partis-bcr 1.0.11__cp312-cp312-macosx_10_13_universal2.whl → 1.0.11.post1.dev7__cp312-cp312-macosx_10_13_universal2.whl

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 (644) hide show
  1. bin/partis +1 -1
  2. bin/partis-test.py +6 -0
  3. bin/partis.py +1 -1
  4. {partis_bcr-1.0.11.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/partis-test.py +6 -0
  5. {partis_bcr-1.0.11.dist-info → partis_bcr-1.0.11.post1.dev7.dist-info}/METADATA +1 -1
  6. {partis_bcr-1.0.11.dist-info → partis_bcr-1.0.11.post1.dev7.dist-info}/RECORD +644 -126
  7. python/recombinator.py +2 -0
  8. python/treegenerator.py +1 -1
  9. test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/d_3p_del.csv +7 -0
  10. test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/d_5p_del.csv +8 -0
  11. test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/dj_insertion.csv +8 -0
  12. test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/fv_insertion.csv +10 -0
  13. test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/j_3p_del.csv +4 -0
  14. test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/j_5p_del.csv +8 -0
  15. test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/jf_insertion.csv +4 -0
  16. test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/shm_indel_length.csv +8 -0
  17. test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/v_3p_del.csv +4 -0
  18. test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/v_5p_del.csv +4 -0
  19. test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/vd_insertion.csv +8 -0
  20. test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/d_allele_fraction_correct_vs_per_gene_support.csv +28 -0
  21. test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/d_fraction_correct_vs_mute_freq.csv +28 -0
  22. test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/d_gene.csv +5 -0
  23. test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/j_allele_fraction_correct_vs_per_gene_support.csv +28 -0
  24. test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/j_fraction_correct_vs_mute_freq.csv +28 -0
  25. test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/j_gene.csv +5 -0
  26. test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/v_allele_fraction_correct_vs_per_gene_support.csv +28 -0
  27. test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/v_fraction_correct_vs_mute_freq.csv +28 -0
  28. test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/v_gene.csv +5 -0
  29. test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/cdr3_hamming_to_true_naive.csv +7 -0
  30. test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/cdr3_muted_bases.csv +7 -0
  31. test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/d_hamming_to_true_naive.csv +5 -0
  32. test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/d_muted_bases.csv +6 -0
  33. test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/hamming_to_true_naive.csv +7 -0
  34. test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/j_hamming_to_true_naive.csv +4 -0
  35. test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/j_muted_bases.csv +5 -0
  36. test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/mute_freqs.csv +28 -0
  37. test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/muted_bases.csv +7 -0
  38. test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/v_hamming_to_true_naive.csv +4 -0
  39. test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/v_muted_bases.csv +4 -0
  40. test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/d_3p_del.csv +8 -0
  41. test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/d_5p_del.csv +6 -0
  42. test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/dj_insertion.csv +7 -0
  43. test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/fv_insertion.csv +4 -0
  44. test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/j_3p_del.csv +4 -0
  45. test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/j_5p_del.csv +9 -0
  46. test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/jf_insertion.csv +4 -0
  47. test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/shm_indel_length.csv +8 -0
  48. test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/v_3p_del.csv +4 -0
  49. test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/v_5p_del.csv +4 -0
  50. test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/vd_insertion.csv +6 -0
  51. test/new-results/annotate-new-simu-annotation-performance/sw/gene-call/d_fraction_correct_vs_mute_freq.csv +28 -0
  52. test/new-results/annotate-new-simu-annotation-performance/sw/gene-call/d_gene.csv +5 -0
  53. test/new-results/annotate-new-simu-annotation-performance/sw/gene-call/j_fraction_correct_vs_mute_freq.csv +28 -0
  54. test/new-results/annotate-new-simu-annotation-performance/sw/gene-call/j_gene.csv +5 -0
  55. test/new-results/annotate-new-simu-annotation-performance/sw/gene-call/v_fraction_correct_vs_mute_freq.csv +28 -0
  56. test/new-results/annotate-new-simu-annotation-performance/sw/gene-call/v_gene.csv +5 -0
  57. test/new-results/annotate-new-simu-annotation-performance/sw/mutation/cdr3_hamming_to_true_naive.csv +6 -0
  58. test/new-results/annotate-new-simu-annotation-performance/sw/mutation/cdr3_muted_bases.csv +7 -0
  59. test/new-results/annotate-new-simu-annotation-performance/sw/mutation/d_hamming_to_true_naive.csv +5 -0
  60. test/new-results/annotate-new-simu-annotation-performance/sw/mutation/d_muted_bases.csv +5 -0
  61. test/new-results/annotate-new-simu-annotation-performance/sw/mutation/hamming_to_true_naive.csv +6 -0
  62. test/new-results/annotate-new-simu-annotation-performance/sw/mutation/j_hamming_to_true_naive.csv +4 -0
  63. test/new-results/annotate-new-simu-annotation-performance/sw/mutation/j_muted_bases.csv +6 -0
  64. test/new-results/annotate-new-simu-annotation-performance/sw/mutation/mute_freqs.csv +28 -0
  65. test/new-results/annotate-new-simu-annotation-performance/sw/mutation/muted_bases.csv +7 -0
  66. test/new-results/annotate-new-simu-annotation-performance/sw/mutation/v_hamming_to_true_naive.csv +4 -0
  67. test/new-results/annotate-new-simu-annotation-performance/sw/mutation/v_muted_bases.csv +4 -0
  68. test/new-results/annotate-new-simu.yaml +1 -0
  69. test/new-results/cache-new-partition.csv +59 -0
  70. test/new-results/get-selection-metrics-new-simu.yaml +1 -0
  71. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/d_3p_del.csv +7 -0
  72. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/d_5p_del.csv +6 -0
  73. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/dj_insertion.csv +8 -0
  74. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/fv_insertion.csv +10 -0
  75. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/j_3p_del.csv +4 -0
  76. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/j_5p_del.csv +8 -0
  77. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/jf_insertion.csv +4 -0
  78. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/shm_indel_length.csv +8 -0
  79. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/v_3p_del.csv +4 -0
  80. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/v_5p_del.csv +4 -0
  81. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/vd_insertion.csv +6 -0
  82. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/gene-call/d_allele_fraction_correct_vs_per_gene_support.csv +28 -0
  83. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/gene-call/d_fraction_correct_vs_mute_freq.csv +28 -0
  84. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/gene-call/d_gene.csv +5 -0
  85. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/gene-call/j_allele_fraction_correct_vs_per_gene_support.csv +28 -0
  86. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/gene-call/j_fraction_correct_vs_mute_freq.csv +28 -0
  87. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/gene-call/j_gene.csv +5 -0
  88. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/gene-call/v_allele_fraction_correct_vs_per_gene_support.csv +28 -0
  89. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/gene-call/v_fraction_correct_vs_mute_freq.csv +28 -0
  90. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/gene-call/v_gene.csv +5 -0
  91. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/cdr3_hamming_to_true_naive.csv +5 -0
  92. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/cdr3_muted_bases.csv +5 -0
  93. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/d_hamming_to_true_naive.csv +4 -0
  94. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/d_muted_bases.csv +4 -0
  95. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/hamming_to_true_naive.csv +5 -0
  96. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/j_hamming_to_true_naive.csv +4 -0
  97. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/j_muted_bases.csv +5 -0
  98. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/mute_freqs.csv +28 -0
  99. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/muted_bases.csv +5 -0
  100. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/v_hamming_to_true_naive.csv +4 -0
  101. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/v_muted_bases.csv +4 -0
  102. test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/d_3p_del.csv +8 -0
  103. test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/d_5p_del.csv +6 -0
  104. test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/dj_insertion.csv +7 -0
  105. test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/fv_insertion.csv +4 -0
  106. test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/j_3p_del.csv +4 -0
  107. test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/j_5p_del.csv +9 -0
  108. test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/jf_insertion.csv +4 -0
  109. test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/shm_indel_length.csv +8 -0
  110. test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/v_3p_del.csv +4 -0
  111. test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/v_5p_del.csv +4 -0
  112. test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/vd_insertion.csv +6 -0
  113. test/new-results/multi-annotate-new-simu-annotation-performance/sw/gene-call/d_fraction_correct_vs_mute_freq.csv +28 -0
  114. test/new-results/multi-annotate-new-simu-annotation-performance/sw/gene-call/d_gene.csv +5 -0
  115. test/new-results/multi-annotate-new-simu-annotation-performance/sw/gene-call/j_fraction_correct_vs_mute_freq.csv +28 -0
  116. test/new-results/multi-annotate-new-simu-annotation-performance/sw/gene-call/j_gene.csv +5 -0
  117. test/new-results/multi-annotate-new-simu-annotation-performance/sw/gene-call/v_fraction_correct_vs_mute_freq.csv +28 -0
  118. test/new-results/multi-annotate-new-simu-annotation-performance/sw/gene-call/v_gene.csv +5 -0
  119. test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/cdr3_hamming_to_true_naive.csv +6 -0
  120. test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/cdr3_muted_bases.csv +7 -0
  121. test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/d_hamming_to_true_naive.csv +5 -0
  122. test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/d_muted_bases.csv +5 -0
  123. test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/hamming_to_true_naive.csv +6 -0
  124. test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/j_hamming_to_true_naive.csv +4 -0
  125. test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/j_muted_bases.csv +6 -0
  126. test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/mute_freqs.csv +28 -0
  127. test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/muted_bases.csv +7 -0
  128. test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/v_hamming_to_true_naive.csv +4 -0
  129. test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/v_muted_bases.csv +4 -0
  130. test/new-results/multi-annotate-new-simu.yaml +1 -0
  131. test/new-results/partition-new-simu/fasttree/iclust-0/fasttree.out +1 -0
  132. test/new-results/partition-new-simu/fasttree/iclust-0/input-seqs.fa +24 -0
  133. test/new-results/partition-new-simu/fasttree/iclust-0/log +23 -0
  134. test/new-results/partition-new-simu/fasttree/iclust-1/fasttree.out +1 -0
  135. test/new-results/partition-new-simu/fasttree/iclust-1/input-seqs.fa +16 -0
  136. test/new-results/partition-new-simu/fasttree/iclust-1/log +23 -0
  137. test/new-results/partition-new-simu/fasttree/iclust-2/fasttree.out +1 -0
  138. test/new-results/partition-new-simu/fasttree/iclust-2/input-seqs.fa +16 -0
  139. test/new-results/partition-new-simu/fasttree/iclust-2/log +22 -0
  140. test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/d_3p_del.csv +7 -0
  141. test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/d_5p_del.csv +6 -0
  142. test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/dj_insertion.csv +8 -0
  143. test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/fv_insertion.csv +10 -0
  144. test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/j_3p_del.csv +4 -0
  145. test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/j_5p_del.csv +8 -0
  146. test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/jf_insertion.csv +4 -0
  147. test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/shm_indel_length.csv +8 -0
  148. test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/v_3p_del.csv +4 -0
  149. test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/v_5p_del.csv +4 -0
  150. test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/vd_insertion.csv +6 -0
  151. test/new-results/partition-new-simu-annotation-performance/hmm/gene-call/d_allele_fraction_correct_vs_per_gene_support.csv +28 -0
  152. test/new-results/partition-new-simu-annotation-performance/hmm/gene-call/d_fraction_correct_vs_mute_freq.csv +28 -0
  153. test/new-results/partition-new-simu-annotation-performance/hmm/gene-call/d_gene.csv +5 -0
  154. test/new-results/partition-new-simu-annotation-performance/hmm/gene-call/j_allele_fraction_correct_vs_per_gene_support.csv +28 -0
  155. test/new-results/partition-new-simu-annotation-performance/hmm/gene-call/j_fraction_correct_vs_mute_freq.csv +28 -0
  156. test/new-results/partition-new-simu-annotation-performance/hmm/gene-call/j_gene.csv +5 -0
  157. test/new-results/partition-new-simu-annotation-performance/hmm/gene-call/v_allele_fraction_correct_vs_per_gene_support.csv +28 -0
  158. test/new-results/partition-new-simu-annotation-performance/hmm/gene-call/v_fraction_correct_vs_mute_freq.csv +28 -0
  159. test/new-results/partition-new-simu-annotation-performance/hmm/gene-call/v_gene.csv +5 -0
  160. test/new-results/partition-new-simu-annotation-performance/hmm/mutation/cdr3_hamming_to_true_naive.csv +5 -0
  161. test/new-results/partition-new-simu-annotation-performance/hmm/mutation/cdr3_muted_bases.csv +5 -0
  162. test/new-results/partition-new-simu-annotation-performance/hmm/mutation/d_hamming_to_true_naive.csv +4 -0
  163. test/new-results/partition-new-simu-annotation-performance/hmm/mutation/d_muted_bases.csv +4 -0
  164. test/new-results/partition-new-simu-annotation-performance/hmm/mutation/hamming_to_true_naive.csv +5 -0
  165. test/new-results/partition-new-simu-annotation-performance/hmm/mutation/j_hamming_to_true_naive.csv +4 -0
  166. test/new-results/partition-new-simu-annotation-performance/hmm/mutation/j_muted_bases.csv +5 -0
  167. test/new-results/partition-new-simu-annotation-performance/hmm/mutation/mute_freqs.csv +28 -0
  168. test/new-results/partition-new-simu-annotation-performance/hmm/mutation/muted_bases.csv +5 -0
  169. test/new-results/partition-new-simu-annotation-performance/hmm/mutation/v_hamming_to_true_naive.csv +4 -0
  170. test/new-results/partition-new-simu-annotation-performance/hmm/mutation/v_muted_bases.csv +4 -0
  171. test/new-results/partition-new-simu-annotation-performance/sw/boundaries/d_3p_del.csv +8 -0
  172. test/new-results/partition-new-simu-annotation-performance/sw/boundaries/d_5p_del.csv +6 -0
  173. test/new-results/partition-new-simu-annotation-performance/sw/boundaries/dj_insertion.csv +7 -0
  174. test/new-results/partition-new-simu-annotation-performance/sw/boundaries/fv_insertion.csv +4 -0
  175. test/new-results/partition-new-simu-annotation-performance/sw/boundaries/j_3p_del.csv +4 -0
  176. test/new-results/partition-new-simu-annotation-performance/sw/boundaries/j_5p_del.csv +9 -0
  177. test/new-results/partition-new-simu-annotation-performance/sw/boundaries/jf_insertion.csv +4 -0
  178. test/new-results/partition-new-simu-annotation-performance/sw/boundaries/shm_indel_length.csv +8 -0
  179. test/new-results/partition-new-simu-annotation-performance/sw/boundaries/v_3p_del.csv +4 -0
  180. test/new-results/partition-new-simu-annotation-performance/sw/boundaries/v_5p_del.csv +4 -0
  181. test/new-results/partition-new-simu-annotation-performance/sw/boundaries/vd_insertion.csv +6 -0
  182. test/new-results/partition-new-simu-annotation-performance/sw/gene-call/d_fraction_correct_vs_mute_freq.csv +28 -0
  183. test/new-results/partition-new-simu-annotation-performance/sw/gene-call/d_gene.csv +5 -0
  184. test/new-results/partition-new-simu-annotation-performance/sw/gene-call/j_fraction_correct_vs_mute_freq.csv +28 -0
  185. test/new-results/partition-new-simu-annotation-performance/sw/gene-call/j_gene.csv +5 -0
  186. test/new-results/partition-new-simu-annotation-performance/sw/gene-call/v_fraction_correct_vs_mute_freq.csv +28 -0
  187. test/new-results/partition-new-simu-annotation-performance/sw/gene-call/v_gene.csv +5 -0
  188. test/new-results/partition-new-simu-annotation-performance/sw/mutation/cdr3_hamming_to_true_naive.csv +6 -0
  189. test/new-results/partition-new-simu-annotation-performance/sw/mutation/cdr3_muted_bases.csv +7 -0
  190. test/new-results/partition-new-simu-annotation-performance/sw/mutation/d_hamming_to_true_naive.csv +5 -0
  191. test/new-results/partition-new-simu-annotation-performance/sw/mutation/d_muted_bases.csv +5 -0
  192. test/new-results/partition-new-simu-annotation-performance/sw/mutation/hamming_to_true_naive.csv +6 -0
  193. test/new-results/partition-new-simu-annotation-performance/sw/mutation/j_hamming_to_true_naive.csv +4 -0
  194. test/new-results/partition-new-simu-annotation-performance/sw/mutation/j_muted_bases.csv +6 -0
  195. test/new-results/partition-new-simu-annotation-performance/sw/mutation/mute_freqs.csv +28 -0
  196. test/new-results/partition-new-simu-annotation-performance/sw/mutation/muted_bases.csv +7 -0
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  632. test/trees.nwk +100 -0
  633. {partis_bcr-1.0.11.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/cf-alleles.py +0 -0
  634. {partis_bcr-1.0.11.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/cf-germlines.py +0 -0
  635. {partis_bcr-1.0.11.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/compare-plotdirs.py +0 -0
  636. {partis_bcr-1.0.11.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/extract-pairing-info.py +0 -0
  637. {partis_bcr-1.0.11.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/gctree-run.py +0 -0
  638. {partis_bcr-1.0.11.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/get-naive-probabilities.py +0 -0
  639. {partis_bcr-1.0.11.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/parse-output.py +0 -0
  640. {partis_bcr-1.0.11.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/split-loci.py +0 -0
  641. {partis_bcr-1.0.11.dist-info → partis_bcr-1.0.11.post1.dev7.dist-info}/WHEEL +0 -0
  642. {partis_bcr-1.0.11.dist-info → partis_bcr-1.0.11.post1.dev7.dist-info}/entry_points.txt +0 -0
  643. {partis_bcr-1.0.11.dist-info → partis_bcr-1.0.11.post1.dev7.dist-info}/licenses/COPYING +0 -0
  644. {partis_bcr-1.0.11.dist-info → partis_bcr-1.0.11.post1.dev7.dist-info}/top_level.txt +0 -0
test/new-results/test/parameters/simu/sw/hmms/IGHV3-23_star_01.yaml ADDED
@@ -0,0 +1,4484 @@
1
+ !!python/object:python.hmmwriter.HMM
2
+ extras:
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+ gene_prob: 0.05555555555555555
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+ overall_mute_freq: 0.012222222222222223
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+ per_gene_mute_freq: 0.11408509852555
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+ name: IGHV3-23_star_01
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+ states:
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+ - !!python/object:python.hmmwriter.State
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+ emissions: null
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+ extras: {}
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+ name: init
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+ transitions:
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+ IGHV3-23_star_01_0: 0.6666666666666666
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+ insert_left_N: 0.33333333333333337
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+ - !!python/object:python.hmmwriter.State
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+ emissions:
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+ C: 0.25
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+ track: nukes
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+ extras:
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+ ambiguous_char: N
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+ ambiguous_emission_prob: 0.25
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+ germline: N
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+ name: insert_left_N
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+ transitions:
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+ IGHV3-23_star_01_0: 0.6666666666666666
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+ insert_left_N: 0.33333333333333337
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+ - !!python/object:python.hmmwriter.State
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+ emissions:
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+ germline: G
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+ name: IGHV3-23_star_01_0
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+ transitions:
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+ IGHV3-23_star_01_1: 1.0
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+ - !!python/object:python.hmmwriter.State
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+ emissions:
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+ ambiguous_char: N
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+ germline: A
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+ name: IGHV3-23_star_01_1
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+ transitions:
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+ IGHV3-23_star_01_2: 1.0
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+ - !!python/object:python.hmmwriter.State
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+ emissions:
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+ ambiguous_char: N
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+ ambiguous_emission_prob: 0.25
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+ germline: G
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+ name: IGHV3-23_star_01_2
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+ transitions:
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+ IGHV3-23_star_01_3: 1.0
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+ - !!python/object:python.hmmwriter.State
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+ emissions:
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+ germline: G
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+ name: IGHV3-23_star_01_3
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+ transitions:
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+ IGHV3-23_star_01_4: 1.0
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+ - !!python/object:python.hmmwriter.State
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+ emissions:
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+ ambiguous_char: N
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+ ambiguous_emission_prob: 0.25
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+ germline: T
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+ name: IGHV3-23_star_01_4
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+ transitions:
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+ IGHV3-23_star_01_5: 1.0
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+ - !!python/object:python.hmmwriter.State
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+ emissions:
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+ IGHV3-23_star_01_6: 1.0
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+ IGHV3-23_star_01_7: 1.0
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+ - !!python/object:python.hmmwriter.State
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+ name: IGHV3-23_star_01_7
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+ transitions:
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+ IGHV3-23_star_01_8: 1.0
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+ - !!python/object:python.hmmwriter.State
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+ emissions:
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+ name: IGHV3-23_star_01_8
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+ transitions:
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+ IGHV3-23_star_01_9: 1.0
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+ - !!python/object:python.hmmwriter.State
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+ emissions:
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+ name: IGHV3-23_star_01_9
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+ IGHV3-23_star_01_10: 1.0
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+ - !!python/object:python.hmmwriter.State
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+ emissions:
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+ ambiguous_char: N
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+ ambiguous_emission_prob: 0.25
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+ germline: T
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+ name: IGHV3-23_star_01_10
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+ transitions:
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+ IGHV3-23_star_01_11: 1.0
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+ - !!python/object:python.hmmwriter.State
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+ emissions:
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+ ambiguous_char: N
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+ ambiguous_emission_prob: 0.25
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+ germline: G
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+ name: IGHV3-23_star_01_11
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+ transitions:
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+ IGHV3-23_star_01_12: 1.0
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+ - !!python/object:python.hmmwriter.State
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+ emissions:
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+ ambiguous_char: N
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+ germline: T
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+ name: IGHV3-23_star_01_12
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+ transitions:
225
+ IGHV3-23_star_01_13: 1.0
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+ - !!python/object:python.hmmwriter.State
227
+ emissions:
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+ name: IGHV3-23_star_01_13
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+ IGHV3-23_star_01_14: 1.0
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+ - !!python/object:python.hmmwriter.State
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+ emissions:
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+ name: IGHV3-23_star_01_14
254
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255
+ IGHV3-23_star_01_15: 1.0
256
+ - !!python/object:python.hmmwriter.State
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+ emissions:
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+ name: IGHV3-23_star_01_15
269
+ transitions:
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+ IGHV3-23_star_01_16: 1.0
271
+ - !!python/object:python.hmmwriter.State
272
+ emissions:
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+ IGHV3-23_star_01_17: 1.0
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+ - !!python/object:python.hmmwriter.State
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+ emissions:
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300
+ IGHV3-23_star_01_18: 1.0
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+ - !!python/object:python.hmmwriter.State
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+ emissions:
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561
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571
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576
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620
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635
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650
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659
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661
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662
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665
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674
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704
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706
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749
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767
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779
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794
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796
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809
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1097
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1115
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1116
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1117
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1118
+ track: nukes
1119
+ extras:
1120
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1121
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1122
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1123
+ name: IGHV3-23_star_01_72
1124
+ transitions:
1125
+ IGHV3-23_star_01_73: 1.0
1126
+ - !!python/object:python.hmmwriter.State
1127
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1128
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1129
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1130
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1131
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1132
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1133
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1134
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1135
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1136
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1137
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1138
+ name: IGHV3-23_star_01_73
1139
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1140
+ IGHV3-23_star_01_74: 1.0
1141
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1142
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1143
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1144
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1145
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1146
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1147
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1148
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1149
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1150
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1151
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1152
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1153
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1154
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1155
+ IGHV3-23_star_01_75: 1.0
1156
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1157
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1158
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1159
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1160
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1161
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1162
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1163
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1164
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1165
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1166
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1167
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1168
+ name: IGHV3-23_star_01_75
1169
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1170
+ IGHV3-23_star_01_76: 1.0
1171
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1172
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1173
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1174
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1175
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1176
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1177
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1178
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1179
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1180
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1181
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1182
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1183
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1184
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1185
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1186
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1187
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1188
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1189
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1190
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1191
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1192
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1193
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1194
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1195
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1196
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1197
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1198
+ name: IGHV3-23_star_01_77
1199
+ transitions:
1200
+ IGHV3-23_star_01_78: 1.0
1201
+ - !!python/object:python.hmmwriter.State
1202
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1203
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1204
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1205
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1206
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1207
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1208
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1209
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1210
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1211
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1212
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1213
+ name: IGHV3-23_star_01_78
1214
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1215
+ IGHV3-23_star_01_79: 1.0
1216
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1217
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1218
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1219
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1220
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1221
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1222
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1223
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1224
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1225
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1226
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1227
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1228
+ name: IGHV3-23_star_01_79
1229
+ transitions:
1230
+ IGHV3-23_star_01_80: 1.0
1231
+ - !!python/object:python.hmmwriter.State
1232
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1233
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1234
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1235
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1236
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1237
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1238
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1239
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1240
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1241
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1242
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1243
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1244
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1245
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1246
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1247
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1248
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1249
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1250
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1251
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1252
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1253
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1254
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1255
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1256
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1257
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1258
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1259
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1260
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1261
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1262
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1263
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1264
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1265
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1266
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1267
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1268
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1269
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1270
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1271
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1272
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1273
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1274
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1275
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1276
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1277
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1278
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1279
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1280
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1281
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1282
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1283
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1284
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1285
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1286
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1287
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1288
+ name: IGHV3-23_star_01_83
1289
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1290
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1291
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1292
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1293
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1294
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1295
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1296
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1297
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1298
+ track: nukes
1299
+ extras:
1300
+ ambiguous_char: N
1301
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1302
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1303
+ name: IGHV3-23_star_01_84
1304
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1305
+ IGHV3-23_star_01_85: 1.0
1306
+ - !!python/object:python.hmmwriter.State
1307
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1308
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1309
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1310
+ C: 0.038028366175183334
1311
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1312
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1313
+ track: nukes
1314
+ extras:
1315
+ ambiguous_char: N
1316
+ ambiguous_emission_prob: 0.25
1317
+ germline: T
1318
+ name: IGHV3-23_star_01_85
1319
+ transitions:
1320
+ IGHV3-23_star_01_86: 1.0
1321
+ - !!python/object:python.hmmwriter.State
1322
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1323
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1324
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1325
+ C: 0.038028366175183334
1326
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1327
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1328
+ track: nukes
1329
+ extras:
1330
+ ambiguous_char: N
1331
+ ambiguous_emission_prob: 0.25
1332
+ germline: T
1333
+ name: IGHV3-23_star_01_86
1334
+ transitions:
1335
+ IGHV3-23_star_01_87: 1.0
1336
+ - !!python/object:python.hmmwriter.State
1337
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1338
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1339
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1340
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1341
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1342
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1343
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1344
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1345
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1346
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1347
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1348
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1349
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1350
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1351
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1352
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1353
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1354
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1355
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1356
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1357
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1358
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1359
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1360
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1361
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1362
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1363
+ name: IGHV3-23_star_01_88
1364
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1365
+ IGHV3-23_star_01_89: 1.0
1366
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1367
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1368
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1369
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1370
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1371
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1372
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1373
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1374
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1375
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1376
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1377
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1378
+ name: IGHV3-23_star_01_89
1379
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1380
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1381
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1382
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1383
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1384
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1385
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1386
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1387
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1388
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1389
+ extras:
1390
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1391
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1392
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1393
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1394
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1395
+ IGHV3-23_star_01_91: 1.0
1396
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1397
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1398
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1399
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1400
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1401
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1402
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1403
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1404
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1405
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1406
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1407
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1408
+ name: IGHV3-23_star_01_91
1409
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1410
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1411
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1412
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1413
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1414
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1415
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1416
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1417
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1418
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1419
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1420
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1421
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1422
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1423
+ name: IGHV3-23_star_01_92
1424
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1425
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1426
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1427
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1428
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1429
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1430
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1431
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1432
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1433
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1434
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1435
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1436
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1437
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1438
+ name: IGHV3-23_star_01_93
1439
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1440
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1441
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1442
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1443
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1444
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1445
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1446
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1447
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1448
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1449
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1450
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1451
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1452
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1453
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1454
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1455
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1456
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1457
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1458
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1459
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1460
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1461
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1462
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1463
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1464
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1465
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1466
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1467
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1468
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1469
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1470
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1471
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1472
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1473
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1474
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1475
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1476
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1477
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1478
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1479
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1480
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1481
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1482
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1483
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1484
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1485
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1486
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1487
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1488
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1489
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1490
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1491
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1492
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1493
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1494
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1495
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1496
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1497
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1498
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1499
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1500
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1501
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1502
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1503
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1504
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1505
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1506
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1507
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1508
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1509
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1510
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1511
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1512
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1513
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1514
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1515
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1516
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1517
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1518
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1519
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1520
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1521
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1522
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1523
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1524
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1525
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1526
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1527
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1528
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1529
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1530
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1531
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1532
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1533
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1534
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1535
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1536
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1537
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1538
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1539
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1540
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1541
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1542
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1543
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1544
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1545
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1546
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1547
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1548
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1549
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1550
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1551
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1552
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1553
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1554
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1555
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1556
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1557
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1558
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1559
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1560
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1561
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1562
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1563
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1564
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1565
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1566
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1567
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1568
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1569
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1570
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1571
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1572
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1573
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1574
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1575
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1576
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1577
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1578
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1579
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1580
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1581
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1582
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1583
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1584
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1585
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1586
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1587
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1588
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1589
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1590
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1591
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1592
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1593
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1594
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1595
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1596
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1597
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1598
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1599
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1600
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1601
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1602
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1603
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1604
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1605
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1606
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1607
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1608
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1609
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1610
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1611
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1612
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1613
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1614
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1615
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1616
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1617
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1618
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1619
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1620
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1621
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1622
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1623
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1624
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1625
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1626
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1627
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1628
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1629
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1630
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1631
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1632
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1633
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1634
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1635
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1636
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1637
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1638
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1639
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1640
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1641
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1642
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1643
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1644
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1645
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1646
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1647
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1648
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1649
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1650
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1651
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1652
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1653
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1654
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1655
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1656
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1657
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1658
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1659
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1660
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1661
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1662
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1663
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1664
+ transitions:
1665
+ IGHV3-23_star_01_109: 1.0
1666
+ - !!python/object:python.hmmwriter.State
1667
+ emissions:
1668
+ probs:
1669
+ A: 0.038028366175183334
1670
+ C: 0.038028366175183334
1671
+ G: 0.038028366175183334
1672
+ T: 0.88591490147445
1673
+ track: nukes
1674
+ extras:
1675
+ ambiguous_char: N
1676
+ ambiguous_emission_prob: 0.25
1677
+ germline: T
1678
+ name: IGHV3-23_star_01_109
1679
+ transitions:
1680
+ IGHV3-23_star_01_110: 1.0
1681
+ - !!python/object:python.hmmwriter.State
1682
+ emissions:
1683
+ probs:
1684
+ A: 0.038028366175183334
1685
+ C: 0.88591490147445
1686
+ G: 0.038028366175183334
1687
+ T: 0.038028366175183334
1688
+ track: nukes
1689
+ extras:
1690
+ ambiguous_char: N
1691
+ ambiguous_emission_prob: 0.25
1692
+ germline: C
1693
+ name: IGHV3-23_star_01_110
1694
+ transitions:
1695
+ IGHV3-23_star_01_111: 1.0
1696
+ - !!python/object:python.hmmwriter.State
1697
+ emissions:
1698
+ probs:
1699
+ A: 0.038028366175183334
1700
+ C: 0.88591490147445
1701
+ G: 0.038028366175183334
1702
+ T: 0.038028366175183334
1703
+ track: nukes
1704
+ extras:
1705
+ ambiguous_char: N
1706
+ ambiguous_emission_prob: 0.25
1707
+ germline: C
1708
+ name: IGHV3-23_star_01_111
1709
+ transitions:
1710
+ IGHV3-23_star_01_112: 1.0
1711
+ - !!python/object:python.hmmwriter.State
1712
+ emissions:
1713
+ probs:
1714
+ A: 0.038028366175183334
1715
+ C: 0.038028366175183334
1716
+ G: 0.88591490147445
1717
+ T: 0.038028366175183334
1718
+ track: nukes
1719
+ extras:
1720
+ ambiguous_char: N
1721
+ ambiguous_emission_prob: 0.25
1722
+ germline: G
1723
+ name: IGHV3-23_star_01_112
1724
+ transitions:
1725
+ IGHV3-23_star_01_113: 1.0
1726
+ - !!python/object:python.hmmwriter.State
1727
+ emissions:
1728
+ probs:
1729
+ A: 0.038028366175183334
1730
+ C: 0.88591490147445
1731
+ G: 0.038028366175183334
1732
+ T: 0.038028366175183334
1733
+ track: nukes
1734
+ extras:
1735
+ ambiguous_char: N
1736
+ ambiguous_emission_prob: 0.25
1737
+ germline: C
1738
+ name: IGHV3-23_star_01_113
1739
+ transitions:
1740
+ IGHV3-23_star_01_114: 1.0
1741
+ - !!python/object:python.hmmwriter.State
1742
+ emissions:
1743
+ probs:
1744
+ A: 0.038028366175183334
1745
+ C: 0.88591490147445
1746
+ G: 0.038028366175183334
1747
+ T: 0.038028366175183334
1748
+ track: nukes
1749
+ extras:
1750
+ ambiguous_char: N
1751
+ ambiguous_emission_prob: 0.25
1752
+ germline: C
1753
+ name: IGHV3-23_star_01_114
1754
+ transitions:
1755
+ IGHV3-23_star_01_115: 1.0
1756
+ - !!python/object:python.hmmwriter.State
1757
+ emissions:
1758
+ probs:
1759
+ A: 0.88591490147445
1760
+ C: 0.038028366175183334
1761
+ G: 0.038028366175183334
1762
+ T: 0.038028366175183334
1763
+ track: nukes
1764
+ extras:
1765
+ ambiguous_char: N
1766
+ ambiguous_emission_prob: 0.25
1767
+ germline: A
1768
+ name: IGHV3-23_star_01_115
1769
+ transitions:
1770
+ IGHV3-23_star_01_116: 1.0
1771
+ - !!python/object:python.hmmwriter.State
1772
+ emissions:
1773
+ probs:
1774
+ A: 0.038028366175183334
1775
+ C: 0.038028366175183334
1776
+ G: 0.88591490147445
1777
+ T: 0.038028366175183334
1778
+ track: nukes
1779
+ extras:
1780
+ ambiguous_char: N
1781
+ ambiguous_emission_prob: 0.25
1782
+ germline: G
1783
+ name: IGHV3-23_star_01_116
1784
+ transitions:
1785
+ IGHV3-23_star_01_117: 1.0
1786
+ - !!python/object:python.hmmwriter.State
1787
+ emissions:
1788
+ probs:
1789
+ A: 0.038028366175183334
1790
+ C: 0.038028366175183334
1791
+ G: 0.88591490147445
1792
+ T: 0.038028366175183334
1793
+ track: nukes
1794
+ extras:
1795
+ ambiguous_char: N
1796
+ ambiguous_emission_prob: 0.25
1797
+ germline: G
1798
+ name: IGHV3-23_star_01_117
1799
+ transitions:
1800
+ IGHV3-23_star_01_118: 1.0
1801
+ - !!python/object:python.hmmwriter.State
1802
+ emissions:
1803
+ probs:
1804
+ A: 0.038028366175183334
1805
+ C: 0.88591490147445
1806
+ G: 0.038028366175183334
1807
+ T: 0.038028366175183334
1808
+ track: nukes
1809
+ extras:
1810
+ ambiguous_char: N
1811
+ ambiguous_emission_prob: 0.25
1812
+ germline: C
1813
+ name: IGHV3-23_star_01_118
1814
+ transitions:
1815
+ IGHV3-23_star_01_119: 1.0
1816
+ - !!python/object:python.hmmwriter.State
1817
+ emissions:
1818
+ probs:
1819
+ A: 0.038028366175183334
1820
+ C: 0.038028366175183334
1821
+ G: 0.038028366175183334
1822
+ T: 0.88591490147445
1823
+ track: nukes
1824
+ extras:
1825
+ ambiguous_char: N
1826
+ ambiguous_emission_prob: 0.25
1827
+ germline: T
1828
+ name: IGHV3-23_star_01_119
1829
+ transitions:
1830
+ IGHV3-23_star_01_120: 1.0
1831
+ - !!python/object:python.hmmwriter.State
1832
+ emissions:
1833
+ probs:
1834
+ A: 0.038028366175183334
1835
+ C: 0.88591490147445
1836
+ G: 0.038028366175183334
1837
+ T: 0.038028366175183334
1838
+ track: nukes
1839
+ extras:
1840
+ ambiguous_char: N
1841
+ ambiguous_emission_prob: 0.25
1842
+ germline: C
1843
+ name: IGHV3-23_star_01_120
1844
+ transitions:
1845
+ IGHV3-23_star_01_121: 1.0
1846
+ - !!python/object:python.hmmwriter.State
1847
+ emissions:
1848
+ probs:
1849
+ A: 0.038028366175183334
1850
+ C: 0.88591490147445
1851
+ G: 0.038028366175183334
1852
+ T: 0.038028366175183334
1853
+ track: nukes
1854
+ extras:
1855
+ ambiguous_char: N
1856
+ ambiguous_emission_prob: 0.25
1857
+ germline: C
1858
+ name: IGHV3-23_star_01_121
1859
+ transitions:
1860
+ IGHV3-23_star_01_122: 1.0
1861
+ - !!python/object:python.hmmwriter.State
1862
+ emissions:
1863
+ probs:
1864
+ A: 0.88591490147445
1865
+ C: 0.038028366175183334
1866
+ G: 0.038028366175183334
1867
+ T: 0.038028366175183334
1868
+ track: nukes
1869
+ extras:
1870
+ ambiguous_char: N
1871
+ ambiguous_emission_prob: 0.25
1872
+ germline: A
1873
+ name: IGHV3-23_star_01_122
1874
+ transitions:
1875
+ IGHV3-23_star_01_123: 1.0
1876
+ - !!python/object:python.hmmwriter.State
1877
+ emissions:
1878
+ probs:
1879
+ A: 0.038028366175183334
1880
+ C: 0.038028366175183334
1881
+ G: 0.88591490147445
1882
+ T: 0.038028366175183334
1883
+ track: nukes
1884
+ extras:
1885
+ ambiguous_char: N
1886
+ ambiguous_emission_prob: 0.25
1887
+ germline: G
1888
+ name: IGHV3-23_star_01_123
1889
+ transitions:
1890
+ IGHV3-23_star_01_124: 1.0
1891
+ - !!python/object:python.hmmwriter.State
1892
+ emissions:
1893
+ probs:
1894
+ A: 0.038028366175183334
1895
+ C: 0.038028366175183334
1896
+ G: 0.88591490147445
1897
+ T: 0.038028366175183334
1898
+ track: nukes
1899
+ extras:
1900
+ ambiguous_char: N
1901
+ ambiguous_emission_prob: 0.25
1902
+ germline: G
1903
+ name: IGHV3-23_star_01_124
1904
+ transitions:
1905
+ IGHV3-23_star_01_125: 1.0
1906
+ - !!python/object:python.hmmwriter.State
1907
+ emissions:
1908
+ probs:
1909
+ A: 0.038028366175183334
1910
+ C: 0.038028366175183334
1911
+ G: 0.88591490147445
1912
+ T: 0.038028366175183334
1913
+ track: nukes
1914
+ extras:
1915
+ ambiguous_char: N
1916
+ ambiguous_emission_prob: 0.25
1917
+ germline: G
1918
+ name: IGHV3-23_star_01_125
1919
+ transitions:
1920
+ IGHV3-23_star_01_126: 1.0
1921
+ - !!python/object:python.hmmwriter.State
1922
+ emissions:
1923
+ probs:
1924
+ A: 0.88591490147445
1925
+ C: 0.038028366175183334
1926
+ G: 0.038028366175183334
1927
+ T: 0.038028366175183334
1928
+ track: nukes
1929
+ extras:
1930
+ ambiguous_char: N
1931
+ ambiguous_emission_prob: 0.25
1932
+ germline: A
1933
+ name: IGHV3-23_star_01_126
1934
+ transitions:
1935
+ IGHV3-23_star_01_127: 1.0
1936
+ - !!python/object:python.hmmwriter.State
1937
+ emissions:
1938
+ probs:
1939
+ A: 0.88591490147445
1940
+ C: 0.038028366175183334
1941
+ G: 0.038028366175183334
1942
+ T: 0.038028366175183334
1943
+ track: nukes
1944
+ extras:
1945
+ ambiguous_char: N
1946
+ ambiguous_emission_prob: 0.25
1947
+ germline: A
1948
+ name: IGHV3-23_star_01_127
1949
+ transitions:
1950
+ IGHV3-23_star_01_128: 1.0
1951
+ - !!python/object:python.hmmwriter.State
1952
+ emissions:
1953
+ probs:
1954
+ A: 0.038028366175183334
1955
+ C: 0.038028366175183334
1956
+ G: 0.88591490147445
1957
+ T: 0.038028366175183334
1958
+ track: nukes
1959
+ extras:
1960
+ ambiguous_char: N
1961
+ ambiguous_emission_prob: 0.25
1962
+ germline: G
1963
+ name: IGHV3-23_star_01_128
1964
+ transitions:
1965
+ IGHV3-23_star_01_129: 1.0
1966
+ - !!python/object:python.hmmwriter.State
1967
+ emissions:
1968
+ probs:
1969
+ A: 0.038028366175183334
1970
+ C: 0.038028366175183334
1971
+ G: 0.88591490147445
1972
+ T: 0.038028366175183334
1973
+ track: nukes
1974
+ extras:
1975
+ ambiguous_char: N
1976
+ ambiguous_emission_prob: 0.25
1977
+ germline: G
1978
+ name: IGHV3-23_star_01_129
1979
+ transitions:
1980
+ IGHV3-23_star_01_130: 1.0
1981
+ - !!python/object:python.hmmwriter.State
1982
+ emissions:
1983
+ probs:
1984
+ A: 0.038028366175183334
1985
+ C: 0.038028366175183334
1986
+ G: 0.88591490147445
1987
+ T: 0.038028366175183334
1988
+ track: nukes
1989
+ extras:
1990
+ ambiguous_char: N
1991
+ ambiguous_emission_prob: 0.25
1992
+ germline: G
1993
+ name: IGHV3-23_star_01_130
1994
+ transitions:
1995
+ IGHV3-23_star_01_131: 1.0
1996
+ - !!python/object:python.hmmwriter.State
1997
+ emissions:
1998
+ probs:
1999
+ A: 0.038028366175183334
2000
+ C: 0.038028366175183334
2001
+ G: 0.88591490147445
2002
+ T: 0.038028366175183334
2003
+ track: nukes
2004
+ extras:
2005
+ ambiguous_char: N
2006
+ ambiguous_emission_prob: 0.25
2007
+ germline: G
2008
+ name: IGHV3-23_star_01_131
2009
+ transitions:
2010
+ IGHV3-23_star_01_132: 1.0
2011
+ - !!python/object:python.hmmwriter.State
2012
+ emissions:
2013
+ probs:
2014
+ A: 0.038028366175183334
2015
+ C: 0.88591490147445
2016
+ G: 0.038028366175183334
2017
+ T: 0.038028366175183334
2018
+ track: nukes
2019
+ extras:
2020
+ ambiguous_char: N
2021
+ ambiguous_emission_prob: 0.25
2022
+ germline: C
2023
+ name: IGHV3-23_star_01_132
2024
+ transitions:
2025
+ IGHV3-23_star_01_133: 1.0
2026
+ - !!python/object:python.hmmwriter.State
2027
+ emissions:
2028
+ probs:
2029
+ A: 0.038028366175183334
2030
+ C: 0.038028366175183334
2031
+ G: 0.038028366175183334
2032
+ T: 0.88591490147445
2033
+ track: nukes
2034
+ extras:
2035
+ ambiguous_char: N
2036
+ ambiguous_emission_prob: 0.25
2037
+ germline: T
2038
+ name: IGHV3-23_star_01_133
2039
+ transitions:
2040
+ IGHV3-23_star_01_134: 1.0
2041
+ - !!python/object:python.hmmwriter.State
2042
+ emissions:
2043
+ probs:
2044
+ A: 0.038028366175183334
2045
+ C: 0.038028366175183334
2046
+ G: 0.88591490147445
2047
+ T: 0.038028366175183334
2048
+ track: nukes
2049
+ extras:
2050
+ ambiguous_char: N
2051
+ ambiguous_emission_prob: 0.25
2052
+ germline: G
2053
+ name: IGHV3-23_star_01_134
2054
+ transitions:
2055
+ IGHV3-23_star_01_135: 1.0
2056
+ - !!python/object:python.hmmwriter.State
2057
+ emissions:
2058
+ probs:
2059
+ A: 0.038028366175183334
2060
+ C: 0.038028366175183334
2061
+ G: 0.88591490147445
2062
+ T: 0.038028366175183334
2063
+ track: nukes
2064
+ extras:
2065
+ ambiguous_char: N
2066
+ ambiguous_emission_prob: 0.25
2067
+ germline: G
2068
+ name: IGHV3-23_star_01_135
2069
+ transitions:
2070
+ IGHV3-23_star_01_136: 1.0
2071
+ - !!python/object:python.hmmwriter.State
2072
+ emissions:
2073
+ probs:
2074
+ A: 0.88591490147445
2075
+ C: 0.038028366175183334
2076
+ G: 0.038028366175183334
2077
+ T: 0.038028366175183334
2078
+ track: nukes
2079
+ extras:
2080
+ ambiguous_char: N
2081
+ ambiguous_emission_prob: 0.25
2082
+ germline: A
2083
+ name: IGHV3-23_star_01_136
2084
+ transitions:
2085
+ IGHV3-23_star_01_137: 1.0
2086
+ - !!python/object:python.hmmwriter.State
2087
+ emissions:
2088
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2089
+ A: 0.038028366175183334
2090
+ C: 0.038028366175183334
2091
+ G: 0.88591490147445
2092
+ T: 0.038028366175183334
2093
+ track: nukes
2094
+ extras:
2095
+ ambiguous_char: N
2096
+ ambiguous_emission_prob: 0.25
2097
+ germline: G
2098
+ name: IGHV3-23_star_01_137
2099
+ transitions:
2100
+ IGHV3-23_star_01_138: 1.0
2101
+ - !!python/object:python.hmmwriter.State
2102
+ emissions:
2103
+ probs:
2104
+ A: 0.038028366175183334
2105
+ C: 0.038028366175183334
2106
+ G: 0.038028366175183334
2107
+ T: 0.88591490147445
2108
+ track: nukes
2109
+ extras:
2110
+ ambiguous_char: N
2111
+ ambiguous_emission_prob: 0.25
2112
+ germline: T
2113
+ name: IGHV3-23_star_01_138
2114
+ transitions:
2115
+ IGHV3-23_star_01_139: 1.0
2116
+ - !!python/object:python.hmmwriter.State
2117
+ emissions:
2118
+ probs:
2119
+ A: 0.038028366175183334
2120
+ C: 0.038028366175183334
2121
+ G: 0.88591490147445
2122
+ T: 0.038028366175183334
2123
+ track: nukes
2124
+ extras:
2125
+ ambiguous_char: N
2126
+ ambiguous_emission_prob: 0.25
2127
+ germline: G
2128
+ name: IGHV3-23_star_01_139
2129
+ transitions:
2130
+ IGHV3-23_star_01_140: 1.0
2131
+ - !!python/object:python.hmmwriter.State
2132
+ emissions:
2133
+ probs:
2134
+ A: 0.038028366175183334
2135
+ C: 0.038028366175183334
2136
+ G: 0.88591490147445
2137
+ T: 0.038028366175183334
2138
+ track: nukes
2139
+ extras:
2140
+ ambiguous_char: N
2141
+ ambiguous_emission_prob: 0.25
2142
+ germline: G
2143
+ name: IGHV3-23_star_01_140
2144
+ transitions:
2145
+ IGHV3-23_star_01_141: 1.0
2146
+ - !!python/object:python.hmmwriter.State
2147
+ emissions:
2148
+ probs:
2149
+ A: 0.038028366175183334
2150
+ C: 0.038028366175183334
2151
+ G: 0.88591490147445
2152
+ T: 0.038028366175183334
2153
+ track: nukes
2154
+ extras:
2155
+ ambiguous_char: N
2156
+ ambiguous_emission_prob: 0.25
2157
+ germline: G
2158
+ name: IGHV3-23_star_01_141
2159
+ transitions:
2160
+ IGHV3-23_star_01_142: 1.0
2161
+ - !!python/object:python.hmmwriter.State
2162
+ emissions:
2163
+ probs:
2164
+ A: 0.038028366175183334
2165
+ C: 0.038028366175183334
2166
+ G: 0.038028366175183334
2167
+ T: 0.88591490147445
2168
+ track: nukes
2169
+ extras:
2170
+ ambiguous_char: N
2171
+ ambiguous_emission_prob: 0.25
2172
+ germline: T
2173
+ name: IGHV3-23_star_01_142
2174
+ transitions:
2175
+ IGHV3-23_star_01_143: 1.0
2176
+ - !!python/object:python.hmmwriter.State
2177
+ emissions:
2178
+ probs:
2179
+ A: 0.038028366175183334
2180
+ C: 0.88591490147445
2181
+ G: 0.038028366175183334
2182
+ T: 0.038028366175183334
2183
+ track: nukes
2184
+ extras:
2185
+ ambiguous_char: N
2186
+ ambiguous_emission_prob: 0.25
2187
+ germline: C
2188
+ name: IGHV3-23_star_01_143
2189
+ transitions:
2190
+ IGHV3-23_star_01_144: 1.0
2191
+ - !!python/object:python.hmmwriter.State
2192
+ emissions:
2193
+ probs:
2194
+ A: 0.038028366175183334
2195
+ C: 0.038028366175183334
2196
+ G: 0.038028366175183334
2197
+ T: 0.88591490147445
2198
+ track: nukes
2199
+ extras:
2200
+ ambiguous_char: N
2201
+ ambiguous_emission_prob: 0.25
2202
+ germline: T
2203
+ name: IGHV3-23_star_01_144
2204
+ transitions:
2205
+ IGHV3-23_star_01_145: 1.0
2206
+ - !!python/object:python.hmmwriter.State
2207
+ emissions:
2208
+ probs:
2209
+ A: 0.038028366175183334
2210
+ C: 0.88591490147445
2211
+ G: 0.038028366175183334
2212
+ T: 0.038028366175183334
2213
+ track: nukes
2214
+ extras:
2215
+ ambiguous_char: N
2216
+ ambiguous_emission_prob: 0.25
2217
+ germline: C
2218
+ name: IGHV3-23_star_01_145
2219
+ transitions:
2220
+ IGHV3-23_star_01_146: 1.0
2221
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2222
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2223
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2224
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2225
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2226
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2227
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2228
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2229
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2230
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2231
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2232
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2233
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2234
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2235
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2236
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2237
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2238
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2239
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2240
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2241
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2242
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2243
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2244
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2245
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2246
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2247
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2248
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2249
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2250
+ IGHV3-23_star_01_148: 1.0
2251
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2252
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2253
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2254
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2255
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2256
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2257
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2258
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2259
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2260
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2261
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2262
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2263
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2264
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2265
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2266
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2267
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2268
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2269
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2270
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2271
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2272
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2273
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2274
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2275
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2276
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2277
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2278
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2279
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2280
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2281
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2282
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2283
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2284
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2285
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2286
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2287
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2288
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2289
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2290
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2291
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2292
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2293
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2294
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2295
+ IGHV3-23_star_01_151: 1.0
2296
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2297
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2298
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2299
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2300
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2301
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2302
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2303
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2304
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2305
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2306
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2307
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2308
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2309
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2310
+ IGHV3-23_star_01_152: 1.0
2311
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2312
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2313
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2314
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2315
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2316
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2317
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2318
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2319
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2320
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2321
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2322
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2323
+ name: IGHV3-23_star_01_152
2324
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2325
+ IGHV3-23_star_01_153: 1.0
2326
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2327
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2328
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2329
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2330
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2331
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2332
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2333
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2334
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2335
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2336
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2337
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2338
+ name: IGHV3-23_star_01_153
2339
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2340
+ IGHV3-23_star_01_154: 1.0
2341
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2342
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2343
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2344
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2345
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2346
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2347
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2348
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2349
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2350
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2351
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2352
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2353
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2354
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2355
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2356
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2357
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2358
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2359
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2360
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2361
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2362
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2363
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2364
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2365
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2366
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2367
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2368
+ name: IGHV3-23_star_01_155
2369
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2370
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2371
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2372
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2373
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2374
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2375
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2376
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2377
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2378
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2379
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2380
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2381
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2382
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2383
+ name: IGHV3-23_star_01_156
2384
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2385
+ IGHV3-23_star_01_157: 1.0
2386
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2387
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2388
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2389
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2390
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2391
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2392
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2393
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2394
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2395
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2396
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2397
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2398
+ name: IGHV3-23_star_01_157
2399
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2400
+ IGHV3-23_star_01_158: 1.0
2401
+ - !!python/object:python.hmmwriter.State
2402
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2403
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2404
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2405
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2406
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2407
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2408
+ track: nukes
2409
+ extras:
2410
+ ambiguous_char: N
2411
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2412
+ germline: T
2413
+ name: IGHV3-23_star_01_158
2414
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2415
+ IGHV3-23_star_01_159: 1.0
2416
+ - !!python/object:python.hmmwriter.State
2417
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2418
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2419
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2420
+ C: 0.038028366175183334
2421
+ G: 0.038028366175183334
2422
+ T: 0.038028366175183334
2423
+ track: nukes
2424
+ extras:
2425
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2426
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2427
+ germline: A
2428
+ name: IGHV3-23_star_01_159
2429
+ transitions:
2430
+ IGHV3-23_star_01_160: 1.0
2431
+ - !!python/object:python.hmmwriter.State
2432
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2433
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2434
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2435
+ C: 0.038028366175183334
2436
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2437
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2438
+ track: nukes
2439
+ extras:
2440
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2441
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2442
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2443
+ name: IGHV3-23_star_01_160
2444
+ transitions:
2445
+ IGHV3-23_star_01_161: 1.0
2446
+ - !!python/object:python.hmmwriter.State
2447
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2448
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2449
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2450
+ C: 0.038028366175183334
2451
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2452
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2453
+ track: nukes
2454
+ extras:
2455
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2456
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2457
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2458
+ name: IGHV3-23_star_01_161
2459
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2460
+ IGHV3-23_star_01_162: 1.0
2461
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2462
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2463
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2464
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2465
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2466
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2467
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2468
+ track: nukes
2469
+ extras:
2470
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2471
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2472
+ germline: G
2473
+ name: IGHV3-23_star_01_162
2474
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2475
+ IGHV3-23_star_01_163: 1.0
2476
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2477
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2478
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2479
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2480
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2481
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2482
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2483
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2484
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2485
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2486
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2487
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2488
+ name: IGHV3-23_star_01_163
2489
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2490
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2491
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2492
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2493
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2494
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2495
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2496
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2497
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2498
+ track: nukes
2499
+ extras:
2500
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2501
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2502
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2503
+ name: IGHV3-23_star_01_164
2504
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2505
+ IGHV3-23_star_01_165: 1.0
2506
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2507
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2508
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2509
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2510
+ C: 0.038028366175183334
2511
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2512
+ T: 0.038028366175183334
2513
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2514
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2515
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2516
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2517
+ germline: G
2518
+ name: IGHV3-23_star_01_165
2519
+ transitions:
2520
+ IGHV3-23_star_01_166: 1.0
2521
+ - !!python/object:python.hmmwriter.State
2522
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2523
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2524
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2525
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2526
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2527
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2528
+ track: nukes
2529
+ extras:
2530
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2531
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2532
+ germline: G
2533
+ name: IGHV3-23_star_01_166
2534
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2535
+ IGHV3-23_star_01_167: 1.0
2536
+ - !!python/object:python.hmmwriter.State
2537
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2538
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2539
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2540
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2541
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2542
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2543
+ track: nukes
2544
+ extras:
2545
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2546
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2547
+ germline: T
2548
+ name: IGHV3-23_star_01_167
2549
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2550
+ IGHV3-23_star_01_168: 1.0
2551
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2552
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2553
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2554
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2555
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2556
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2557
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2558
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2559
+ extras:
2560
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2561
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2562
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2563
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2564
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2565
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2566
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2567
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2568
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2569
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2570
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2571
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2572
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2573
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2574
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2575
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2576
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2577
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2578
+ name: IGHV3-23_star_01_169
2579
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2580
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2581
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2582
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2583
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2584
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2585
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2586
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2587
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2588
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2589
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2590
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2591
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2592
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2593
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2594
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2595
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2596
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2597
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2598
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2599
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2600
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2601
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2602
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2603
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2604
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2605
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2606
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2607
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2608
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2609
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2610
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2611
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2612
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2613
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2614
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2615
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2616
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2617
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2618
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2619
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2620
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2621
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2622
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2623
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2624
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2625
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2626
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2627
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2628
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2629
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2630
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2631
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2632
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2633
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2634
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2635
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2636
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2637
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2638
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2639
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2640
+ IGHV3-23_star_01_174: 1.0
2641
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2642
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2643
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2644
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2645
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2646
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2647
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2648
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2649
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2650
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2651
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2652
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2653
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2654
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2655
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2656
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2657
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2658
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2659
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2660
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2661
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2662
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2663
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2664
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2665
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2666
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2667
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2668
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2669
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2670
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2671
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2672
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2673
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2674
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2675
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2676
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2677
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2678
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2679
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2680
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2681
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2682
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2683
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2684
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2685
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2686
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2687
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2688
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2689
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2690
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2691
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2692
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2693
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2694
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2695
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2696
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2697
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2698
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2699
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2700
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2701
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2702
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2703
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2704
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2705
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2706
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2707
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2708
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2709
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2710
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2711
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2712
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2713
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2714
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2715
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2716
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2717
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2718
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2719
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2720
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2721
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2722
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2723
+ track: nukes
2724
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2725
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2726
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2727
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2728
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2729
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2730
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2731
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2732
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2733
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2734
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2735
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2736
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2737
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2738
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2739
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2740
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2741
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2742
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2743
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2744
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2745
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2746
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2747
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2748
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2749
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2750
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2751
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2752
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2753
+ track: nukes
2754
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2755
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2756
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2757
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2758
+ name: IGHV3-23_star_01_181
2759
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2760
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2761
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2762
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2763
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2764
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2765
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2766
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2767
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2768
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2769
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2770
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2771
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2772
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2773
+ name: IGHV3-23_star_01_182
2774
+ transitions:
2775
+ IGHV3-23_star_01_183: 1.0
2776
+ - !!python/object:python.hmmwriter.State
2777
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2778
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2779
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2780
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2781
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2782
+ T: 0.038028366175183334
2783
+ track: nukes
2784
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2785
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2786
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2787
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2788
+ name: IGHV3-23_star_01_183
2789
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2790
+ IGHV3-23_star_01_184: 1.0
2791
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2792
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2793
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2794
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2795
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2796
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2797
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2798
+ track: nukes
2799
+ extras:
2800
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2801
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2802
+ germline: A
2803
+ name: IGHV3-23_star_01_184
2804
+ transitions:
2805
+ IGHV3-23_star_01_185: 1.0
2806
+ - !!python/object:python.hmmwriter.State
2807
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2808
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2809
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2810
+ C: 0.88591490147445
2811
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2812
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2813
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2814
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2815
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2816
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2817
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2818
+ name: IGHV3-23_star_01_185
2819
+ transitions:
2820
+ IGHV3-23_star_01_186: 1.0
2821
+ - !!python/object:python.hmmwriter.State
2822
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2823
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2824
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2825
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2826
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2827
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2828
+ track: nukes
2829
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2830
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2831
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2832
+ germline: T
2833
+ name: IGHV3-23_star_01_186
2834
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2835
+ IGHV3-23_star_01_187: 1.0
2836
+ - !!python/object:python.hmmwriter.State
2837
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2838
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2839
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2840
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2841
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2842
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2843
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2844
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2845
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2846
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2847
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2848
+ name: IGHV3-23_star_01_187
2849
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2850
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2851
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2852
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2853
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2854
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2855
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2856
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2857
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2858
+ track: nukes
2859
+ extras:
2860
+ ambiguous_char: N
2861
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2862
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2863
+ name: IGHV3-23_star_01_188
2864
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2865
+ IGHV3-23_star_01_189: 1.0
2866
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2867
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2868
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2869
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2870
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2871
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2872
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2873
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2874
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2875
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2876
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2877
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2878
+ name: IGHV3-23_star_01_189
2879
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2880
+ IGHV3-23_star_01_190: 1.0
2881
+ - !!python/object:python.hmmwriter.State
2882
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2883
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2884
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2885
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2886
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2887
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2888
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2889
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2890
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2891
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2892
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2893
+ name: IGHV3-23_star_01_190
2894
+ transitions:
2895
+ IGHV3-23_star_01_191: 1.0
2896
+ - !!python/object:python.hmmwriter.State
2897
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2898
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2899
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2900
+ C: 0.038028366175183334
2901
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2902
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2903
+ track: nukes
2904
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2905
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2906
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2907
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2908
+ name: IGHV3-23_star_01_191
2909
+ transitions:
2910
+ IGHV3-23_star_01_192: 1.0
2911
+ - !!python/object:python.hmmwriter.State
2912
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2913
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2914
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2915
+ C: 0.038028366175183334
2916
+ G: 0.038028366175183334
2917
+ T: 0.038028366175183334
2918
+ track: nukes
2919
+ extras:
2920
+ ambiguous_char: N
2921
+ ambiguous_emission_prob: 0.25
2922
+ germline: A
2923
+ name: IGHV3-23_star_01_192
2924
+ transitions:
2925
+ IGHV3-23_star_01_193: 1.0
2926
+ - !!python/object:python.hmmwriter.State
2927
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2928
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2929
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2930
+ C: 0.038028366175183334
2931
+ G: 0.038028366175183334
2932
+ T: 0.038028366175183334
2933
+ track: nukes
2934
+ extras:
2935
+ ambiguous_char: N
2936
+ ambiguous_emission_prob: 0.25
2937
+ germline: A
2938
+ name: IGHV3-23_star_01_193
2939
+ transitions:
2940
+ IGHV3-23_star_01_194: 1.0
2941
+ - !!python/object:python.hmmwriter.State
2942
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2943
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2944
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2945
+ C: 0.038028366175183334
2946
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2947
+ T: 0.038028366175183334
2948
+ track: nukes
2949
+ extras:
2950
+ ambiguous_char: N
2951
+ ambiguous_emission_prob: 0.25
2952
+ germline: G
2953
+ name: IGHV3-23_star_01_194
2954
+ transitions:
2955
+ IGHV3-23_star_01_195: 1.0
2956
+ - !!python/object:python.hmmwriter.State
2957
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2958
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2959
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2960
+ C: 0.038028366175183334
2961
+ G: 0.88591490147445
2962
+ T: 0.038028366175183334
2963
+ track: nukes
2964
+ extras:
2965
+ ambiguous_char: N
2966
+ ambiguous_emission_prob: 0.25
2967
+ germline: G
2968
+ name: IGHV3-23_star_01_195
2969
+ transitions:
2970
+ IGHV3-23_star_01_196: 1.0
2971
+ - !!python/object:python.hmmwriter.State
2972
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2973
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2974
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2975
+ C: 0.038028366175183334
2976
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2977
+ T: 0.038028366175183334
2978
+ track: nukes
2979
+ extras:
2980
+ ambiguous_char: N
2981
+ ambiguous_emission_prob: 0.25
2982
+ germline: G
2983
+ name: IGHV3-23_star_01_196
2984
+ transitions:
2985
+ IGHV3-23_star_01_197: 1.0
2986
+ - !!python/object:python.hmmwriter.State
2987
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2988
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2989
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2990
+ C: 0.88591490147445
2991
+ G: 0.038028366175183334
2992
+ T: 0.038028366175183334
2993
+ track: nukes
2994
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2995
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2996
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2997
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2998
+ name: IGHV3-23_star_01_197
2999
+ transitions:
3000
+ IGHV3-23_star_01_198: 1.0
3001
+ - !!python/object:python.hmmwriter.State
3002
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3003
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3004
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3005
+ C: 0.88591490147445
3006
+ G: 0.038028366175183334
3007
+ T: 0.038028366175183334
3008
+ track: nukes
3009
+ extras:
3010
+ ambiguous_char: N
3011
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3012
+ germline: C
3013
+ name: IGHV3-23_star_01_198
3014
+ transitions:
3015
+ IGHV3-23_star_01_199: 1.0
3016
+ - !!python/object:python.hmmwriter.State
3017
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3018
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3019
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3020
+ C: 0.038028366175183334
3021
+ G: 0.88591490147445
3022
+ T: 0.038028366175183334
3023
+ track: nukes
3024
+ extras:
3025
+ ambiguous_char: N
3026
+ ambiguous_emission_prob: 0.25
3027
+ germline: G
3028
+ name: IGHV3-23_star_01_199
3029
+ transitions:
3030
+ IGHV3-23_star_01_200: 1.0
3031
+ - !!python/object:python.hmmwriter.State
3032
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3033
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3034
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3035
+ C: 0.038028366175183334
3036
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3037
+ T: 0.038028366175183334
3038
+ track: nukes
3039
+ extras:
3040
+ ambiguous_char: N
3041
+ ambiguous_emission_prob: 0.25
3042
+ germline: G
3043
+ name: IGHV3-23_star_01_200
3044
+ transitions:
3045
+ IGHV3-23_star_01_201: 1.0
3046
+ - !!python/object:python.hmmwriter.State
3047
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3048
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3049
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3050
+ C: 0.038028366175183334
3051
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3052
+ T: 0.88591490147445
3053
+ track: nukes
3054
+ extras:
3055
+ ambiguous_char: N
3056
+ ambiguous_emission_prob: 0.25
3057
+ germline: T
3058
+ name: IGHV3-23_star_01_201
3059
+ transitions:
3060
+ IGHV3-23_star_01_202: 1.0
3061
+ - !!python/object:python.hmmwriter.State
3062
+ emissions:
3063
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3064
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3065
+ C: 0.038028366175183334
3066
+ G: 0.038028366175183334
3067
+ T: 0.88591490147445
3068
+ track: nukes
3069
+ extras:
3070
+ ambiguous_char: N
3071
+ ambiguous_emission_prob: 0.25
3072
+ germline: T
3073
+ name: IGHV3-23_star_01_202
3074
+ transitions:
3075
+ IGHV3-23_star_01_203: 1.0
3076
+ - !!python/object:python.hmmwriter.State
3077
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3078
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3079
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3080
+ C: 0.88591490147445
3081
+ G: 0.038028366175183334
3082
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3083
+ track: nukes
3084
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3085
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3086
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3087
+ germline: C
3088
+ name: IGHV3-23_star_01_203
3089
+ transitions:
3090
+ IGHV3-23_star_01_204: 1.0
3091
+ - !!python/object:python.hmmwriter.State
3092
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3093
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3094
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3095
+ C: 0.038028366175183334
3096
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3097
+ T: 0.038028366175183334
3098
+ track: nukes
3099
+ extras:
3100
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3101
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3102
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3103
+ name: IGHV3-23_star_01_204
3104
+ transitions:
3105
+ IGHV3-23_star_01_205: 1.0
3106
+ - !!python/object:python.hmmwriter.State
3107
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3108
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3109
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3110
+ C: 0.88591490147445
3111
+ G: 0.038028366175183334
3112
+ T: 0.038028366175183334
3113
+ track: nukes
3114
+ extras:
3115
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3116
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3117
+ germline: C
3118
+ name: IGHV3-23_star_01_205
3119
+ transitions:
3120
+ IGHV3-23_star_01_206: 1.0
3121
+ - !!python/object:python.hmmwriter.State
3122
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3123
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3124
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3125
+ C: 0.88591490147445
3126
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3127
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3128
+ track: nukes
3129
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3130
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3131
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3132
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3133
+ name: IGHV3-23_star_01_206
3134
+ transitions:
3135
+ IGHV3-23_star_01_207: 1.0
3136
+ - !!python/object:python.hmmwriter.State
3137
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3138
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3139
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3140
+ C: 0.038028366175183334
3141
+ G: 0.038028366175183334
3142
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3143
+ track: nukes
3144
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3145
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3146
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3147
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3148
+ name: IGHV3-23_star_01_207
3149
+ transitions:
3150
+ IGHV3-23_star_01_208: 1.0
3151
+ - !!python/object:python.hmmwriter.State
3152
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3153
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3154
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3155
+ C: 0.038028366175183334
3156
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3157
+ T: 0.88591490147445
3158
+ track: nukes
3159
+ extras:
3160
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3161
+ ambiguous_emission_prob: 0.25
3162
+ germline: T
3163
+ name: IGHV3-23_star_01_208
3164
+ transitions:
3165
+ IGHV3-23_star_01_209: 1.0
3166
+ - !!python/object:python.hmmwriter.State
3167
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3168
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3169
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3170
+ C: 0.88591490147445
3171
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3172
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3173
+ track: nukes
3174
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3175
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3176
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3177
+ germline: C
3178
+ name: IGHV3-23_star_01_209
3179
+ transitions:
3180
+ IGHV3-23_star_01_210: 1.0
3181
+ - !!python/object:python.hmmwriter.State
3182
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3183
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3184
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3185
+ C: 0.038028366175183334
3186
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3187
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3188
+ track: nukes
3189
+ extras:
3190
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3191
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3192
+ germline: T
3193
+ name: IGHV3-23_star_01_210
3194
+ transitions:
3195
+ IGHV3-23_star_01_211: 1.0
3196
+ - !!python/object:python.hmmwriter.State
3197
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3198
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3199
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3200
+ C: 0.88591490147445
3201
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3202
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3203
+ track: nukes
3204
+ extras:
3205
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3206
+ ambiguous_emission_prob: 0.25
3207
+ germline: C
3208
+ name: IGHV3-23_star_01_211
3209
+ transitions:
3210
+ IGHV3-23_star_01_212: 1.0
3211
+ - !!python/object:python.hmmwriter.State
3212
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3213
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3214
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3215
+ C: 0.88591490147445
3216
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3217
+ T: 0.038028366175183334
3218
+ track: nukes
3219
+ extras:
3220
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3221
+ ambiguous_emission_prob: 0.25
3222
+ germline: C
3223
+ name: IGHV3-23_star_01_212
3224
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3225
+ IGHV3-23_star_01_213: 1.0
3226
+ - !!python/object:python.hmmwriter.State
3227
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3228
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3229
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3230
+ C: 0.038028366175183334
3231
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3232
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3233
+ track: nukes
3234
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3235
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3236
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3237
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3238
+ name: IGHV3-23_star_01_213
3239
+ transitions:
3240
+ IGHV3-23_star_01_214: 1.0
3241
+ - !!python/object:python.hmmwriter.State
3242
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3243
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3244
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3245
+ C: 0.038028366175183334
3246
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3247
+ T: 0.038028366175183334
3248
+ track: nukes
3249
+ extras:
3250
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3251
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3252
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3253
+ name: IGHV3-23_star_01_214
3254
+ transitions:
3255
+ IGHV3-23_star_01_215: 1.0
3256
+ - !!python/object:python.hmmwriter.State
3257
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3258
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3259
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3260
+ C: 0.038028366175183334
3261
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3262
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3263
+ track: nukes
3264
+ extras:
3265
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3266
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3267
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3268
+ name: IGHV3-23_star_01_215
3269
+ transitions:
3270
+ IGHV3-23_star_01_216: 1.0
3271
+ - !!python/object:python.hmmwriter.State
3272
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3273
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3274
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3275
+ C: 0.038028366175183334
3276
+ G: 0.88591490147445
3277
+ T: 0.038028366175183334
3278
+ track: nukes
3279
+ extras:
3280
+ ambiguous_char: N
3281
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3282
+ germline: G
3283
+ name: IGHV3-23_star_01_216
3284
+ transitions:
3285
+ IGHV3-23_star_01_217: 1.0
3286
+ - !!python/object:python.hmmwriter.State
3287
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3288
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3289
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3290
+ C: 0.038028366175183334
3291
+ G: 0.038028366175183334
3292
+ T: 0.038028366175183334
3293
+ track: nukes
3294
+ extras:
3295
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3296
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3297
+ germline: A
3298
+ name: IGHV3-23_star_01_217
3299
+ transitions:
3300
+ IGHV3-23_star_01_218: 1.0
3301
+ - !!python/object:python.hmmwriter.State
3302
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3303
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3304
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3305
+ C: 0.88591490147445
3306
+ G: 0.038028366175183334
3307
+ T: 0.038028366175183334
3308
+ track: nukes
3309
+ extras:
3310
+ ambiguous_char: N
3311
+ ambiguous_emission_prob: 0.25
3312
+ germline: C
3313
+ name: IGHV3-23_star_01_218
3314
+ transitions:
3315
+ IGHV3-23_star_01_219: 1.0
3316
+ - !!python/object:python.hmmwriter.State
3317
+ emissions:
3318
+ probs:
3319
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3320
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3321
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3322
+ T: 0.038028366175183334
3323
+ track: nukes
3324
+ extras:
3325
+ ambiguous_char: N
3326
+ ambiguous_emission_prob: 0.25
3327
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3328
+ name: IGHV3-23_star_01_219
3329
+ transitions:
3330
+ IGHV3-23_star_01_220: 1.0
3331
+ - !!python/object:python.hmmwriter.State
3332
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3333
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3334
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3335
+ C: 0.038028366175183334
3336
+ G: 0.038028366175183334
3337
+ T: 0.038028366175183334
3338
+ track: nukes
3339
+ extras:
3340
+ ambiguous_char: N
3341
+ ambiguous_emission_prob: 0.25
3342
+ germline: A
3343
+ name: IGHV3-23_star_01_220
3344
+ transitions:
3345
+ IGHV3-23_star_01_221: 1.0
3346
+ - !!python/object:python.hmmwriter.State
3347
+ emissions:
3348
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3349
+ A: 0.038028366175183334
3350
+ C: 0.038028366175183334
3351
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3352
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3353
+ track: nukes
3354
+ extras:
3355
+ ambiguous_char: N
3356
+ ambiguous_emission_prob: 0.25
3357
+ germline: T
3358
+ name: IGHV3-23_star_01_221
3359
+ transitions:
3360
+ IGHV3-23_star_01_222: 1.0
3361
+ - !!python/object:python.hmmwriter.State
3362
+ emissions:
3363
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3364
+ A: 0.038028366175183334
3365
+ C: 0.038028366175183334
3366
+ G: 0.038028366175183334
3367
+ T: 0.88591490147445
3368
+ track: nukes
3369
+ extras:
3370
+ ambiguous_char: N
3371
+ ambiguous_emission_prob: 0.25
3372
+ germline: T
3373
+ name: IGHV3-23_star_01_222
3374
+ transitions:
3375
+ IGHV3-23_star_01_223: 1.0
3376
+ - !!python/object:python.hmmwriter.State
3377
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3378
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3379
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3380
+ C: 0.88591490147445
3381
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3382
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3383
+ track: nukes
3384
+ extras:
3385
+ ambiguous_char: N
3386
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3387
+ germline: C
3388
+ name: IGHV3-23_star_01_223
3389
+ transitions:
3390
+ IGHV3-23_star_01_224: 1.0
3391
+ - !!python/object:python.hmmwriter.State
3392
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3393
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3394
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3395
+ C: 0.88591490147445
3396
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3397
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3398
+ track: nukes
3399
+ extras:
3400
+ ambiguous_char: N
3401
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3402
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3403
+ name: IGHV3-23_star_01_224
3404
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3405
+ IGHV3-23_star_01_225: 1.0
3406
+ - !!python/object:python.hmmwriter.State
3407
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3408
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3409
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3410
+ C: 0.038028366175183334
3411
+ G: 0.038028366175183334
3412
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3413
+ track: nukes
3414
+ extras:
3415
+ ambiguous_char: N
3416
+ ambiguous_emission_prob: 0.25
3417
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3418
+ name: IGHV3-23_star_01_225
3419
+ transitions:
3420
+ IGHV3-23_star_01_226: 1.0
3421
+ - !!python/object:python.hmmwriter.State
3422
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3423
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3424
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3425
+ C: 0.038028366175183334
3426
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3427
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3428
+ track: nukes
3429
+ extras:
3430
+ ambiguous_char: N
3431
+ ambiguous_emission_prob: 0.25
3432
+ germline: A
3433
+ name: IGHV3-23_star_01_226
3434
+ transitions:
3435
+ IGHV3-23_star_01_227: 1.0
3436
+ - !!python/object:python.hmmwriter.State
3437
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3438
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3439
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3440
+ C: 0.038028366175183334
3441
+ G: 0.88591490147445
3442
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3443
+ track: nukes
3444
+ extras:
3445
+ ambiguous_char: N
3446
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3447
+ germline: G
3448
+ name: IGHV3-23_star_01_227
3449
+ transitions:
3450
+ IGHV3-23_star_01_228: 1.0
3451
+ - !!python/object:python.hmmwriter.State
3452
+ emissions:
3453
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3454
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3455
+ C: 0.038028366175183334
3456
+ G: 0.038028366175183334
3457
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3458
+ track: nukes
3459
+ extras:
3460
+ ambiguous_char: N
3461
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3462
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3463
+ name: IGHV3-23_star_01_228
3464
+ transitions:
3465
+ IGHV3-23_star_01_229: 1.0
3466
+ - !!python/object:python.hmmwriter.State
3467
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3468
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3469
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3470
+ C: 0.038028366175183334
3471
+ G: 0.038028366175183334
3472
+ T: 0.038028366175183334
3473
+ track: nukes
3474
+ extras:
3475
+ ambiguous_char: N
3476
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3477
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3478
+ name: IGHV3-23_star_01_229
3479
+ transitions:
3480
+ IGHV3-23_star_01_230: 1.0
3481
+ - !!python/object:python.hmmwriter.State
3482
+ emissions:
3483
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3484
+ A: 0.038028366175183334
3485
+ C: 0.88591490147445
3486
+ G: 0.038028366175183334
3487
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3488
+ track: nukes
3489
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3490
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3491
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3492
+ germline: C
3493
+ name: IGHV3-23_star_01_230
3494
+ transitions:
3495
+ IGHV3-23_star_01_231: 1.0
3496
+ - !!python/object:python.hmmwriter.State
3497
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3498
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3499
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3500
+ C: 0.038028366175183334
3501
+ G: 0.038028366175183334
3502
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3503
+ track: nukes
3504
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3505
+ ambiguous_char: N
3506
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3507
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3508
+ name: IGHV3-23_star_01_231
3509
+ transitions:
3510
+ IGHV3-23_star_01_232: 1.0
3511
+ - !!python/object:python.hmmwriter.State
3512
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3513
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3514
+ A: 0.038028366175183334
3515
+ C: 0.88591490147445
3516
+ G: 0.038028366175183334
3517
+ T: 0.038028366175183334
3518
+ track: nukes
3519
+ extras:
3520
+ ambiguous_char: N
3521
+ ambiguous_emission_prob: 0.25
3522
+ germline: C
3523
+ name: IGHV3-23_star_01_232
3524
+ transitions:
3525
+ IGHV3-23_star_01_233: 1.0
3526
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3527
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3528
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3529
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3530
+ C: 0.038028366175183334
3531
+ G: 0.88591490147445
3532
+ T: 0.038028366175183334
3533
+ track: nukes
3534
+ extras:
3535
+ ambiguous_char: N
3536
+ ambiguous_emission_prob: 0.25
3537
+ germline: G
3538
+ name: IGHV3-23_star_01_233
3539
+ transitions:
3540
+ IGHV3-23_star_01_234: 1.0
3541
+ - !!python/object:python.hmmwriter.State
3542
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3543
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3544
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3545
+ C: 0.88591490147445
3546
+ G: 0.038028366175183334
3547
+ T: 0.038028366175183334
3548
+ track: nukes
3549
+ extras:
3550
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3551
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3552
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3553
+ name: IGHV3-23_star_01_234
3554
+ transitions:
3555
+ IGHV3-23_star_01_235: 1.0
3556
+ - !!python/object:python.hmmwriter.State
3557
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3558
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3559
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3560
+ C: 0.038028366175183334
3561
+ G: 0.038028366175183334
3562
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3563
+ track: nukes
3564
+ extras:
3565
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3566
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3567
+ germline: T
3568
+ name: IGHV3-23_star_01_235
3569
+ transitions:
3570
+ IGHV3-23_star_01_236: 1.0
3571
+ - !!python/object:python.hmmwriter.State
3572
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3573
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3574
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3575
+ C: 0.038028366175183334
3576
+ G: 0.88591490147445
3577
+ T: 0.038028366175183334
3578
+ track: nukes
3579
+ extras:
3580
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3581
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3582
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3583
+ name: IGHV3-23_star_01_236
3584
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3585
+ IGHV3-23_star_01_237: 1.0
3586
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3587
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3588
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3589
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3590
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3591
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3592
+ T: 0.88591490147445
3593
+ track: nukes
3594
+ extras:
3595
+ ambiguous_char: N
3596
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3597
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3598
+ name: IGHV3-23_star_01_237
3599
+ transitions:
3600
+ IGHV3-23_star_01_238: 1.0
3601
+ - !!python/object:python.hmmwriter.State
3602
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3603
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3604
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3605
+ C: 0.038028366175183334
3606
+ G: 0.038028366175183334
3607
+ T: 0.038028366175183334
3608
+ track: nukes
3609
+ extras:
3610
+ ambiguous_char: N
3611
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3612
+ germline: A
3613
+ name: IGHV3-23_star_01_238
3614
+ transitions:
3615
+ IGHV3-23_star_01_239: 1.0
3616
+ - !!python/object:python.hmmwriter.State
3617
+ emissions:
3618
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3619
+ A: 0.038028366175183334
3620
+ C: 0.038028366175183334
3621
+ G: 0.038028366175183334
3622
+ T: 0.88591490147445
3623
+ track: nukes
3624
+ extras:
3625
+ ambiguous_char: N
3626
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3627
+ germline: T
3628
+ name: IGHV3-23_star_01_239
3629
+ transitions:
3630
+ IGHV3-23_star_01_240: 1.0
3631
+ - !!python/object:python.hmmwriter.State
3632
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3633
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3634
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3635
+ C: 0.88591490147445
3636
+ G: 0.038028366175183334
3637
+ T: 0.038028366175183334
3638
+ track: nukes
3639
+ extras:
3640
+ ambiguous_char: N
3641
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3642
+ germline: C
3643
+ name: IGHV3-23_star_01_240
3644
+ transitions:
3645
+ IGHV3-23_star_01_241: 1.0
3646
+ - !!python/object:python.hmmwriter.State
3647
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3648
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3649
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3650
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3651
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3652
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3653
+ track: nukes
3654
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3655
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3656
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3657
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3658
+ name: IGHV3-23_star_01_241
3659
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3660
+ IGHV3-23_star_01_242: 1.0
3661
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3662
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3663
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3664
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3665
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3666
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3667
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3668
+ track: nukes
3669
+ extras:
3670
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3671
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3672
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3673
+ name: IGHV3-23_star_01_242
3674
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3675
+ IGHV3-23_star_01_243: 1.0
3676
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3677
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3678
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3679
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3680
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3681
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3682
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3683
+ track: nukes
3684
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3685
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3686
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3687
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3688
+ name: IGHV3-23_star_01_243
3689
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3690
+ IGHV3-23_star_01_244: 1.0
3691
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3692
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3693
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3694
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3695
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3696
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3697
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3698
+ track: nukes
3699
+ extras:
3700
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3701
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3702
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3703
+ name: IGHV3-23_star_01_244
3704
+ transitions:
3705
+ IGHV3-23_star_01_245: 1.0
3706
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3707
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3708
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3709
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3710
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3711
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3712
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3713
+ track: nukes
3714
+ extras:
3715
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3716
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3717
+ germline: A
3718
+ name: IGHV3-23_star_01_245
3719
+ transitions:
3720
+ IGHV3-23_star_01_246: 1.0
3721
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3722
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3723
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3724
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3725
+ C: 0.038028366175183334
3726
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3727
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3728
+ track: nukes
3729
+ extras:
3730
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3731
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3732
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3733
+ name: IGHV3-23_star_01_246
3734
+ transitions:
3735
+ IGHV3-23_star_01_247: 1.0
3736
+ - !!python/object:python.hmmwriter.State
3737
+ emissions:
3738
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3739
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3740
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3741
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3742
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3743
+ track: nukes
3744
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3745
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3746
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3747
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3748
+ name: IGHV3-23_star_01_247
3749
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3750
+ IGHV3-23_star_01_248: 1.0
3751
+ - !!python/object:python.hmmwriter.State
3752
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3753
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3754
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3755
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3756
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3757
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3758
+ track: nukes
3759
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3760
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3761
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3762
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3763
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3764
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3765
+ IGHV3-23_star_01_249: 1.0
3766
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3767
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3768
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3769
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3770
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3771
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3772
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3773
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3774
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3775
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3776
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3777
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3778
+ name: IGHV3-23_star_01_249
3779
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3780
+ IGHV3-23_star_01_250: 1.0
3781
+ - !!python/object:python.hmmwriter.State
3782
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3783
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3784
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3785
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3786
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3787
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3788
+ track: nukes
3789
+ extras:
3790
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3791
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3792
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3793
+ name: IGHV3-23_star_01_250
3794
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3795
+ IGHV3-23_star_01_251: 1.0
3796
+ - !!python/object:python.hmmwriter.State
3797
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3798
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3799
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3800
+ C: 0.88591490147445
3801
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3802
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3803
+ track: nukes
3804
+ extras:
3805
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3806
+ ambiguous_emission_prob: 0.25
3807
+ germline: C
3808
+ name: IGHV3-23_star_01_251
3809
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3810
+ IGHV3-23_star_01_252: 1.0
3811
+ - !!python/object:python.hmmwriter.State
3812
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3813
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3814
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3815
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3816
+ G: 0.038028366175183334
3817
+ T: 0.038028366175183334
3818
+ track: nukes
3819
+ extras:
3820
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3821
+ ambiguous_emission_prob: 0.25
3822
+ germline: A
3823
+ name: IGHV3-23_star_01_252
3824
+ transitions:
3825
+ IGHV3-23_star_01_253: 1.0
3826
+ - !!python/object:python.hmmwriter.State
3827
+ emissions:
3828
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3829
+ A: 0.038028366175183334
3830
+ C: 0.038028366175183334
3831
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3832
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3833
+ track: nukes
3834
+ extras:
3835
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3836
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3837
+ germline: G
3838
+ name: IGHV3-23_star_01_253
3839
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3840
+ IGHV3-23_star_01_254: 1.0
3841
+ - !!python/object:python.hmmwriter.State
3842
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3843
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3844
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3845
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3846
+ G: 0.038028366175183334
3847
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3848
+ track: nukes
3849
+ extras:
3850
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3851
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3852
+ germline: C
3853
+ name: IGHV3-23_star_01_254
3854
+ transitions:
3855
+ IGHV3-23_star_01_255: 1.0
3856
+ - !!python/object:python.hmmwriter.State
3857
+ emissions:
3858
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3859
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3860
+ C: 0.88591490147445
3861
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3862
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3863
+ track: nukes
3864
+ extras:
3865
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3866
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3867
+ germline: C
3868
+ name: IGHV3-23_star_01_255
3869
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3870
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3871
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3872
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3873
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3874
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3875
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3876
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3877
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3878
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3879
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3880
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3881
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3882
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3883
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3884
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3885
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3886
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3887
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3888
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3889
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3890
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3891
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3892
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3893
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3894
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3895
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3896
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3897
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3898
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3899
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3900
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3901
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3902
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3903
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3904
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3905
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3906
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3907
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3908
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3909
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3910
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3911
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3912
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3913
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3914
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3915
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3916
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3917
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3918
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3919
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3920
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3921
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3922
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3923
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3924
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3925
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3926
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3927
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3928
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3929
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3930
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3931
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3932
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3933
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3934
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3935
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3936
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3937
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3938
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3939
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3940
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3941
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3942
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3943
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3944
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3945
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3946
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3947
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3948
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3949
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3950
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3951
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3952
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3953
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3954
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3955
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3956
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3957
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3958
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3959
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3960
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3961
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3962
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3963
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3964
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3965
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3966
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3967
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3968
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3969
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3970
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3971
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3972
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3973
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3974
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3975
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3976
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3977
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3978
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3979
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3980
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3981
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3982
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3983
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3984
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3985
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3986
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3987
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3988
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3989
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3990
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3991
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3992
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3993
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3994
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3995
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3996
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3997
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3998
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3999
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4000
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4001
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4002
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4003
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4004
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4005
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4006
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4007
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4008
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4009
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4010
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4011
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4012
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4013
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4014
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4015
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4016
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4017
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4018
+ name: IGHV3-23_star_01_265
4019
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4020
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4021
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4022
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4023
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4024
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4025
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4026
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4027
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4028
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4029
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4030
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4031
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4032
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4033
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4034
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4035
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4036
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4037
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4038
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4039
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4040
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4041
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4042
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4043
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4044
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4045
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4046
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4047
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4048
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4049
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4050
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4051
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4052
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4053
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4054
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4055
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4056
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4057
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4058
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4059
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4060
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4061
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4062
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4063
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4064
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4065
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4066
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4067
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4068
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4069
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4070
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4071
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4072
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4073
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4074
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4075
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4076
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4077
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4078
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4079
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4080
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4081
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4082
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4083
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4084
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4085
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4086
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4087
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4088
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4089
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4090
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4091
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4092
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4093
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4094
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4095
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4096
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4097
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4098
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4099
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4100
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4101
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4102
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4103
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4104
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4105
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4106
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4107
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4108
+ name: IGHV3-23_star_01_271
4109
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4110
+ IGHV3-23_star_01_272: 1.0
4111
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4112
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4113
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4114
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4115
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4116
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4117
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4118
+ track: nukes
4119
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4120
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4121
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4122
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4123
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4124
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4125
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4126
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4127
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4128
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4129
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4130
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4131
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4132
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4133
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4134
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4135
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4136
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4137
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4138
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4139
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4140
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4141
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4142
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4143
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4144
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4145
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4146
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4147
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4148
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4149
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4150
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4151
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4152
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4153
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4154
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4155
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4156
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4157
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4158
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4159
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4160
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4161
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4162
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4163
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4164
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4165
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4166
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4167
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4168
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4169
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4170
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4171
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4172
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4173
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4174
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4175
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4176
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4177
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4178
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4179
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4180
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4181
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4182
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4183
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4184
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4185
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4186
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4187
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4188
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4189
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4190
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4191
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4192
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4193
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4194
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4195
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4196
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4197
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4198
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4199
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4200
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4201
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4202
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4203
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4204
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4205
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4206
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4207
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4208
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4209
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4210
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4211
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4212
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4213
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4214
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4215
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4216
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4217
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4218
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4219
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4220
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4221
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4222
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4223
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4224
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4225
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4226
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4227
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4228
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4229
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4230
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4231
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4232
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4233
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4234
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4235
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4236
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4237
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4238
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4239
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4240
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4241
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4242
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4243
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4244
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4245
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4246
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4247
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4248
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4249
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4250
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4251
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4252
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4253
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4254
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4255
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4256
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4257
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4258
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4259
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4260
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4261
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4262
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4263
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4264
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4265
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4266
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4267
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4268
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4269
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4270
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4271
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4272
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4273
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4274
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4275
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4276
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4277
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4278
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4279
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4280
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4281
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4282
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4283
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4284
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4285
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4286
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4287
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4288
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4289
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4290
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4291
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4292
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4293
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4294
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4295
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4296
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4297
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4298
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4299
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4300
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4301
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4302
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4303
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4304
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4305
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4306
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4307
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4309
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4310
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4311
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4312
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4313
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4314
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4315
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4316
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4317
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4318
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4319
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4320
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4321
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4322
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4324
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4325
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4326
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4327
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4328
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4329
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4330
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4331
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4332
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4333
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4334
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4335
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4336
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4337
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4338
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4339
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4340
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4341
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4342
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4343
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4344
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4345
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4346
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4347
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4348
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4349
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4350
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4351
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4352
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4353
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4354
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4355
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4356
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4357
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4358
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4359
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4360
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4361
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4362
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4363
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4364
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4365
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4366
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4367
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4368
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4369
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4370
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4371
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4372
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4373
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4374
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4375
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4376
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4378
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4379
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4380
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4381
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4383
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4384
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4385
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4386
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4387
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4388
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4389
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4390
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4391
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4392
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4394
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4395
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4396
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4397
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4399
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4400
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4401
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4402
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4403
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4404
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4405
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4406
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4407
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4408
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4409
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4410
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4411
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4412
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4413
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4414
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4415
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4416
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4417
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4418
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4419
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4420
+ C: 0.038028366175183334
4421
+ G: 0.038028366175183334
4422
+ T: 0.038028366175183334
4423
+ track: nukes
4424
+ extras:
4425
+ ambiguous_char: N
4426
+ ambiguous_emission_prob: 0.25
4427
+ germline: A
4428
+ name: IGHV3-23_star_01_292
4429
+ transitions:
4430
+ IGHV3-23_star_01_293: 0.9
4431
+ end: 0.1
4432
+ - !!python/object:python.hmmwriter.State
4433
+ emissions:
4434
+ probs:
4435
+ A: 0.88591490147445
4436
+ C: 0.038028366175183334
4437
+ G: 0.038028366175183334
4438
+ T: 0.038028366175183334
4439
+ track: nukes
4440
+ extras:
4441
+ ambiguous_char: N
4442
+ ambiguous_emission_prob: 0.25
4443
+ germline: A
4444
+ name: IGHV3-23_star_01_293
4445
+ transitions:
4446
+ IGHV3-23_star_01_294: 0.9
4447
+ end: 0.1
4448
+ - !!python/object:python.hmmwriter.State
4449
+ emissions:
4450
+ probs:
4451
+ A: 0.038028366175183334
4452
+ C: 0.038028366175183334
4453
+ G: 0.88591490147445
4454
+ T: 0.038028366175183334
4455
+ track: nukes
4456
+ extras:
4457
+ ambiguous_char: N
4458
+ ambiguous_emission_prob: 0.25
4459
+ germline: G
4460
+ name: IGHV3-23_star_01_294
4461
+ transitions:
4462
+ IGHV3-23_star_01_295: 0.9
4463
+ end: 0.1
4464
+ - !!python/object:python.hmmwriter.State
4465
+ emissions:
4466
+ probs:
4467
+ A: 0.88591490147445
4468
+ C: 0.038028366175183334
4469
+ G: 0.038028366175183334
4470
+ T: 0.038028366175183334
4471
+ track: nukes
4472
+ extras:
4473
+ ambiguous_char: N
4474
+ ambiguous_emission_prob: 0.25
4475
+ germline: A
4476
+ name: IGHV3-23_star_01_295
4477
+ transitions:
4478
+ end: 1.0
4479
+ tracks:
4480
+ nukes:
4481
+ - A
4482
+ - C
4483
+ - G
4484
+ - T