partis-bcr 1.0.11.post1.dev1__cp312-cp312-macosx_10_13_universal2.whl → 1.0.12__cp312-cp312-macosx_10_13_universal2.whl

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Files changed (647) 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.post1.dev1.data → partis_bcr-1.0.12.data}/scripts/partis-test.py +6 -0
  5. {partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.12.dist-info}/METADATA +1 -1
  6. {partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.12.dist-info}/RECORD +647 -129
  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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  633. test/paired/new-results/test.log +142 -133
  634. test/test.py +6 -0
  635. test/trees.nwk +100 -0
  636. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.12.data}/scripts/cf-alleles.py +0 -0
  637. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.12.data}/scripts/cf-germlines.py +0 -0
  638. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.12.data}/scripts/compare-plotdirs.py +0 -0
  639. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.12.data}/scripts/extract-pairing-info.py +0 -0
  640. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.12.data}/scripts/gctree-run.py +0 -0
  641. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.12.data}/scripts/get-naive-probabilities.py +0 -0
  642. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.12.data}/scripts/parse-output.py +0 -0
  643. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.12.data}/scripts/split-loci.py +0 -0
  644. {partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.12.dist-info}/WHEEL +0 -0
  645. {partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.12.dist-info}/entry_points.txt +0 -0
  646. {partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.12.dist-info}/licenses/COPYING +0 -0
  647. {partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.12.dist-info}/top_level.txt +0 -0
test/new-results/test/parameters/data/hmm/hmms/IGHV2-70D_star_04.yaml ADDED
@@ -0,0 +1,4561 @@
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+ !!python/object:python.hmmwriter.HMM
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+ extras:
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+ gene_prob: 0.021739130434782608
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+ overall_mute_freq: 0.08760869565217394
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+ per_gene_mute_freq: 0.10222647775802059
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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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+ IGHV2-70D_star_04_0: 0.6666666666666666
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+ insert_left_N: 0.33333333333333337
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+ emissions:
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+ transitions:
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+ IGHV2-70D_star_04_0: 0.6666666666666666
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+ insert_left_N: 0.33333333333333337
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+ germline: C
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+ name: IGHV2-70D_star_04_0
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+ IGHV2-70D_star_04_1: 1.0
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+ IGHV2-70D_star_04_5: 1.0
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1184
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1186
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1190
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1199
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1200
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1201
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1228
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1229
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1230
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1231
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1232
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1246
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1259
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1262
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1273
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1274
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1276
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1277
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1288
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1289
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1291
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1292
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1301
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1303
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1306
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1307
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1313
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1316
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1318
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1319
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1322
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1333
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1334
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1336
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1348
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1349
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1351
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1352
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1378
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1379
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1381
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1391
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1393
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1394
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1396
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1397
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1406
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1408
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1409
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1411
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1412
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1421
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1423
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1424
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1426
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1427
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1436
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1438
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1439
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1441
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1442
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1453
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1454
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1456
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1457
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1468
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1469
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1471
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1472
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1483
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1484
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1487
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1741
+ - !!python/object:python.hmmwriter.State
1742
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1743
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1744
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1745
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1746
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1747
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1748
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1749
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1750
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1751
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1752
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1753
+ name: IGHV2-70D_star_04_114
1754
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1755
+ IGHV2-70D_star_04_115: 1.0
1756
+ - !!python/object:python.hmmwriter.State
1757
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1758
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1759
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1760
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1761
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1762
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1763
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1764
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1765
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1766
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1767
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1768
+ name: IGHV2-70D_star_04_115
1769
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1770
+ IGHV2-70D_star_04_116: 1.0
1771
+ - !!python/object:python.hmmwriter.State
1772
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1773
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1774
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1775
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1776
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1777
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1778
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1779
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1780
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1781
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1782
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1783
+ name: IGHV2-70D_star_04_116
1784
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1785
+ IGHV2-70D_star_04_117: 1.0
1786
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1787
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1788
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1789
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1790
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1791
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1792
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1793
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1794
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1795
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1796
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1797
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1798
+ name: IGHV2-70D_star_04_117
1799
+ transitions:
1800
+ IGHV2-70D_star_04_118: 1.0
1801
+ - !!python/object:python.hmmwriter.State
1802
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1803
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1804
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1805
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1806
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1807
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1808
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1809
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1810
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1811
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1812
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1813
+ name: IGHV2-70D_star_04_118
1814
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1815
+ IGHV2-70D_star_04_119: 1.0
1816
+ - !!python/object:python.hmmwriter.State
1817
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1818
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1819
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1820
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1821
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1822
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1823
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1824
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1825
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1826
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1827
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1828
+ name: IGHV2-70D_star_04_119
1829
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1830
+ IGHV2-70D_star_04_120: 1.0
1831
+ - !!python/object:python.hmmwriter.State
1832
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1833
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1834
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1835
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1836
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1837
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1838
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1839
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1840
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1841
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1842
+ germline: C
1843
+ name: IGHV2-70D_star_04_120
1844
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1845
+ IGHV2-70D_star_04_121: 1.0
1846
+ - !!python/object:python.hmmwriter.State
1847
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1848
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1849
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1850
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1851
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1852
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1853
+ track: nukes
1854
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1855
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1856
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1857
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1858
+ name: IGHV2-70D_star_04_121
1859
+ transitions:
1860
+ IGHV2-70D_star_04_122: 1.0
1861
+ - !!python/object:python.hmmwriter.State
1862
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1863
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1864
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1865
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1866
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1867
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1868
+ track: nukes
1869
+ extras:
1870
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1871
+ ambiguous_emission_prob: 0.25
1872
+ germline: G
1873
+ name: IGHV2-70D_star_04_122
1874
+ transitions:
1875
+ IGHV2-70D_star_04_123: 1.0
1876
+ - !!python/object:python.hmmwriter.State
1877
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1878
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1879
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1880
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1881
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1882
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1883
+ track: nukes
1884
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1885
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1886
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1887
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1888
+ name: IGHV2-70D_star_04_123
1889
+ transitions:
1890
+ IGHV2-70D_star_04_124: 1.0
1891
+ - !!python/object:python.hmmwriter.State
1892
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1893
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1894
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1895
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1896
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1897
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1898
+ track: nukes
1899
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1900
+ ambiguous_char: N
1901
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1902
+ germline: C
1903
+ name: IGHV2-70D_star_04_124
1904
+ transitions:
1905
+ IGHV2-70D_star_04_125: 1.0
1906
+ - !!python/object:python.hmmwriter.State
1907
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1908
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1909
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1910
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1911
+ G: 0.03333333333333333
1912
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1913
+ track: nukes
1914
+ extras:
1915
+ ambiguous_char: N
1916
+ ambiguous_emission_prob: 0.25
1917
+ germline: C
1918
+ name: IGHV2-70D_star_04_125
1919
+ transitions:
1920
+ IGHV2-70D_star_04_126: 1.0
1921
+ - !!python/object:python.hmmwriter.State
1922
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1923
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1924
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1925
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1926
+ G: 0.03333333333333333
1927
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1928
+ track: nukes
1929
+ extras:
1930
+ ambiguous_char: N
1931
+ ambiguous_emission_prob: 0.25
1932
+ germline: C
1933
+ name: IGHV2-70D_star_04_126
1934
+ transitions:
1935
+ IGHV2-70D_star_04_127: 1.0
1936
+ - !!python/object:python.hmmwriter.State
1937
+ emissions:
1938
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1939
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1940
+ C: 0.9
1941
+ G: 0.03333333333333333
1942
+ T: 0.03333333333333333
1943
+ track: nukes
1944
+ extras:
1945
+ ambiguous_char: N
1946
+ ambiguous_emission_prob: 0.25
1947
+ germline: C
1948
+ name: IGHV2-70D_star_04_127
1949
+ transitions:
1950
+ IGHV2-70D_star_04_128: 1.0
1951
+ - !!python/object:python.hmmwriter.State
1952
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1953
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1954
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1955
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1956
+ G: 0.03333333333333333
1957
+ T: 0.03333333333333333
1958
+ track: nukes
1959
+ extras:
1960
+ ambiguous_char: N
1961
+ ambiguous_emission_prob: 0.25
1962
+ germline: A
1963
+ name: IGHV2-70D_star_04_128
1964
+ transitions:
1965
+ IGHV2-70D_star_04_129: 1.0
1966
+ - !!python/object:python.hmmwriter.State
1967
+ emissions:
1968
+ probs:
1969
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1970
+ C: 0.03333333333333333
1971
+ G: 0.9
1972
+ T: 0.03333333333333333
1973
+ track: nukes
1974
+ extras:
1975
+ ambiguous_char: N
1976
+ ambiguous_emission_prob: 0.25
1977
+ germline: G
1978
+ name: IGHV2-70D_star_04_129
1979
+ transitions:
1980
+ IGHV2-70D_star_04_130: 1.0
1981
+ - !!python/object:python.hmmwriter.State
1982
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1983
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1984
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1985
+ C: 0.03333333333333333
1986
+ G: 0.9
1987
+ T: 0.03333333333333333
1988
+ track: nukes
1989
+ extras:
1990
+ ambiguous_char: N
1991
+ ambiguous_emission_prob: 0.25
1992
+ germline: G
1993
+ name: IGHV2-70D_star_04_130
1994
+ transitions:
1995
+ IGHV2-70D_star_04_131: 1.0
1996
+ - !!python/object:python.hmmwriter.State
1997
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1998
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1999
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2000
+ C: 0.03333333333333333
2001
+ G: 0.9
2002
+ T: 0.03333333333333333
2003
+ track: nukes
2004
+ extras:
2005
+ ambiguous_char: N
2006
+ ambiguous_emission_prob: 0.25
2007
+ germline: G
2008
+ name: IGHV2-70D_star_04_131
2009
+ transitions:
2010
+ IGHV2-70D_star_04_132: 1.0
2011
+ - !!python/object:python.hmmwriter.State
2012
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2013
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2014
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2015
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2016
+ G: 0.03333333333333333
2017
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2018
+ track: nukes
2019
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2020
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2021
+ ambiguous_emission_prob: 0.25
2022
+ germline: A
2023
+ name: IGHV2-70D_star_04_132
2024
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2025
+ IGHV2-70D_star_04_133: 1.0
2026
+ - !!python/object:python.hmmwriter.State
2027
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2028
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2029
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2030
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2031
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2032
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2033
+ track: nukes
2034
+ extras:
2035
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2036
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2037
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2038
+ name: IGHV2-70D_star_04_133
2039
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2040
+ IGHV2-70D_star_04_134: 1.0
2041
+ - !!python/object:python.hmmwriter.State
2042
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2043
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2044
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2045
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2046
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2047
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2048
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2049
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2050
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2051
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2052
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2053
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2054
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2055
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2056
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2057
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2058
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2059
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2060
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2061
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2062
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2063
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2064
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2065
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2066
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2067
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2068
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2069
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2070
+ IGHV2-70D_star_04_136: 1.0
2071
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2072
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2073
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2074
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2075
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2076
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2077
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2078
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2079
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2080
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2081
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2082
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2083
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2084
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2085
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2086
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2087
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2088
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2089
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2090
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2091
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2092
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2093
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2094
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2095
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2096
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2097
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2098
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2099
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2100
+ IGHV2-70D_star_04_138: 1.0
2101
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2102
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2103
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2104
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2105
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2106
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2107
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2108
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2109
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2110
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2111
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2112
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2113
+ name: IGHV2-70D_star_04_138
2114
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2115
+ IGHV2-70D_star_04_139: 1.0
2116
+ - !!python/object:python.hmmwriter.State
2117
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2118
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2119
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2120
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2121
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2122
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2123
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2124
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2125
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2126
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2127
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2128
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2129
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2130
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2131
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2132
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2133
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2134
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2135
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2136
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2137
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2138
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2139
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2140
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2141
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2142
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2143
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2144
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2145
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2146
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2147
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2148
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2149
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2150
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2151
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2152
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2153
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2154
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2155
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2156
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2157
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2158
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2159
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2160
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2161
+ - !!python/object:python.hmmwriter.State
2162
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2163
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2164
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2165
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2166
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2167
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2168
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2169
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2170
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2171
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2172
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2173
+ name: IGHV2-70D_star_04_142
2174
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2175
+ IGHV2-70D_star_04_143: 1.0
2176
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2177
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2178
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2179
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2180
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2181
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2182
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2183
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2184
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2185
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2186
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2187
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2188
+ name: IGHV2-70D_star_04_143
2189
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2190
+ IGHV2-70D_star_04_144: 1.0
2191
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2192
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2193
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2194
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2195
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2196
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2197
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2198
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2199
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2200
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2201
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2202
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2203
+ name: IGHV2-70D_star_04_144
2204
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2205
+ IGHV2-70D_star_04_145: 1.0
2206
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2207
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2208
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2209
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2210
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2211
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2212
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2213
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2214
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2215
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2216
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2217
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2218
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2219
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2220
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2221
+ - !!python/object:python.hmmwriter.State
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
+ IGHV2-70D_star_04_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
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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
+ name: IGHV2-70D_star_04_151
2309
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2310
+ IGHV2-70D_star_04_152: 1.0
2311
+ - !!python/object:python.hmmwriter.State
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
+ track: nukes
2319
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2320
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2321
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2322
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2323
+ name: IGHV2-70D_star_04_152
2324
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2325
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2326
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2327
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2330
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2331
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2332
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2333
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2336
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2338
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2339
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2340
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2341
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2342
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2345
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2346
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2348
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2351
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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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2360
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2361
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2362
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2363
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2366
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2367
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2368
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2369
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2370
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2371
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2372
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2376
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2378
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2381
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2382
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2383
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2384
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2385
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2386
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2387
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2390
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2391
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2393
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2396
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2398
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2399
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2400
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2401
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2402
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2405
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2406
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2408
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2411
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2413
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2414
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2415
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2416
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2417
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2419
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2420
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2421
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2422
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2423
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2424
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2426
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2427
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2428
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2429
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2430
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2431
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2432
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2434
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2435
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2436
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2437
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2438
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2439
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2441
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2442
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2443
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2444
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2445
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2446
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2447
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2450
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2451
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2452
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2453
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2454
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2456
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2457
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2458
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2459
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2460
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2461
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2462
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2465
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2466
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2468
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2469
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2471
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2473
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2474
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2475
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2476
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2477
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2479
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2480
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2481
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2483
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2486
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2487
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2488
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2489
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2490
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2491
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2492
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2494
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2495
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2496
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2498
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2500
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2501
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2503
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2504
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2505
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2506
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2507
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2509
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2510
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2511
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2512
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2513
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2514
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2516
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2517
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2518
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2519
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2520
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2521
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2522
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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
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2529
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2530
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2531
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2532
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2533
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2534
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2535
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2536
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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
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2544
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2546
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2547
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2548
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2549
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2550
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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
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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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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
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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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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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2636
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2637
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2638
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2639
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2640
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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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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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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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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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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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2690
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2691
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2692
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2693
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2696
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2697
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2698
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2699
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2701
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2702
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2705
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2706
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2708
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2709
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2711
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2713
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2714
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2716
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2717
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2720
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2721
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2723
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2724
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2726
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2727
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2728
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2729
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2731
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2732
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2741
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2743
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2744
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2746
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2747
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2756
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2758
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2759
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2761
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2762
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2765
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2771
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2773
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2774
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2776
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2777
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2781
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2786
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2788
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2789
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2791
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2792
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2795
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2803
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2804
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2805
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2806
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2807
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2818
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2819
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2821
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2822
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2831
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2833
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2834
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2836
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2837
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2846
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2848
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2849
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2851
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2852
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2863
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2866
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2867
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2878
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2879
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2881
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2882
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2891
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2893
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2896
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2897
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2903
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2904
+ extras:
2905
+ ambiguous_char: N
2906
+ ambiguous_emission_prob: 0.25
2907
+ germline: T
2908
+ name: IGHV2-70D_star_04_191
2909
+ transitions:
2910
+ IGHV2-70D_star_04_192: 1.0
2911
+ - !!python/object:python.hmmwriter.State
2912
+ emissions:
2913
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2914
+ A: 0.03333333333333333
2915
+ C: 0.9
2916
+ G: 0.03333333333333333
2917
+ T: 0.03333333333333333
2918
+ track: nukes
2919
+ extras:
2920
+ ambiguous_char: N
2921
+ ambiguous_emission_prob: 0.25
2922
+ germline: C
2923
+ name: IGHV2-70D_star_04_192
2924
+ transitions:
2925
+ IGHV2-70D_star_04_193: 1.0
2926
+ - !!python/object:python.hmmwriter.State
2927
+ emissions:
2928
+ probs:
2929
+ A: 0.03333333333333333
2930
+ C: 0.03333333333333333
2931
+ G: 0.03333333333333333
2932
+ T: 0.9
2933
+ track: nukes
2934
+ extras:
2935
+ ambiguous_char: N
2936
+ ambiguous_emission_prob: 0.25
2937
+ germline: T
2938
+ name: IGHV2-70D_star_04_193
2939
+ transitions:
2940
+ IGHV2-70D_star_04_194: 1.0
2941
+ - !!python/object:python.hmmwriter.State
2942
+ emissions:
2943
+ probs:
2944
+ A: 0.03333333333333333
2945
+ C: 0.03333333333333333
2946
+ G: 0.9
2947
+ T: 0.03333333333333333
2948
+ track: nukes
2949
+ extras:
2950
+ ambiguous_char: N
2951
+ ambiguous_emission_prob: 0.25
2952
+ germline: G
2953
+ name: IGHV2-70D_star_04_194
2954
+ transitions:
2955
+ IGHV2-70D_star_04_195: 1.0
2956
+ - !!python/object:python.hmmwriter.State
2957
+ emissions:
2958
+ probs:
2959
+ A: 0.9
2960
+ C: 0.03333333333333333
2961
+ G: 0.03333333333333333
2962
+ T: 0.03333333333333333
2963
+ track: nukes
2964
+ extras:
2965
+ ambiguous_char: N
2966
+ ambiguous_emission_prob: 0.25
2967
+ germline: A
2968
+ name: IGHV2-70D_star_04_195
2969
+ transitions:
2970
+ IGHV2-70D_star_04_196: 1.0
2971
+ - !!python/object:python.hmmwriter.State
2972
+ emissions:
2973
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2974
+ A: 0.9
2975
+ C: 0.03333333333333333
2976
+ G: 0.03333333333333333
2977
+ T: 0.03333333333333333
2978
+ track: nukes
2979
+ extras:
2980
+ ambiguous_char: N
2981
+ ambiguous_emission_prob: 0.25
2982
+ germline: A
2983
+ name: IGHV2-70D_star_04_196
2984
+ transitions:
2985
+ IGHV2-70D_star_04_197: 1.0
2986
+ - !!python/object:python.hmmwriter.State
2987
+ emissions:
2988
+ probs:
2989
+ A: 0.03333333333333333
2990
+ C: 0.03333333333333333
2991
+ G: 0.9
2992
+ T: 0.03333333333333333
2993
+ track: nukes
2994
+ extras:
2995
+ ambiguous_char: N
2996
+ ambiguous_emission_prob: 0.25
2997
+ germline: G
2998
+ name: IGHV2-70D_star_04_197
2999
+ transitions:
3000
+ IGHV2-70D_star_04_198: 1.0
3001
+ - !!python/object:python.hmmwriter.State
3002
+ emissions:
3003
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3004
+ A: 0.9
3005
+ C: 0.03333333333333333
3006
+ G: 0.03333333333333333
3007
+ T: 0.03333333333333333
3008
+ track: nukes
3009
+ extras:
3010
+ ambiguous_char: N
3011
+ ambiguous_emission_prob: 0.25
3012
+ germline: A
3013
+ name: IGHV2-70D_star_04_198
3014
+ transitions:
3015
+ IGHV2-70D_star_04_199: 1.0
3016
+ - !!python/object:python.hmmwriter.State
3017
+ emissions:
3018
+ probs:
3019
+ A: 0.03333333333333333
3020
+ C: 0.9
3021
+ G: 0.03333333333333333
3022
+ T: 0.03333333333333333
3023
+ track: nukes
3024
+ extras:
3025
+ ambiguous_char: N
3026
+ ambiguous_emission_prob: 0.25
3027
+ germline: C
3028
+ name: IGHV2-70D_star_04_199
3029
+ transitions:
3030
+ IGHV2-70D_star_04_200: 1.0
3031
+ - !!python/object:python.hmmwriter.State
3032
+ emissions:
3033
+ probs:
3034
+ A: 0.03333333333333333
3035
+ C: 0.9
3036
+ G: 0.03333333333333333
3037
+ T: 0.03333333333333333
3038
+ track: nukes
3039
+ extras:
3040
+ ambiguous_char: N
3041
+ ambiguous_emission_prob: 0.25
3042
+ germline: C
3043
+ name: IGHV2-70D_star_04_200
3044
+ transitions:
3045
+ IGHV2-70D_star_04_201: 1.0
3046
+ - !!python/object:python.hmmwriter.State
3047
+ emissions:
3048
+ probs:
3049
+ A: 0.9
3050
+ C: 0.03333333333333333
3051
+ G: 0.03333333333333333
3052
+ T: 0.03333333333333333
3053
+ track: nukes
3054
+ extras:
3055
+ ambiguous_char: N
3056
+ ambiguous_emission_prob: 0.25
3057
+ germline: A
3058
+ name: IGHV2-70D_star_04_201
3059
+ transitions:
3060
+ IGHV2-70D_star_04_202: 1.0
3061
+ - !!python/object:python.hmmwriter.State
3062
+ emissions:
3063
+ probs:
3064
+ A: 0.03333333333333333
3065
+ C: 0.03333333333333333
3066
+ G: 0.9
3067
+ T: 0.03333333333333333
3068
+ track: nukes
3069
+ extras:
3070
+ ambiguous_char: N
3071
+ ambiguous_emission_prob: 0.25
3072
+ germline: G
3073
+ name: IGHV2-70D_star_04_202
3074
+ transitions:
3075
+ IGHV2-70D_star_04_203: 1.0
3076
+ - !!python/object:python.hmmwriter.State
3077
+ emissions:
3078
+ probs:
3079
+ A: 0.03333333333333333
3080
+ C: 0.03333333333333333
3081
+ G: 0.9
3082
+ T: 0.03333333333333333
3083
+ track: nukes
3084
+ extras:
3085
+ ambiguous_char: N
3086
+ ambiguous_emission_prob: 0.25
3087
+ germline: G
3088
+ name: IGHV2-70D_star_04_203
3089
+ transitions:
3090
+ IGHV2-70D_star_04_204: 1.0
3091
+ - !!python/object:python.hmmwriter.State
3092
+ emissions:
3093
+ probs:
3094
+ A: 0.03333333333333333
3095
+ C: 0.9
3096
+ G: 0.03333333333333333
3097
+ T: 0.03333333333333333
3098
+ track: nukes
3099
+ extras:
3100
+ ambiguous_char: N
3101
+ ambiguous_emission_prob: 0.25
3102
+ germline: C
3103
+ name: IGHV2-70D_star_04_204
3104
+ transitions:
3105
+ IGHV2-70D_star_04_205: 1.0
3106
+ - !!python/object:python.hmmwriter.State
3107
+ emissions:
3108
+ probs:
3109
+ A: 0.03333333333333333
3110
+ C: 0.03333333333333333
3111
+ G: 0.03333333333333333
3112
+ T: 0.9
3113
+ track: nukes
3114
+ extras:
3115
+ ambiguous_char: N
3116
+ ambiguous_emission_prob: 0.25
3117
+ germline: T
3118
+ name: IGHV2-70D_star_04_205
3119
+ transitions:
3120
+ IGHV2-70D_star_04_206: 1.0
3121
+ - !!python/object:python.hmmwriter.State
3122
+ emissions:
3123
+ probs:
3124
+ A: 0.03333333333333333
3125
+ C: 0.9
3126
+ G: 0.03333333333333333
3127
+ T: 0.03333333333333333
3128
+ track: nukes
3129
+ extras:
3130
+ ambiguous_char: N
3131
+ ambiguous_emission_prob: 0.25
3132
+ germline: C
3133
+ name: IGHV2-70D_star_04_206
3134
+ transitions:
3135
+ IGHV2-70D_star_04_207: 1.0
3136
+ - !!python/object:python.hmmwriter.State
3137
+ emissions:
3138
+ probs:
3139
+ A: 0.9
3140
+ C: 0.03333333333333333
3141
+ G: 0.03333333333333333
3142
+ T: 0.03333333333333333
3143
+ track: nukes
3144
+ extras:
3145
+ ambiguous_char: N
3146
+ ambiguous_emission_prob: 0.25
3147
+ germline: A
3148
+ name: IGHV2-70D_star_04_207
3149
+ transitions:
3150
+ IGHV2-70D_star_04_208: 1.0
3151
+ - !!python/object:python.hmmwriter.State
3152
+ emissions:
3153
+ probs:
3154
+ A: 0.03333333333333333
3155
+ C: 0.9
3156
+ G: 0.03333333333333333
3157
+ T: 0.03333333333333333
3158
+ track: nukes
3159
+ extras:
3160
+ ambiguous_char: N
3161
+ ambiguous_emission_prob: 0.25
3162
+ germline: C
3163
+ name: IGHV2-70D_star_04_208
3164
+ transitions:
3165
+ IGHV2-70D_star_04_209: 1.0
3166
+ - !!python/object:python.hmmwriter.State
3167
+ emissions:
3168
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3169
+ A: 0.03587185532259167
3170
+ C: 0.892384434032225
3171
+ G: 0.03587185532259167
3172
+ T: 0.03587185532259167
3173
+ track: nukes
3174
+ extras:
3175
+ ambiguous_char: N
3176
+ ambiguous_emission_prob: 0.25
3177
+ germline: C
3178
+ name: IGHV2-70D_star_04_209
3179
+ transitions:
3180
+ IGHV2-70D_star_04_210: 1.0
3181
+ - !!python/object:python.hmmwriter.State
3182
+ emissions:
3183
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3184
+ A: 0.892384434032225
3185
+ C: 0.03587185532259167
3186
+ G: 0.03587185532259167
3187
+ T: 0.03587185532259167
3188
+ track: nukes
3189
+ extras:
3190
+ ambiguous_char: N
3191
+ ambiguous_emission_prob: 0.25
3192
+ germline: A
3193
+ name: IGHV2-70D_star_04_210
3194
+ transitions:
3195
+ IGHV2-70D_star_04_211: 1.0
3196
+ - !!python/object:python.hmmwriter.State
3197
+ emissions:
3198
+ probs:
3199
+ A: 0.03587185532259167
3200
+ C: 0.03587185532259167
3201
+ G: 0.03587185532259167
3202
+ T: 0.892384434032225
3203
+ track: nukes
3204
+ extras:
3205
+ ambiguous_char: N
3206
+ ambiguous_emission_prob: 0.25
3207
+ germline: T
3208
+ name: IGHV2-70D_star_04_211
3209
+ transitions:
3210
+ IGHV2-70D_star_04_212: 1.0
3211
+ - !!python/object:python.hmmwriter.State
3212
+ emissions:
3213
+ probs:
3214
+ A: 0.03587185532259167
3215
+ C: 0.892384434032225
3216
+ G: 0.03587185532259167
3217
+ T: 0.03587185532259167
3218
+ track: nukes
3219
+ extras:
3220
+ ambiguous_char: N
3221
+ ambiguous_emission_prob: 0.25
3222
+ germline: C
3223
+ name: IGHV2-70D_star_04_212
3224
+ transitions:
3225
+ IGHV2-70D_star_04_213: 1.0
3226
+ - !!python/object:python.hmmwriter.State
3227
+ emissions:
3228
+ probs:
3229
+ A: 0.03587185532259167
3230
+ C: 0.03587185532259167
3231
+ G: 0.03587185532259167
3232
+ T: 0.892384434032225
3233
+ track: nukes
3234
+ extras:
3235
+ ambiguous_char: N
3236
+ ambiguous_emission_prob: 0.25
3237
+ germline: T
3238
+ name: IGHV2-70D_star_04_213
3239
+ transitions:
3240
+ IGHV2-70D_star_04_214: 1.0
3241
+ - !!python/object:python.hmmwriter.State
3242
+ emissions:
3243
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3244
+ A: 0.03587185532259167
3245
+ C: 0.892384434032225
3246
+ G: 0.03587185532259167
3247
+ T: 0.03587185532259167
3248
+ track: nukes
3249
+ extras:
3250
+ ambiguous_char: N
3251
+ ambiguous_emission_prob: 0.25
3252
+ germline: C
3253
+ name: IGHV2-70D_star_04_214
3254
+ transitions:
3255
+ IGHV2-70D_star_04_215: 1.0
3256
+ - !!python/object:python.hmmwriter.State
3257
+ emissions:
3258
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3259
+ A: 0.03587185532259167
3260
+ C: 0.892384434032225
3261
+ G: 0.03587185532259167
3262
+ T: 0.03587185532259167
3263
+ track: nukes
3264
+ extras:
3265
+ ambiguous_char: N
3266
+ ambiguous_emission_prob: 0.25
3267
+ germline: C
3268
+ name: IGHV2-70D_star_04_215
3269
+ transitions:
3270
+ IGHV2-70D_star_04_216: 1.0
3271
+ - !!python/object:python.hmmwriter.State
3272
+ emissions:
3273
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3274
+ A: 0.892384434032225
3275
+ C: 0.03587185532259167
3276
+ G: 0.03587185532259167
3277
+ T: 0.03587185532259167
3278
+ track: nukes
3279
+ extras:
3280
+ ambiguous_char: N
3281
+ ambiguous_emission_prob: 0.25
3282
+ germline: A
3283
+ name: IGHV2-70D_star_04_216
3284
+ transitions:
3285
+ IGHV2-70D_star_04_217: 1.0
3286
+ - !!python/object:python.hmmwriter.State
3287
+ emissions:
3288
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3289
+ A: 0.892384434032225
3290
+ C: 0.03587185532259167
3291
+ G: 0.03587185532259167
3292
+ T: 0.03587185532259167
3293
+ track: nukes
3294
+ extras:
3295
+ ambiguous_char: N
3296
+ ambiguous_emission_prob: 0.25
3297
+ germline: A
3298
+ name: IGHV2-70D_star_04_217
3299
+ transitions:
3300
+ IGHV2-70D_star_04_218: 1.0
3301
+ - !!python/object:python.hmmwriter.State
3302
+ emissions:
3303
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3304
+ A: 0.03587185532259167
3305
+ C: 0.03587185532259167
3306
+ G: 0.892384434032225
3307
+ T: 0.03587185532259167
3308
+ track: nukes
3309
+ extras:
3310
+ ambiguous_char: N
3311
+ ambiguous_emission_prob: 0.25
3312
+ germline: G
3313
+ name: IGHV2-70D_star_04_218
3314
+ transitions:
3315
+ IGHV2-70D_star_04_219: 1.0
3316
+ - !!python/object:python.hmmwriter.State
3317
+ emissions:
3318
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3319
+ A: 0.03587185532259167
3320
+ C: 0.03587185532259167
3321
+ G: 0.892384434032225
3322
+ T: 0.03587185532259167
3323
+ track: nukes
3324
+ extras:
3325
+ ambiguous_char: N
3326
+ ambiguous_emission_prob: 0.25
3327
+ germline: G
3328
+ name: IGHV2-70D_star_04_219
3329
+ transitions:
3330
+ IGHV2-70D_star_04_220: 1.0
3331
+ - !!python/object:python.hmmwriter.State
3332
+ emissions:
3333
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3334
+ A: 0.892384434032225
3335
+ C: 0.03587185532259167
3336
+ G: 0.03587185532259167
3337
+ T: 0.03587185532259167
3338
+ track: nukes
3339
+ extras:
3340
+ ambiguous_char: N
3341
+ ambiguous_emission_prob: 0.25
3342
+ germline: A
3343
+ name: IGHV2-70D_star_04_220
3344
+ transitions:
3345
+ IGHV2-70D_star_04_221: 1.0
3346
+ - !!python/object:python.hmmwriter.State
3347
+ emissions:
3348
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3349
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3350
+ C: 0.892384434032225
3351
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3352
+ T: 0.03587185532259167
3353
+ track: nukes
3354
+ extras:
3355
+ ambiguous_char: N
3356
+ ambiguous_emission_prob: 0.25
3357
+ germline: C
3358
+ name: IGHV2-70D_star_04_221
3359
+ transitions:
3360
+ IGHV2-70D_star_04_222: 1.0
3361
+ - !!python/object:python.hmmwriter.State
3362
+ emissions:
3363
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3364
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3365
+ C: 0.03587185532259167
3366
+ G: 0.03587185532259167
3367
+ T: 0.03587185532259167
3368
+ track: nukes
3369
+ extras:
3370
+ ambiguous_char: N
3371
+ ambiguous_emission_prob: 0.25
3372
+ germline: A
3373
+ name: IGHV2-70D_star_04_222
3374
+ transitions:
3375
+ IGHV2-70D_star_04_223: 1.0
3376
+ - !!python/object:python.hmmwriter.State
3377
+ emissions:
3378
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3379
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3380
+ C: 0.892384434032225
3381
+ G: 0.03587185532259167
3382
+ T: 0.03587185532259167
3383
+ track: nukes
3384
+ extras:
3385
+ ambiguous_char: N
3386
+ ambiguous_emission_prob: 0.25
3387
+ germline: C
3388
+ name: IGHV2-70D_star_04_223
3389
+ transitions:
3390
+ IGHV2-70D_star_04_224: 1.0
3391
+ - !!python/object:python.hmmwriter.State
3392
+ emissions:
3393
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3394
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3395
+ C: 0.892384434032225
3396
+ G: 0.03587185532259167
3397
+ T: 0.03587185532259167
3398
+ track: nukes
3399
+ extras:
3400
+ ambiguous_char: N
3401
+ ambiguous_emission_prob: 0.25
3402
+ germline: C
3403
+ name: IGHV2-70D_star_04_224
3404
+ transitions:
3405
+ IGHV2-70D_star_04_225: 1.0
3406
+ - !!python/object:python.hmmwriter.State
3407
+ emissions:
3408
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3409
+ A: 0.03587185532259167
3410
+ C: 0.03587185532259167
3411
+ G: 0.03587185532259167
3412
+ T: 0.892384434032225
3413
+ track: nukes
3414
+ extras:
3415
+ ambiguous_char: N
3416
+ ambiguous_emission_prob: 0.25
3417
+ germline: T
3418
+ name: IGHV2-70D_star_04_225
3419
+ transitions:
3420
+ IGHV2-70D_star_04_226: 1.0
3421
+ - !!python/object:python.hmmwriter.State
3422
+ emissions:
3423
+ probs:
3424
+ A: 0.03587185532259167
3425
+ C: 0.892384434032225
3426
+ G: 0.03587185532259167
3427
+ T: 0.03587185532259167
3428
+ track: nukes
3429
+ extras:
3430
+ ambiguous_char: N
3431
+ ambiguous_emission_prob: 0.25
3432
+ germline: C
3433
+ name: IGHV2-70D_star_04_226
3434
+ transitions:
3435
+ IGHV2-70D_star_04_227: 1.0
3436
+ - !!python/object:python.hmmwriter.State
3437
+ emissions:
3438
+ probs:
3439
+ A: 0.03587185532259167
3440
+ C: 0.892384434032225
3441
+ G: 0.03587185532259167
3442
+ T: 0.03587185532259167
3443
+ track: nukes
3444
+ extras:
3445
+ ambiguous_char: N
3446
+ ambiguous_emission_prob: 0.25
3447
+ germline: C
3448
+ name: IGHV2-70D_star_04_227
3449
+ transitions:
3450
+ IGHV2-70D_star_04_228: 1.0
3451
+ - !!python/object:python.hmmwriter.State
3452
+ emissions:
3453
+ probs:
3454
+ A: 0.892384434032225
3455
+ C: 0.03587185532259167
3456
+ G: 0.03587185532259167
3457
+ T: 0.03587185532259167
3458
+ track: nukes
3459
+ extras:
3460
+ ambiguous_char: N
3461
+ ambiguous_emission_prob: 0.25
3462
+ germline: A
3463
+ name: IGHV2-70D_star_04_228
3464
+ transitions:
3465
+ IGHV2-70D_star_04_229: 1.0
3466
+ - !!python/object:python.hmmwriter.State
3467
+ emissions:
3468
+ probs:
3469
+ A: 0.892384434032225
3470
+ C: 0.03587185532259167
3471
+ G: 0.03587185532259167
3472
+ T: 0.03587185532259167
3473
+ track: nukes
3474
+ extras:
3475
+ ambiguous_char: N
3476
+ ambiguous_emission_prob: 0.25
3477
+ germline: A
3478
+ name: IGHV2-70D_star_04_229
3479
+ transitions:
3480
+ IGHV2-70D_star_04_230: 1.0
3481
+ - !!python/object:python.hmmwriter.State
3482
+ emissions:
3483
+ probs:
3484
+ A: 0.892384434032225
3485
+ C: 0.03587185532259167
3486
+ G: 0.03587185532259167
3487
+ T: 0.03587185532259167
3488
+ track: nukes
3489
+ extras:
3490
+ ambiguous_char: N
3491
+ ambiguous_emission_prob: 0.25
3492
+ germline: A
3493
+ name: IGHV2-70D_star_04_230
3494
+ transitions:
3495
+ IGHV2-70D_star_04_231: 1.0
3496
+ - !!python/object:python.hmmwriter.State
3497
+ emissions:
3498
+ probs:
3499
+ A: 0.892384434032225
3500
+ C: 0.03587185532259167
3501
+ G: 0.03587185532259167
3502
+ T: 0.03587185532259167
3503
+ track: nukes
3504
+ extras:
3505
+ ambiguous_char: N
3506
+ ambiguous_emission_prob: 0.25
3507
+ germline: A
3508
+ name: IGHV2-70D_star_04_231
3509
+ transitions:
3510
+ IGHV2-70D_star_04_232: 1.0
3511
+ - !!python/object:python.hmmwriter.State
3512
+ emissions:
3513
+ probs:
3514
+ A: 0.892384434032225
3515
+ C: 0.03587185532259167
3516
+ G: 0.03587185532259167
3517
+ T: 0.03587185532259167
3518
+ track: nukes
3519
+ extras:
3520
+ ambiguous_char: N
3521
+ ambiguous_emission_prob: 0.25
3522
+ germline: A
3523
+ name: IGHV2-70D_star_04_232
3524
+ transitions:
3525
+ IGHV2-70D_star_04_233: 1.0
3526
+ - !!python/object:python.hmmwriter.State
3527
+ emissions:
3528
+ probs:
3529
+ A: 0.03587185532259167
3530
+ C: 0.892384434032225
3531
+ G: 0.03587185532259167
3532
+ T: 0.03587185532259167
3533
+ track: nukes
3534
+ extras:
3535
+ ambiguous_char: N
3536
+ ambiguous_emission_prob: 0.25
3537
+ germline: C
3538
+ name: IGHV2-70D_star_04_233
3539
+ transitions:
3540
+ IGHV2-70D_star_04_234: 1.0
3541
+ - !!python/object:python.hmmwriter.State
3542
+ emissions:
3543
+ probs:
3544
+ A: 0.03587185532259167
3545
+ C: 0.892384434032225
3546
+ G: 0.03587185532259167
3547
+ T: 0.03587185532259167
3548
+ track: nukes
3549
+ extras:
3550
+ ambiguous_char: N
3551
+ ambiguous_emission_prob: 0.25
3552
+ germline: C
3553
+ name: IGHV2-70D_star_04_234
3554
+ transitions:
3555
+ IGHV2-70D_star_04_235: 1.0
3556
+ - !!python/object:python.hmmwriter.State
3557
+ emissions:
3558
+ probs:
3559
+ A: 0.892384434032225
3560
+ C: 0.03587185532259167
3561
+ G: 0.03587185532259167
3562
+ T: 0.03587185532259167
3563
+ track: nukes
3564
+ extras:
3565
+ ambiguous_char: N
3566
+ ambiguous_emission_prob: 0.25
3567
+ germline: A
3568
+ name: IGHV2-70D_star_04_235
3569
+ transitions:
3570
+ IGHV2-70D_star_04_236: 1.0
3571
+ - !!python/object:python.hmmwriter.State
3572
+ emissions:
3573
+ probs:
3574
+ A: 0.03587185532259167
3575
+ C: 0.03587185532259167
3576
+ G: 0.892384434032225
3577
+ T: 0.03587185532259167
3578
+ track: nukes
3579
+ extras:
3580
+ ambiguous_char: N
3581
+ ambiguous_emission_prob: 0.25
3582
+ germline: G
3583
+ name: IGHV2-70D_star_04_236
3584
+ transitions:
3585
+ IGHV2-70D_star_04_237: 1.0
3586
+ - !!python/object:python.hmmwriter.State
3587
+ emissions:
3588
+ probs:
3589
+ A: 0.03587185532259167
3590
+ C: 0.03587185532259167
3591
+ G: 0.892384434032225
3592
+ T: 0.03587185532259167
3593
+ track: nukes
3594
+ extras:
3595
+ ambiguous_char: N
3596
+ ambiguous_emission_prob: 0.25
3597
+ germline: G
3598
+ name: IGHV2-70D_star_04_237
3599
+ transitions:
3600
+ IGHV2-70D_star_04_238: 1.0
3601
+ - !!python/object:python.hmmwriter.State
3602
+ emissions:
3603
+ probs:
3604
+ A: 0.03587185532259167
3605
+ C: 0.03587185532259167
3606
+ G: 0.03587185532259167
3607
+ T: 0.892384434032225
3608
+ track: nukes
3609
+ extras:
3610
+ ambiguous_char: N
3611
+ ambiguous_emission_prob: 0.25
3612
+ germline: T
3613
+ name: IGHV2-70D_star_04_238
3614
+ transitions:
3615
+ IGHV2-70D_star_04_239: 1.0
3616
+ - !!python/object:python.hmmwriter.State
3617
+ emissions:
3618
+ probs:
3619
+ A: 0.03587185532259167
3620
+ C: 0.03587185532259167
3621
+ G: 0.892384434032225
3622
+ T: 0.03587185532259167
3623
+ track: nukes
3624
+ extras:
3625
+ ambiguous_char: N
3626
+ ambiguous_emission_prob: 0.25
3627
+ germline: G
3628
+ name: IGHV2-70D_star_04_239
3629
+ transitions:
3630
+ IGHV2-70D_star_04_240: 1.0
3631
+ - !!python/object:python.hmmwriter.State
3632
+ emissions:
3633
+ probs:
3634
+ A: 0.03587185532259167
3635
+ C: 0.03587185532259167
3636
+ G: 0.892384434032225
3637
+ T: 0.03587185532259167
3638
+ track: nukes
3639
+ extras:
3640
+ ambiguous_char: N
3641
+ ambiguous_emission_prob: 0.25
3642
+ germline: G
3643
+ name: IGHV2-70D_star_04_240
3644
+ transitions:
3645
+ IGHV2-70D_star_04_241: 1.0
3646
+ - !!python/object:python.hmmwriter.State
3647
+ emissions:
3648
+ probs:
3649
+ A: 0.03587185532259167
3650
+ C: 0.03587185532259167
3651
+ G: 0.03587185532259167
3652
+ T: 0.892384434032225
3653
+ track: nukes
3654
+ extras:
3655
+ ambiguous_char: N
3656
+ ambiguous_emission_prob: 0.25
3657
+ germline: T
3658
+ name: IGHV2-70D_star_04_241
3659
+ transitions:
3660
+ IGHV2-70D_star_04_242: 1.0
3661
+ - !!python/object:python.hmmwriter.State
3662
+ emissions:
3663
+ probs:
3664
+ A: 0.03587185532259167
3665
+ C: 0.892384434032225
3666
+ G: 0.03587185532259167
3667
+ T: 0.03587185532259167
3668
+ track: nukes
3669
+ extras:
3670
+ ambiguous_char: N
3671
+ ambiguous_emission_prob: 0.25
3672
+ germline: C
3673
+ name: IGHV2-70D_star_04_242
3674
+ transitions:
3675
+ IGHV2-70D_star_04_243: 1.0
3676
+ - !!python/object:python.hmmwriter.State
3677
+ emissions:
3678
+ probs:
3679
+ A: 0.03587185532259167
3680
+ C: 0.892384434032225
3681
+ G: 0.03587185532259167
3682
+ T: 0.03587185532259167
3683
+ track: nukes
3684
+ extras:
3685
+ ambiguous_char: N
3686
+ ambiguous_emission_prob: 0.25
3687
+ germline: C
3688
+ name: IGHV2-70D_star_04_243
3689
+ transitions:
3690
+ IGHV2-70D_star_04_244: 1.0
3691
+ - !!python/object:python.hmmwriter.State
3692
+ emissions:
3693
+ probs:
3694
+ A: 0.03587185532259167
3695
+ C: 0.03587185532259167
3696
+ G: 0.03587185532259167
3697
+ T: 0.892384434032225
3698
+ track: nukes
3699
+ extras:
3700
+ ambiguous_char: N
3701
+ ambiguous_emission_prob: 0.25
3702
+ germline: T
3703
+ name: IGHV2-70D_star_04_244
3704
+ transitions:
3705
+ IGHV2-70D_star_04_245: 1.0
3706
+ - !!python/object:python.hmmwriter.State
3707
+ emissions:
3708
+ probs:
3709
+ A: 0.03587185532259167
3710
+ C: 0.03587185532259167
3711
+ G: 0.03587185532259167
3712
+ T: 0.892384434032225
3713
+ track: nukes
3714
+ extras:
3715
+ ambiguous_char: N
3716
+ ambiguous_emission_prob: 0.25
3717
+ germline: T
3718
+ name: IGHV2-70D_star_04_245
3719
+ transitions:
3720
+ IGHV2-70D_star_04_246: 1.0
3721
+ - !!python/object:python.hmmwriter.State
3722
+ emissions:
3723
+ probs:
3724
+ A: 0.892384434032225
3725
+ C: 0.03587185532259167
3726
+ G: 0.03587185532259167
3727
+ T: 0.03587185532259167
3728
+ track: nukes
3729
+ extras:
3730
+ ambiguous_char: N
3731
+ ambiguous_emission_prob: 0.25
3732
+ germline: A
3733
+ name: IGHV2-70D_star_04_246
3734
+ transitions:
3735
+ IGHV2-70D_star_04_247: 1.0
3736
+ - !!python/object:python.hmmwriter.State
3737
+ emissions:
3738
+ probs:
3739
+ A: 0.03587185532259167
3740
+ C: 0.892384434032225
3741
+ G: 0.03587185532259167
3742
+ T: 0.03587185532259167
3743
+ track: nukes
3744
+ extras:
3745
+ ambiguous_char: N
3746
+ ambiguous_emission_prob: 0.25
3747
+ germline: C
3748
+ name: IGHV2-70D_star_04_247
3749
+ transitions:
3750
+ IGHV2-70D_star_04_248: 1.0
3751
+ - !!python/object:python.hmmwriter.State
3752
+ emissions:
3753
+ probs:
3754
+ A: 0.892384434032225
3755
+ C: 0.03587185532259167
3756
+ G: 0.03587185532259167
3757
+ T: 0.03587185532259167
3758
+ track: nukes
3759
+ extras:
3760
+ ambiguous_char: N
3761
+ ambiguous_emission_prob: 0.25
3762
+ germline: A
3763
+ name: IGHV2-70D_star_04_248
3764
+ transitions:
3765
+ IGHV2-70D_star_04_249: 1.0
3766
+ - !!python/object:python.hmmwriter.State
3767
+ emissions:
3768
+ probs:
3769
+ A: 0.892384434032225
3770
+ C: 0.03587185532259167
3771
+ G: 0.03587185532259167
3772
+ T: 0.03587185532259167
3773
+ track: nukes
3774
+ extras:
3775
+ ambiguous_char: N
3776
+ ambiguous_emission_prob: 0.25
3777
+ germline: A
3778
+ name: IGHV2-70D_star_04_249
3779
+ transitions:
3780
+ IGHV2-70D_star_04_250: 1.0
3781
+ - !!python/object:python.hmmwriter.State
3782
+ emissions:
3783
+ probs:
3784
+ A: 0.03587185532259167
3785
+ C: 0.03587185532259167
3786
+ G: 0.03587185532259167
3787
+ T: 0.892384434032225
3788
+ track: nukes
3789
+ extras:
3790
+ ambiguous_char: N
3791
+ ambiguous_emission_prob: 0.25
3792
+ germline: T
3793
+ name: IGHV2-70D_star_04_250
3794
+ transitions:
3795
+ IGHV2-70D_star_04_251: 1.0
3796
+ - !!python/object:python.hmmwriter.State
3797
+ emissions:
3798
+ probs:
3799
+ A: 0.03587185532259167
3800
+ C: 0.03587185532259167
3801
+ G: 0.892384434032225
3802
+ T: 0.03587185532259167
3803
+ track: nukes
3804
+ extras:
3805
+ ambiguous_char: N
3806
+ ambiguous_emission_prob: 0.25
3807
+ germline: G
3808
+ name: IGHV2-70D_star_04_251
3809
+ transitions:
3810
+ IGHV2-70D_star_04_252: 1.0
3811
+ - !!python/object:python.hmmwriter.State
3812
+ emissions:
3813
+ probs:
3814
+ A: 0.892384434032225
3815
+ C: 0.03587185532259167
3816
+ G: 0.03587185532259167
3817
+ T: 0.03587185532259167
3818
+ track: nukes
3819
+ extras:
3820
+ ambiguous_char: N
3821
+ ambiguous_emission_prob: 0.25
3822
+ germline: A
3823
+ name: IGHV2-70D_star_04_252
3824
+ transitions:
3825
+ IGHV2-70D_star_04_253: 1.0
3826
+ - !!python/object:python.hmmwriter.State
3827
+ emissions:
3828
+ probs:
3829
+ A: 0.03587185532259167
3830
+ C: 0.892384434032225
3831
+ G: 0.03587185532259167
3832
+ T: 0.03587185532259167
3833
+ track: nukes
3834
+ extras:
3835
+ ambiguous_char: N
3836
+ ambiguous_emission_prob: 0.25
3837
+ germline: C
3838
+ name: IGHV2-70D_star_04_253
3839
+ transitions:
3840
+ IGHV2-70D_star_04_254: 1.0
3841
+ - !!python/object:python.hmmwriter.State
3842
+ emissions:
3843
+ probs:
3844
+ A: 0.03587185532259167
3845
+ C: 0.892384434032225
3846
+ G: 0.03587185532259167
3847
+ T: 0.03587185532259167
3848
+ track: nukes
3849
+ extras:
3850
+ ambiguous_char: N
3851
+ ambiguous_emission_prob: 0.25
3852
+ germline: C
3853
+ name: IGHV2-70D_star_04_254
3854
+ transitions:
3855
+ IGHV2-70D_star_04_255: 1.0
3856
+ - !!python/object:python.hmmwriter.State
3857
+ emissions:
3858
+ probs:
3859
+ A: 0.892384434032225
3860
+ C: 0.03587185532259167
3861
+ G: 0.03587185532259167
3862
+ T: 0.03587185532259167
3863
+ track: nukes
3864
+ extras:
3865
+ ambiguous_char: N
3866
+ ambiguous_emission_prob: 0.25
3867
+ germline: A
3868
+ name: IGHV2-70D_star_04_255
3869
+ transitions:
3870
+ IGHV2-70D_star_04_256: 1.0
3871
+ - !!python/object:python.hmmwriter.State
3872
+ emissions:
3873
+ probs:
3874
+ A: 0.892384434032225
3875
+ C: 0.03587185532259167
3876
+ G: 0.03587185532259167
3877
+ T: 0.03587185532259167
3878
+ track: nukes
3879
+ extras:
3880
+ ambiguous_char: N
3881
+ ambiguous_emission_prob: 0.25
3882
+ germline: A
3883
+ name: IGHV2-70D_star_04_256
3884
+ transitions:
3885
+ IGHV2-70D_star_04_257: 1.0
3886
+ - !!python/object:python.hmmwriter.State
3887
+ emissions:
3888
+ probs:
3889
+ A: 0.03587185532259167
3890
+ C: 0.892384434032225
3891
+ G: 0.03587185532259167
3892
+ T: 0.03587185532259167
3893
+ track: nukes
3894
+ extras:
3895
+ ambiguous_char: N
3896
+ ambiguous_emission_prob: 0.25
3897
+ germline: C
3898
+ name: IGHV2-70D_star_04_257
3899
+ transitions:
3900
+ IGHV2-70D_star_04_258: 1.0
3901
+ - !!python/object:python.hmmwriter.State
3902
+ emissions:
3903
+ probs:
3904
+ A: 0.892384434032225
3905
+ C: 0.03587185532259167
3906
+ G: 0.03587185532259167
3907
+ T: 0.03587185532259167
3908
+ track: nukes
3909
+ extras:
3910
+ ambiguous_char: N
3911
+ ambiguous_emission_prob: 0.25
3912
+ germline: A
3913
+ name: IGHV2-70D_star_04_258
3914
+ transitions:
3915
+ IGHV2-70D_star_04_259: 1.0
3916
+ - !!python/object:python.hmmwriter.State
3917
+ emissions:
3918
+ probs:
3919
+ A: 0.03587185532259167
3920
+ C: 0.03587185532259167
3921
+ G: 0.03587185532259167
3922
+ T: 0.892384434032225
3923
+ track: nukes
3924
+ extras:
3925
+ ambiguous_char: N
3926
+ ambiguous_emission_prob: 0.25
3927
+ germline: T
3928
+ name: IGHV2-70D_star_04_259
3929
+ transitions:
3930
+ IGHV2-70D_star_04_260: 1.0
3931
+ - !!python/object:python.hmmwriter.State
3932
+ emissions:
3933
+ probs:
3934
+ A: 0.03587185532259167
3935
+ C: 0.03587185532259167
3936
+ G: 0.892384434032225
3937
+ T: 0.03587185532259167
3938
+ track: nukes
3939
+ extras:
3940
+ ambiguous_char: N
3941
+ ambiguous_emission_prob: 0.25
3942
+ germline: G
3943
+ name: IGHV2-70D_star_04_260
3944
+ transitions:
3945
+ IGHV2-70D_star_04_261: 1.0
3946
+ - !!python/object:python.hmmwriter.State
3947
+ emissions:
3948
+ probs:
3949
+ A: 0.03587185532259167
3950
+ C: 0.03587185532259167
3951
+ G: 0.892384434032225
3952
+ T: 0.03587185532259167
3953
+ track: nukes
3954
+ extras:
3955
+ ambiguous_char: N
3956
+ ambiguous_emission_prob: 0.25
3957
+ germline: G
3958
+ name: IGHV2-70D_star_04_261
3959
+ transitions:
3960
+ IGHV2-70D_star_04_262: 1.0
3961
+ - !!python/object:python.hmmwriter.State
3962
+ emissions:
3963
+ probs:
3964
+ A: 0.892384434032225
3965
+ C: 0.03587185532259167
3966
+ G: 0.03587185532259167
3967
+ T: 0.03587185532259167
3968
+ track: nukes
3969
+ extras:
3970
+ ambiguous_char: N
3971
+ ambiguous_emission_prob: 0.25
3972
+ germline: A
3973
+ name: IGHV2-70D_star_04_262
3974
+ transitions:
3975
+ IGHV2-70D_star_04_263: 1.0
3976
+ - !!python/object:python.hmmwriter.State
3977
+ emissions:
3978
+ probs:
3979
+ A: 0.03587185532259167
3980
+ C: 0.892384434032225
3981
+ G: 0.03587185532259167
3982
+ T: 0.03587185532259167
3983
+ track: nukes
3984
+ extras:
3985
+ ambiguous_char: N
3986
+ ambiguous_emission_prob: 0.25
3987
+ germline: C
3988
+ name: IGHV2-70D_star_04_263
3989
+ transitions:
3990
+ IGHV2-70D_star_04_264: 1.0
3991
+ - !!python/object:python.hmmwriter.State
3992
+ emissions:
3993
+ probs:
3994
+ A: 0.03587185532259167
3995
+ C: 0.892384434032225
3996
+ G: 0.03587185532259167
3997
+ T: 0.03587185532259167
3998
+ track: nukes
3999
+ extras:
4000
+ ambiguous_char: N
4001
+ ambiguous_emission_prob: 0.25
4002
+ germline: C
4003
+ name: IGHV2-70D_star_04_264
4004
+ transitions:
4005
+ IGHV2-70D_star_04_265: 1.0
4006
+ - !!python/object:python.hmmwriter.State
4007
+ emissions:
4008
+ probs:
4009
+ A: 0.03587185532259167
4010
+ C: 0.892384434032225
4011
+ G: 0.03587185532259167
4012
+ T: 0.03587185532259167
4013
+ track: nukes
4014
+ extras:
4015
+ ambiguous_char: N
4016
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4017
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4018
+ name: IGHV2-70D_star_04_265
4019
+ transitions:
4020
+ IGHV2-70D_star_04_266: 1.0
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
+ track: nukes
4029
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4030
+ ambiguous_char: N
4031
+ ambiguous_emission_prob: 0.25
4032
+ germline: T
4033
+ name: IGHV2-70D_star_04_266
4034
+ transitions:
4035
+ IGHV2-70D_star_04_267: 1.0
4036
+ - !!python/object:python.hmmwriter.State
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
+ track: nukes
4044
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4045
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4046
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4047
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4048
+ name: IGHV2-70D_star_04_267
4049
+ transitions:
4050
+ IGHV2-70D_star_04_268: 1.0
4051
+ - !!python/object:python.hmmwriter.State
4052
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4053
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4054
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4055
+ C: 0.03587185532259167
4056
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4057
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4058
+ track: nukes
4059
+ extras:
4060
+ ambiguous_char: N
4061
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4062
+ germline: T
4063
+ name: IGHV2-70D_star_04_268
4064
+ transitions:
4065
+ IGHV2-70D_star_04_269: 1.0
4066
+ - !!python/object:python.hmmwriter.State
4067
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4068
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4069
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4070
+ C: 0.03587185532259167
4071
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4072
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4073
+ track: nukes
4074
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4075
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4076
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4077
+ germline: G
4078
+ name: IGHV2-70D_star_04_269
4079
+ transitions:
4080
+ IGHV2-70D_star_04_270: 1.0
4081
+ - !!python/object:python.hmmwriter.State
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
+ name: IGHV2-70D_star_04_270
4094
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4095
+ IGHV2-70D_star_04_271: 1.0
4096
+ - !!python/object:python.hmmwriter.State
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
+ track: nukes
4104
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4105
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4106
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4107
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4108
+ name: IGHV2-70D_star_04_271
4109
+ transitions:
4110
+ IGHV2-70D_star_04_272: 1.0
4111
+ - !!python/object:python.hmmwriter.State
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
+ name: IGHV2-70D_star_04_272
4124
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4125
+ IGHV2-70D_star_04_273: 1.0
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
+ track: nukes
4134
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4135
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4136
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4137
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4138
+ name: IGHV2-70D_star_04_273
4139
+ transitions:
4140
+ IGHV2-70D_star_04_274: 1.0
4141
+ - !!python/object:python.hmmwriter.State
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
+ track: nukes
4149
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4150
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4151
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4152
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4153
+ name: IGHV2-70D_star_04_274
4154
+ transitions:
4155
+ IGHV2-70D_star_04_275: 1.0
4156
+ - !!python/object:python.hmmwriter.State
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
+ track: nukes
4164
+ extras:
4165
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4166
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4167
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4168
+ name: IGHV2-70D_star_04_275
4169
+ transitions:
4170
+ IGHV2-70D_star_04_276: 1.0
4171
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4172
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4173
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4174
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4175
+ C: 0.03587185532259167
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
+ name: IGHV2-70D_star_04_276
4184
+ transitions:
4185
+ IGHV2-70D_star_04_277: 1.0
4186
+ - !!python/object:python.hmmwriter.State
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
+ name: IGHV2-70D_star_04_277
4199
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4200
+ IGHV2-70D_star_04_278: 1.0
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
+ track: nukes
4209
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4210
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4211
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4212
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4213
+ name: IGHV2-70D_star_04_278
4214
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4215
+ IGHV2-70D_star_04_279: 1.0
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
+ track: nukes
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
+ IGHV2-70D_star_04_280: 1.0
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
+ IGHV2-70D_star_04_282: 1.0
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
+ name: IGHV2-70D_star_04_282
4274
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4275
+ IGHV2-70D_star_04_283: 1.0
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
+ track: nukes
4284
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4285
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4286
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4287
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4288
+ name: IGHV2-70D_star_04_283
4289
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4290
+ IGHV2-70D_star_04_284: 1.0
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
+ track: nukes
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
+ IGHV2-70D_star_04_285: 1.0
4306
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4307
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4308
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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
+ IGHV2-70D_star_04_286: 1.0
4321
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4322
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4323
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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
+ IGHV2-70D_star_04_287: 1.0
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
+ transitions:
4365
+ IGHV2-70D_star_04_289: 1.0
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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4377
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4378
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4379
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4380
+ IGHV2-70D_star_04_290: 1.0
4381
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4382
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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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4393
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4394
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4395
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4396
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4397
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4398
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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
+ end: 0.10526315789473684
4413
+ - !!python/object:python.hmmwriter.State
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
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4421
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4422
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4423
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4424
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4425
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4426
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4427
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4428
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4429
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4430
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4431
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4432
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4433
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4434
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4435
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4436
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4437
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4438
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4439
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4440
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4441
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4442
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4443
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4444
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4445
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4446
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4447
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4448
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4449
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4450
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4451
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4452
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4453
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4455
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4456
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4457
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4458
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4459
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4460
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4461
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4462
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4463
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4464
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4465
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4466
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4467
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4468
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4469
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4470
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4471
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4472
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4473
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4474
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4475
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4476
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4477
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4478
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4479
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4480
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4481
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4482
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4483
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4484
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4485
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4486
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4487
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4488
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4489
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4490
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4491
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4492
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4493
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4494
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4495
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4496
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4497
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4498
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4499
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4500
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4501
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4502
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4503
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4504
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4505
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4506
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4507
+ IGHV2-70D_star_04_298: 0.8947368421052632
4508
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4509
+ - !!python/object:python.hmmwriter.State
4510
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4512
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4513
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4514
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4515
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4516
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4517
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4518
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4519
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4520
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4521
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4522
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4523
+ IGHV2-70D_star_04_299: 0.8947368421052632
4524
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4525
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4526
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4527
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4528
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4529
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4530
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4531
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4532
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4533
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4534
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4535
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4536
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4537
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4538
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4539
+ IGHV2-70D_star_04_300: 0.8947368421052632
4540
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4541
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4542
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4543
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4545
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4546
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4547
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4548
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4549
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4550
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4551
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4552
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4553
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4554
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4555
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4556
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4557
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4558
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4559
+ - C
4560
+ - G
4561
+ - T