests.csv +201 -0
  164. data/test/data/test_from_mutant.csv +3 -0
  165. data/test/data/test_iselect.csv +196 -0
  166. data/test/data/test_iselect_reference.fa +1868 -0
  167. data/test/data/test_iselect_reference.fa.fai +934 -0
  168. data/test/data/test_primer3_error.csv +4 -0
  169. data/test/data/test_primer3_error_contigs.fa +10 -0
  170. data/test/test_bfr.rb +135 -0
  171. data/test/test_blast.rb +47 -0
  172. data/test/test_exon_container.rb +17 -0
  173. data/test/test_exonearate.rb +48 -0
  174. data/test/test_integration.rb +76 -0
  175. data/test/test_snp_parsing.rb +121 -0
  176. data/test/test_wrong_selection.sh +5 -0
  177. metadata +356 -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 0
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 0
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 0
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 0
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 0
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 0
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 0
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 0
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 0
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 0
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 0
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 0
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 0
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 0
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 0
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 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
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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
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119
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120
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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
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137
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138
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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
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179
+ GT_AG inf
180
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181
+ GT_CA inf
182
+ GT_CC 78
183
+ GT_CG 161
184
+ GT_CT 212
185
+ GT_GA 21
186
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187
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188
+ GT_GT inf
189
+ GT_TA 94
190
+ GT_TC inf
191
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192
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193
+ TA_AA 63
194
+ TA_AC 59
195
+ TA_AG 47
196
+ TA_AT inf
197
+ TA_CA inf
198
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199
+ TA_CG inf
200
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201
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202
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203
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204
+ TA_GT 105
205
+ TA_TA inf
206
+ TA_TC inf
207
+ TA_TG inf
208
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209
+ TC_AA 70
210
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211
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212
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213
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214
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215
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216
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217
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218
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219
+ TC_GG 159
220
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221
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222
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223
+ TC_TG 212
224
+ TC_TT inf
225
+ TG_AA 58
226
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227
+ TG_AG 27
228
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229
+ TG_CA inf
230
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231
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232
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233
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234
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235
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236
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237
+ TG_TA inf
238
+ TG_TC 169
239
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240
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241
+ TT_AA inf
242
+ TT_AC 12
243
+ TT_AG 98
244
+ TT_AT 89
245
+ TT_CA 17
246
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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