bio-polymarker 1.3.2

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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 +1,934 @@
1
+ IWGSC_CSS_3DL_scaff_6953496 6703 29 6703 6704
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+ IWGSC_CSS_3AL_scaff_4449935 6868 6762 6868 6869
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+ IWGSC_CSS_3B_scaff_10395023 11761 13660 11761 11762
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+ IWGSC_CSS_2DL_scaff_9907526 12925 25451 12925 12926
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+ IWGSC_CSS_2DL_scaff_9906638 10931 62158 10931 10932
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+ IWGSC_CSS_5DL_scaff_4508109 14875 73119 14875 14876
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+ IWGSC_CSS_6DL_scaff_3307803 13359 88024 13359 13360
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+ IWGSC_CSS_2BL_scaff_8054628 2283 101413 2283 2284
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+ IWGSC_CSS_7DL_scaff_3393324 16264 103726 16264 16265
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+ IWGSC_CSS_7BL_scaff_6721572 11516 131068 11516 11517
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+ IWGSC_CSS_7BL_scaff_6697193 5077 142614 5077 5078
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+ IWGSC_CSS_4BS_scaff_4882177 13064 147721 13064 13065
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+ IWGSC_CSS_4DS_scaff_2297180 13452 160815 13452 13453
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+ IWGSC_CSS_4AL_scaff_7147639 12724 174297 12724 12725
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+ IWGSC_CSS_6AL_scaff_5823017 28879 187051 28879 28880
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+ IWGSC_CSS_6DL_scaff_3268882 37447 215960 37447 37448
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+ IWGSC_CSS_3DS_scaff_1863191 1805 278959 1805 1806
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+ IWGSC_CSS_4BL_scaff_7039462 3174 282573 3174 3175
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+ IWGSC_CSS_3AS_scaff_3383296 4218 285777 4218 4219
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+ IWGSC_CSS_3DS_scaff_2593977 8941 290025 8941 8942
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+ IWGSC_CSS_7AL_scaff_4521010 3503 302331 3503 3504
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+ IWGSC_CSS_1DS_scaff_1910168 7186 305864 7186 7187
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+ IWGSC_CSS_1AS_scaff_1346349 1693 313080 1693 1694
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+ IWGSC_CSS_1BS_scaff_3257204 6485 314803 6485 6486
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+ IWGSC_CSS_1BS_scaff_3447578 18201 325296 18201 18202
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+ IWGSC_CSS_1DS_scaff_1912151 19999 343527 19999 20000
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+ IWGSC_CSS_1AS_scaff_2605671 6873 390348 6873 6874
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+ IWGSC_CSS_2BL_scaff_7621328 5069 418404 5069 5070
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+ IWGSC_CSS_5DS_scaff_2736327 6626 460692 6626 6627
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+ IWGSC_CSS_1AS_scaff_3315513 9914 482284 9914 9915
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+ IWGSC_CSS_1DS_scaff_1915326 15620 492228 15620 15621
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+ IWGSC_CSS_2AS_scaff_5234765 24510 507878 24510 24511
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+ IWGSC_CSS_2BS_scaff_5140219 8244 532418 8244 8245
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+ IWGSC_CSS_2DS_scaff_5340282 9582 540692 9582 9583
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+ IWGSC_CSS_5DL_scaff_4513874 830 585065 830 831
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+ IWGSC_CSS_5BL_scaff_10788634 3133 591772 3133 3134
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+ IWGSC_CSS_6BS_scaff_2964498 7567 594935 7567 7568
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+ IWGSC_CSS_7BS_scaff_3138303 1581 678093 1581 1582
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+ IWGSC_CSS_7DS_scaff_3962950 1943 684930 1943 1944
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+ IWGSC_CSS_7AS_scaff_4178357 1434 686903 1434 1435
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+ IWGSC_CSS_7BS_scaff_3165063 2601 690353 2601 2602
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+ IWGSC_CSS_1DL_scaff_1188116 261 706019 261 262
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+ IWGSC_CSS_6AS_scaff_4424626 25020 706310 25020 25021
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+ IWGSC_CSS_4BS_scaff_4960021 11323 731360 11323 11324
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+ IWGSC_CSS_4AL_scaff_7175863 9486 742713 9486 9487
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+ IWGSC_CSS_7BL_scaff_6743657 3291 752229 3291 3292
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+ IWGSC_CSS_5BS_scaff_2294273 8529 755550 8529 8530
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+ IWGSC_CSS_2DL_scaff_9907353 5531 764109 5531 5532
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+ IWGSC_CSS_5DL_scaff_4494286 8826 785127 8826 8827
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+ IWGSC_CSS_5AL_scaff_2765649 10462 793983 10462 10463
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+ IWGSC_CSS_5BL_scaff_10807255 6740 804476 6740 6741
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+ IWGSC_CSS_2BS_scaff_1261333 293 811246 293 294
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+ IWGSC_CSS_4DL_scaff_14312177 17932 844747 17932 17933
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+ IWGSC_CSS_4AL_scaff_4984961 13096 862709 13096 13097
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+ IWGSC_CSS_1DS_scaff_1891653 5050 875835 5050 5051
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+ IWGSC_CSS_1DS_scaff_1875577 17011 880915 17011 17012
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+ IWGSC_CSS_1BS_scaff_3472221 11325 897956 11325 11326
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+ IWGSC_CSS_1AS_scaff_3254020 18003 909311 18003 18004
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+ IWGSC_CSS_1AL_scaff_3876593 14292 927344 14292 14293
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+ IWGSC_CSS_2DL_scaff_9906668 10397 961735 10397 10398
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+ IWGSC_CSS_2AL_scaff_6391883 11910 972162 11910 11911
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+ IWGSC_CSS_2BL_scaff_8092637 14338 984102 14338 14339
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+ IWGSC_CSS_2AS_scaff_5210977 14038 1021779 14038 14039
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+ IWGSC_CSS_2AS_scaff_5267865 11618 1077342 11618 11619
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+ IWGSC_CSS_1BS_scaff_395893 3313 8556366 3313 3314
909
+ IWGSC_CSS_1BS_scaff_3432692 6654 8559709 6654 6655
910
+ IWGSC_CSS_1DS_scaff_1285932 1032 8566393 1032 1033
911
+ IWGSC_CSS_5BL_scaff_1287393 349 8567455 349 350
912
+ IWGSC_CSS_1DS_scaff_1285904 491 8567834 491 492
913
+ IWGSC_CSS_3B_scaff_10396096 571 8568355 571 572
914
+ IWGSC_CSS_1DS_scaff_1914681 22229 8568956 22229 22230
915
+ IWGSC_CSS_1AS_scaff_3274088 33473 8591215 33473 33474
916
+ IWGSC_CSS_1AL_scaff_3926846 6504 8624718 6504 6505
917
+ IWGSC_CSS_1BL_scaff_3902666 11608 8631252 11608 11609
918
+ IWGSC_CSS_1DL_scaff_1726702 4681 8642890 4681 4682
919
+ IWGSC_CSS_1AL_scaff_3904706 5427 8647601 5427 5428
920
+ IWGSC_CSS_4AL_scaff_7062439 4996 8653058 4996 4997
921
+ IWGSC_CSS_7AS_scaff_4256402 12904 8658084 12904 12905
922
+ IWGSC_CSS_7DS_scaff_3856393 6050 8671018 6050 6051
923
+ IWGSC_CSS_3B_scaff_850706 9523 8677096 9523 9524
924
+ IWGSC_CSS_3AL_scaff_4251171 3152 8686649 3152 3153
925
+ IWGSC_CSS_2BS_scaff_5243477 3588 8689831 3588 3589
926
+ IWGSC_CSS_2BS_scaff_5177411 14834 8693449 14834 14835
927
+ IWGSC_CSS_2BS_scaff_5191958 16903 8708313 16903 16904
928
+ IWGSC_CSS_3AL_scaff_3773074 5903 8725246 5903 5904
929
+ IWGSC_CSS_3B_scaff_10743253 14514 8731179 14514 14515
930
+ IWGSC_CSS_3B_scaff_10479023 3044 8745723 3044 3045
931
+ IWGSC_CSS_3B_scaff_10776910 8482 8748797 8482 8483
932
+ IWGSC_CSS_3DL_scaff_6918534 8972 8757309 8972 8973
933
+ IWGSC_CSS_3DL_scaff_6931631 10584 8766311 10584 10585
934
+ IWGSC_CSS_3AL_scaff_375972 7161 8776924 7161 7162