partis-bcr 1.0.11.post1.dev1__cp312-cp312-macosx_10_13_universal2.whl → 1.0.11.post1.dev7__cp312-cp312-macosx_10_13_universal2.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (645) 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-1.0.11.post1.dev7.data}/scripts/partis-test.py +6 -0
  5. {partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.11.post1.dev7.dist-info}/METADATA +1 -1
  6. {partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.11.post1.dev7.dist-info}/RECORD +645 -127
  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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  634. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/cf-alleles.py +0 -0
  635. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/cf-germlines.py +0 -0
  636. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/compare-plotdirs.py +0 -0
  637. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/extract-pairing-info.py +0 -0
  638. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/gctree-run.py +0 -0
  639. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/get-naive-probabilities.py +0 -0
  640. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/parse-output.py +0 -0
  641. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev7.data}/scripts/split-loci.py +0 -0
  642. {partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.11.post1.dev7.dist-info}/WHEEL +0 -0
  643. {partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.11.post1.dev7.dist-info}/entry_points.txt +0 -0
  644. {partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.11.post1.dev7.dist-info}/licenses/COPYING +0 -0
  645. {partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.11.post1.dev7.dist-info}/top_level.txt +0 -0
test/new-results/test/parameters/simu/sw/hmms/IGHV4-61_star_01.yaml ADDED
@@ -0,0 +1,4529 @@
1
+ !!python/object:python.hmmwriter.HMM
2
+ extras:
3
+ gene_prob: 0.2222222222222222
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+ overall_mute_freq: 0.012222222222222223
5
+ per_gene_mute_freq: 0.10813409322176055
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+ name: IGHV4-61_star_01
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+ states:
8
+ - !!python/object:python.hmmwriter.State
9
+ emissions: null
10
+ extras: {}
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+ name: init
12
+ transitions:
13
+ IGHV4-61_star_01_0: 0.6666666666666666
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+ insert_left_N: 0.33333333333333337
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+ - !!python/object:python.hmmwriter.State
16
+ emissions:
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+ probs:
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+ A: 0.25
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+ C: 0.25
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+ G: 0.25
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+ T: 0.25
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+ track: nukes
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+ extras:
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+ ambiguous_char: N
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+ ambiguous_emission_prob: 0.25
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+ germline: N
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+ name: insert_left_N
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+ transitions:
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+ IGHV4-61_star_01_0: 0.6666666666666666
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+ insert_left_N: 0.33333333333333337
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+ - !!python/object:python.hmmwriter.State
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+ emissions:
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+ G: 0.0356608468248
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+ track: nukes
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+ extras:
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+ ambiguous_char: N
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+ ambiguous_emission_prob: 0.25
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+ germline: C
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+ name: IGHV4-61_star_01_0
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+ transitions:
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+ IGHV4-61_star_01_1: 1.0
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+ - !!python/object:python.hmmwriter.State
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+ emissions:
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+ probs:
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+ A: 0.8930174595256
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+ ambiguous_char: N
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+ ambiguous_emission_prob: 0.25
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+ germline: A
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+ name: IGHV4-61_star_01_1
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+ transitions:
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+ IGHV4-61_star_01_2: 1.0
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+ - !!python/object:python.hmmwriter.State
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+ emissions:
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+ ambiguous_char: N
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+ ambiguous_emission_prob: 0.25
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+ germline: G
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+ name: IGHV4-61_star_01_2
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+ transitions:
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+ IGHV4-61_star_01_3: 1.0
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+ - !!python/object:python.hmmwriter.State
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+ emissions:
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+ germline: G
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+ name: IGHV4-61_star_01_3
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+ transitions:
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+ IGHV4-61_star_01_4: 1.0
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+ - !!python/object:python.hmmwriter.State
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+ emissions:
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+ ambiguous_char: N
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+ ambiguous_emission_prob: 0.25
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+ germline: T
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+ name: IGHV4-61_star_01_4
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+ transitions:
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+ IGHV4-61_star_01_5: 1.0
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+ - !!python/object:python.hmmwriter.State
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+ emissions:
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+ name: IGHV4-61_star_01_5
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+ transitions:
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+ IGHV4-61_star_01_6: 1.0
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+ - !!python/object:python.hmmwriter.State
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+ germline: C
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+ name: IGHV4-61_star_01_6
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+ transitions:
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+ IGHV4-61_star_01_7: 1.0
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+ - !!python/object:python.hmmwriter.State
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+ emissions:
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+ germline: A
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+ name: IGHV4-61_star_01_7
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+ transitions:
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+ IGHV4-61_star_01_8: 1.0
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+ - !!python/object:python.hmmwriter.State
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+ emissions:
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+ track: nukes
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+ germline: G
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+ name: IGHV4-61_star_01_8
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+ transitions:
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+ IGHV4-61_star_01_9: 1.0
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+ - !!python/object:python.hmmwriter.State
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+ emissions:
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+ germline: C
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+ name: IGHV4-61_star_01_9
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+ transitions:
180
+ IGHV4-61_star_01_10: 1.0
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+ - !!python/object:python.hmmwriter.State
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+ emissions:
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+ track: nukes
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+ extras:
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+ ambiguous_char: N
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+ ambiguous_emission_prob: 0.25
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+ germline: T
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+ name: IGHV4-61_star_01_10
194
+ transitions:
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+ IGHV4-61_star_01_11: 1.0
196
+ - !!python/object:python.hmmwriter.State
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+ emissions:
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+ G: 0.8930174595256
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+ ambiguous_emission_prob: 0.25
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+ germline: G
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+ name: IGHV4-61_star_01_11
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+ transitions:
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+ IGHV4-61_star_01_12: 1.0
211
+ - !!python/object:python.hmmwriter.State
212
+ emissions:
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+ A: 0.0356608468248
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+ C: 0.8930174595256
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+ G: 0.0356608468248
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+ T: 0.0356608468248
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+ track: nukes
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+ extras:
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+ ambiguous_char: N
221
+ ambiguous_emission_prob: 0.25
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+ germline: C
223
+ name: IGHV4-61_star_01_12
224
+ transitions:
225
+ IGHV4-61_star_01_13: 1.0
226
+ - !!python/object:python.hmmwriter.State
227
+ emissions:
228
+ probs:
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+ A: 0.8930174595256
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+ C: 0.0356608468248
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+ G: 0.0356608468248
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+ track: nukes
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+ ambiguous_char: N
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+ ambiguous_emission_prob: 0.25
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+ germline: A
238
+ name: IGHV4-61_star_01_13
239
+ transitions:
240
+ IGHV4-61_star_01_14: 1.0
241
+ - !!python/object:python.hmmwriter.State
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+ emissions:
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+ germline: G
253
+ name: IGHV4-61_star_01_14
254
+ transitions:
255
+ IGHV4-61_star_01_15: 1.0
256
+ - !!python/object:python.hmmwriter.State
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+ emissions:
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266
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+ germline: G
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+ name: IGHV4-61_star_01_15
269
+ transitions:
270
+ IGHV4-61_star_01_16: 1.0
271
+ - !!python/object:python.hmmwriter.State
272
+ emissions:
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+ track: nukes
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+ ambiguous_char: N
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+ germline: A
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+ name: IGHV4-61_star_01_16
284
+ transitions:
285
+ IGHV4-61_star_01_17: 1.0
286
+ - !!python/object:python.hmmwriter.State
287
+ emissions:
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+ germline: G
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+ name: IGHV4-61_star_01_17
299
+ transitions:
300
+ IGHV4-61_star_01_18: 1.0
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+ - !!python/object:python.hmmwriter.State
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+ emissions:
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+ name: IGHV4-61_star_01_18
314
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315
+ IGHV4-61_star_01_19: 1.0
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+ - !!python/object:python.hmmwriter.State
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+ IGHV4-61_star_01_20: 1.0
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+ - !!python/object:python.hmmwriter.State
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+ emissions:
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+ - !!python/object:python.hmmwriter.State
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1172
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1175
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1177
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1186
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1187
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1200
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1201
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1231
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1232
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1235
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1247
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1261
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1262
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1265
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1266
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1276
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1277
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1280
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1281
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1291
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1292
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1301
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1306
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1307
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1310
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1311
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1316
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1319
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1320
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1321
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1322
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1325
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1326
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1334
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1336
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1337
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1341
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1349
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1351
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1352
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1355
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1356
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1367
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1371
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1376
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1379
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1381
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1382
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1385
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1386
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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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1401
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1406
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1409
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1411
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1412
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1415
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1416
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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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1430
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1431
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1432
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1436
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1438
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1439
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1440
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1441
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1442
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1445
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1446
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1453
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1454
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1456
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1457
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1460
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1471
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1472
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1484
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1487
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1490
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1500
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1502
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1517
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1520
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1532
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1546
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1547
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1562
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1577
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1592
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1607
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1622
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1637
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1652
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1667
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1670
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1682
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1697
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1712
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1727
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1730
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1731
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1732
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1733
+ track: nukes
1734
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1735
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1736
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1737
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1738
+ name: IGHV4-61_star_01_113
1739
+ transitions:
1740
+ IGHV4-61_star_01_114: 1.0
1741
+ - !!python/object:python.hmmwriter.State
1742
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1743
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1744
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1745
+ C: 0.0356608468248
1746
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1747
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1748
+ track: nukes
1749
+ extras:
1750
+ ambiguous_char: N
1751
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1752
+ germline: A
1753
+ name: IGHV4-61_star_01_114
1754
+ transitions:
1755
+ IGHV4-61_star_01_115: 1.0
1756
+ - !!python/object:python.hmmwriter.State
1757
+ emissions:
1758
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1759
+ A: 0.0356608468248
1760
+ C: 0.0356608468248
1761
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1762
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1763
+ track: nukes
1764
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1765
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1766
+ ambiguous_emission_prob: 0.25
1767
+ germline: T
1768
+ name: IGHV4-61_star_01_115
1769
+ transitions:
1770
+ IGHV4-61_star_01_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
+ C: 0.8930174595256
1776
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1777
+ T: 0.0356608468248
1778
+ track: nukes
1779
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1780
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1781
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1782
+ germline: C
1783
+ name: IGHV4-61_star_01_116
1784
+ transitions:
1785
+ IGHV4-61_star_01_117: 1.0
1786
+ - !!python/object:python.hmmwriter.State
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
+ track: nukes
1794
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1795
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1796
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1797
+ germline: C
1798
+ name: IGHV4-61_star_01_117
1799
+ transitions:
1800
+ IGHV4-61_star_01_118: 1.0
1801
+ - !!python/object:python.hmmwriter.State
1802
+ emissions:
1803
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1804
+ A: 0.0356608468248
1805
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1806
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1807
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1808
+ track: nukes
1809
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1810
+ ambiguous_char: N
1811
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1812
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1813
+ name: IGHV4-61_star_01_118
1814
+ transitions:
1815
+ IGHV4-61_star_01_119: 1.0
1816
+ - !!python/object:python.hmmwriter.State
1817
+ emissions:
1818
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1819
+ A: 0.0356608468248
1820
+ C: 0.0356608468248
1821
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1822
+ T: 0.0356608468248
1823
+ track: nukes
1824
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1825
+ ambiguous_char: N
1826
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1827
+ germline: G
1828
+ name: IGHV4-61_star_01_119
1829
+ transitions:
1830
+ IGHV4-61_star_01_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
+ T: 0.0356608468248
1838
+ track: nukes
1839
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1840
+ ambiguous_char: N
1841
+ ambiguous_emission_prob: 0.25
1842
+ germline: C
1843
+ name: IGHV4-61_star_01_120
1844
+ transitions:
1845
+ IGHV4-61_star_01_121: 1.0
1846
+ - !!python/object:python.hmmwriter.State
1847
+ emissions:
1848
+ probs:
1849
+ A: 0.8930174595256
1850
+ C: 0.0356608468248
1851
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1852
+ T: 0.0356608468248
1853
+ track: nukes
1854
+ extras:
1855
+ ambiguous_char: N
1856
+ ambiguous_emission_prob: 0.25
1857
+ germline: A
1858
+ name: IGHV4-61_star_01_121
1859
+ transitions:
1860
+ IGHV4-61_star_01_122: 1.0
1861
+ - !!python/object:python.hmmwriter.State
1862
+ emissions:
1863
+ probs:
1864
+ A: 0.0356608468248
1865
+ C: 0.0356608468248
1866
+ G: 0.8930174595256
1867
+ T: 0.0356608468248
1868
+ track: nukes
1869
+ extras:
1870
+ ambiguous_char: N
1871
+ ambiguous_emission_prob: 0.25
1872
+ germline: G
1873
+ name: IGHV4-61_star_01_122
1874
+ transitions:
1875
+ IGHV4-61_star_01_123: 1.0
1876
+ - !!python/object:python.hmmwriter.State
1877
+ emissions:
1878
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1879
+ A: 0.0356608468248
1880
+ C: 0.8930174595256
1881
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1882
+ T: 0.0356608468248
1883
+ track: nukes
1884
+ extras:
1885
+ ambiguous_char: N
1886
+ ambiguous_emission_prob: 0.25
1887
+ germline: C
1888
+ name: IGHV4-61_star_01_123
1889
+ transitions:
1890
+ IGHV4-61_star_01_124: 1.0
1891
+ - !!python/object:python.hmmwriter.State
1892
+ emissions:
1893
+ probs:
1894
+ A: 0.0356608468248
1895
+ C: 0.8930174595256
1896
+ G: 0.0356608468248
1897
+ T: 0.0356608468248
1898
+ track: nukes
1899
+ extras:
1900
+ ambiguous_char: N
1901
+ ambiguous_emission_prob: 0.25
1902
+ germline: C
1903
+ name: IGHV4-61_star_01_124
1904
+ transitions:
1905
+ IGHV4-61_star_01_125: 1.0
1906
+ - !!python/object:python.hmmwriter.State
1907
+ emissions:
1908
+ probs:
1909
+ A: 0.0356608468248
1910
+ C: 0.8930174595256
1911
+ G: 0.0356608468248
1912
+ T: 0.0356608468248
1913
+ track: nukes
1914
+ extras:
1915
+ ambiguous_char: N
1916
+ ambiguous_emission_prob: 0.25
1917
+ germline: C
1918
+ name: IGHV4-61_star_01_125
1919
+ transitions:
1920
+ IGHV4-61_star_01_126: 1.0
1921
+ - !!python/object:python.hmmwriter.State
1922
+ emissions:
1923
+ probs:
1924
+ A: 0.03666666666666667
1925
+ C: 0.89
1926
+ G: 0.03666666666666667
1927
+ T: 0.03666666666666667
1928
+ track: nukes
1929
+ extras:
1930
+ ambiguous_char: N
1931
+ ambiguous_emission_prob: 0.25
1932
+ germline: C
1933
+ name: IGHV4-61_star_01_126
1934
+ transitions:
1935
+ IGHV4-61_star_01_127: 1.0
1936
+ - !!python/object:python.hmmwriter.State
1937
+ emissions:
1938
+ probs:
1939
+ A: 0.0356608468248
1940
+ C: 0.8930174595256
1941
+ G: 0.0356608468248
1942
+ T: 0.0356608468248
1943
+ track: nukes
1944
+ extras:
1945
+ ambiguous_char: N
1946
+ ambiguous_emission_prob: 0.25
1947
+ germline: C
1948
+ name: IGHV4-61_star_01_127
1949
+ transitions:
1950
+ IGHV4-61_star_01_128: 1.0
1951
+ - !!python/object:python.hmmwriter.State
1952
+ emissions:
1953
+ probs:
1954
+ A: 0.8930174595256
1955
+ C: 0.0356608468248
1956
+ G: 0.0356608468248
1957
+ T: 0.0356608468248
1958
+ track: nukes
1959
+ extras:
1960
+ ambiguous_char: N
1961
+ ambiguous_emission_prob: 0.25
1962
+ germline: A
1963
+ name: IGHV4-61_star_01_128
1964
+ transitions:
1965
+ IGHV4-61_star_01_129: 1.0
1966
+ - !!python/object:python.hmmwriter.State
1967
+ emissions:
1968
+ probs:
1969
+ A: 0.0356608468248
1970
+ C: 0.0356608468248
1971
+ G: 0.8930174595256
1972
+ T: 0.0356608468248
1973
+ track: nukes
1974
+ extras:
1975
+ ambiguous_char: N
1976
+ ambiguous_emission_prob: 0.25
1977
+ germline: G
1978
+ name: IGHV4-61_star_01_129
1979
+ transitions:
1980
+ IGHV4-61_star_01_130: 1.0
1981
+ - !!python/object:python.hmmwriter.State
1982
+ emissions:
1983
+ probs:
1984
+ A: 0.0356608468248
1985
+ C: 0.0356608468248
1986
+ G: 0.8930174595256
1987
+ T: 0.0356608468248
1988
+ track: nukes
1989
+ extras:
1990
+ ambiguous_char: N
1991
+ ambiguous_emission_prob: 0.25
1992
+ germline: G
1993
+ name: IGHV4-61_star_01_130
1994
+ transitions:
1995
+ IGHV4-61_star_01_131: 1.0
1996
+ - !!python/object:python.hmmwriter.State
1997
+ emissions:
1998
+ probs:
1999
+ A: 0.0356608468248
2000
+ C: 0.0356608468248
2001
+ G: 0.8930174595256
2002
+ T: 0.0356608468248
2003
+ track: nukes
2004
+ extras:
2005
+ ambiguous_char: N
2006
+ ambiguous_emission_prob: 0.25
2007
+ germline: G
2008
+ name: IGHV4-61_star_01_131
2009
+ transitions:
2010
+ IGHV4-61_star_01_132: 1.0
2011
+ - !!python/object:python.hmmwriter.State
2012
+ emissions:
2013
+ probs:
2014
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2015
+ C: 0.0356608468248
2016
+ G: 0.0356608468248
2017
+ T: 0.0356608468248
2018
+ track: nukes
2019
+ extras:
2020
+ ambiguous_char: N
2021
+ ambiguous_emission_prob: 0.25
2022
+ germline: A
2023
+ name: IGHV4-61_star_01_132
2024
+ transitions:
2025
+ IGHV4-61_star_01_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
+ C: 0.0356608468248
2031
+ G: 0.0356608468248
2032
+ T: 0.0356608468248
2033
+ track: nukes
2034
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2035
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2036
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2037
+ germline: A
2038
+ name: IGHV4-61_star_01_133
2039
+ transitions:
2040
+ IGHV4-61_star_01_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
+ T: 0.0356608468248
2048
+ track: nukes
2049
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2050
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2051
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2052
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2053
+ name: IGHV4-61_star_01_134
2054
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2055
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2056
+ - !!python/object:python.hmmwriter.State
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
+ name: IGHV4-61_star_01_135
2069
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2070
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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
+ name: IGHV4-61_star_01_136
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
+ name: IGHV4-61_star_01_137
2099
+ transitions:
2100
+ IGHV4-61_star_01_138: 1.0
2101
+ - !!python/object:python.hmmwriter.State
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
+ track: nukes
2109
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2110
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2111
+ ambiguous_emission_prob: 0.25
2112
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2113
+ name: IGHV4-61_star_01_138
2114
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2115
+ IGHV4-61_star_01_139: 1.0
2116
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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
+ track: nukes
2124
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2125
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2126
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2127
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2128
+ name: IGHV4-61_star_01_139
2129
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2130
+ IGHV4-61_star_01_140: 1.0
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
+ track: nukes
2139
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2140
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2141
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2142
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2143
+ name: IGHV4-61_star_01_140
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
+ track: nukes
2154
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2155
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2156
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2157
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2158
+ name: IGHV4-61_star_01_141
2159
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2160
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2161
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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
+ track: nukes
2169
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2170
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2171
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2172
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2173
+ name: IGHV4-61_star_01_142
2174
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2175
+ IGHV4-61_star_01_143: 1.0
2176
+ - !!python/object:python.hmmwriter.State
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
+ track: nukes
2184
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2185
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2186
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2187
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2188
+ name: IGHV4-61_star_01_143
2189
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2190
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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: IGHV4-61_star_01_144
2204
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2205
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2206
+ - !!python/object:python.hmmwriter.State
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
+ name: IGHV4-61_star_01_145
2219
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2220
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2221
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2222
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2223
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2224
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2225
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2226
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2227
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2228
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2229
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2230
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2231
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2232
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2233
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2234
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2235
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2236
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2237
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2238
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2239
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2240
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2241
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2242
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2243
+ track: nukes
2244
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2245
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2246
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2247
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2248
+ name: IGHV4-61_star_01_147
2249
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2250
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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
+ name: IGHV4-61_star_01_148
2264
+ transitions:
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
+ name: IGHV4-61_star_01_149
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
+ track: nukes
2289
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2290
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2291
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2292
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2293
+ name: IGHV4-61_star_01_150
2294
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2295
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2296
+ - !!python/object:python.hmmwriter.State
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
+ track: nukes
2304
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2305
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2306
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2307
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2308
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2309
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2310
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2311
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2312
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2313
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2314
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2315
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2316
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2317
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2318
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2319
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2320
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2321
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2322
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2323
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2324
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2325
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2326
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2327
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2328
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2329
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2330
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2331
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2332
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2333
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2334
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2335
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2336
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2337
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2338
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2339
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2340
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2341
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2342
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2343
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2344
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2345
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2346
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2347
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2348
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2349
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2350
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2351
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2352
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2353
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2354
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2355
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2356
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2357
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2358
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2359
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2360
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2361
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2362
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2363
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2364
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2365
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2366
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2367
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2368
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2369
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2370
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2371
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2372
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2373
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2374
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2375
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2376
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2377
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2378
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2379
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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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2388
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2389
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2390
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2391
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2392
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2393
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2394
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2395
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2396
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2397
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2398
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2399
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2400
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2401
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2402
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2403
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2404
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2405
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2406
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2407
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2408
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2409
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2411
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2412
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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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2418
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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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2425
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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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2433
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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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2440
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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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2448
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2449
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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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2455
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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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2463
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2464
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2465
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2466
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2467
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2468
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2469
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2470
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2471
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2472
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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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2478
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2479
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2480
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2481
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2482
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2483
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2484
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2485
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2486
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2487
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2488
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2489
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2490
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2491
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2492
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2493
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2494
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2495
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2496
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2497
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2498
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2499
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2500
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2501
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2502
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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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2508
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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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2515
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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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2523
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2524
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2525
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2526
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2527
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2528
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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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2545
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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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2568
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2569
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2570
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2571
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2572
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2573
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2574
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2575
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2576
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2577
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2578
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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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2628
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2629
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2630
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2631
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2632
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2633
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2634
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2635
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2636
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2637
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2638
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2639
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2640
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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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2650
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2651
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2652
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2653
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2654
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2655
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2656
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2657
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2658
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2659
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2660
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2661
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2662
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2663
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2664
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2665
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2666
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2667
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2668
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2669
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2670
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2671
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2672
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2673
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2674
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2675
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2676
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2677
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2678
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2679
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2680
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2681
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2682
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2683
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2684
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2685
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2686
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2687
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2688
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2689
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2690
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2691
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2692
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2693
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2694
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2695
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2696
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2697
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2698
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2699
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2700
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2701
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2702
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2703
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2704
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2705
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2706
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2707
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2708
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2709
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2710
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2711
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2712
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2713
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2714
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2715
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2716
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2717
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2718
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2719
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2720
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2721
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2722
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2723
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2724
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2725
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2726
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2727
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2728
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2729
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2730
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2731
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2732
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2733
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2734
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2735
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2736
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2737
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2738
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2739
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2740
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2741
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2742
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2743
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2744
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2745
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2746
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2747
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2748
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2749
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2750
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2751
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2752
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2753
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2754
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2755
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2756
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2757
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2758
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2759
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2760
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2761
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2762
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2763
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2764
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2765
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2766
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2767
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2768
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2769
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2771
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2772
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2773
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2774
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2775
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2776
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2777
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2778
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2779
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2780
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2781
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2782
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2783
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2784
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2785
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2786
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2787
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2788
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2789
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2790
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2791
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2792
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2793
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2794
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2795
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2796
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2797
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2798
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2799
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2800
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2801
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2802
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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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2808
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2809
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2810
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2811
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2812
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2813
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2814
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2816
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2817
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2818
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2819
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2820
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2821
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2822
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2823
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2824
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2825
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2826
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2827
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2828
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2829
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2831
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2832
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2833
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2834
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2835
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2836
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2837
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2838
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2839
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2840
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2841
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2842
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2843
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2844
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2846
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2847
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2848
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2849
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2850
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2851
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2852
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2853
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2854
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2855
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2856
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2857
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2858
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2859
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2861
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2862
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2863
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2864
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2865
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2866
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2867
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2868
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2869
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2870
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2871
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2872
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2873
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2874
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2876
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2877
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2878
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2879
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2880
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2881
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2882
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2883
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2884
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2885
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2886
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2887
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2888
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2889
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2890
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2891
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2892
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2893
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2894
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2895
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2896
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2897
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2898
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2899
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2900
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2901
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2902
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2903
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2904
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2905
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2906
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2907
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2908
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2909
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2910
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2911
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2912
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2913
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2914
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2915
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2916
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2917
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2918
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2919
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2920
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2921
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2922
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2923
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2924
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2925
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2926
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2927
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2928
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2929
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2930
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2931
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2932
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2933
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2934
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2935
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2936
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2937
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2938
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2939
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2940
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2941
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2942
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2943
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2944
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2945
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2946
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2947
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2948
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2949
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2950
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2951
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2952
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2953
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2954
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2955
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2956
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2957
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2958
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2959
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2960
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2961
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2962
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2963
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2964
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2965
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2966
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2967
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2968
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2969
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2970
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2971
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2972
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2973
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2974
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2975
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2976
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2977
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2978
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2979
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2980
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2981
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2982
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2983
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2984
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2985
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2986
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2987
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2988
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2989
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2990
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2991
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2992
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2993
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2994
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2995
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2996
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2997
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2998
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2999
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3000
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3001
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3002
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3003
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3004
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3005
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3006
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3007
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3008
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3009
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3010
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3011
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3012
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3013
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3014
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3015
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3016
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3017
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3018
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3019
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3020
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3021
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3022
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3023
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3024
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3025
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3026
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3027
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3028
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3029
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3030
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3031
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3032
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3033
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3034
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3035
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3036
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3037
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3038
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3039
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3040
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3041
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3042
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3043
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3044
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3045
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3046
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3047
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3048
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3049
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3050
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3051
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3052
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3053
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3054
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3055
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3056
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3057
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3058
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3059
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3060
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3061
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3062
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3063
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3064
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3065
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3066
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3067
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3068
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3069
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3070
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3071
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3072
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3073
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3074
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3075
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3076
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3077
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3078
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3079
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3080
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3081
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3082
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3083
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3084
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3085
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3086
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3087
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3088
+ name: IGHV4-61_star_01_203
3089
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3090
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3091
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3092
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3093
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3094
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3095
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3096
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3097
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3098
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3099
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3100
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3101
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3102
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3103
+ name: IGHV4-61_star_01_204
3104
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3105
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3106
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3107
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3108
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3109
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3110
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3111
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3112
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3113
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3114
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3115
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3116
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3117
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3118
+ name: IGHV4-61_star_01_205
3119
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3120
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3121
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3122
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3123
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3124
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3125
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3126
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3127
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3128
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3129
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3130
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3131
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3132
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3133
+ name: IGHV4-61_star_01_206
3134
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3135
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3136
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3137
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3138
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3139
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3140
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3141
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3142
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3143
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3144
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3145
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3146
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3147
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3148
+ name: IGHV4-61_star_01_207
3149
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3150
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3151
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3152
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3153
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3154
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3155
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3156
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3157
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3158
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3159
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3160
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3161
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3162
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3163
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3164
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3165
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3166
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3167
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3168
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3169
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3170
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3171
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3172
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3173
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3174
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3175
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3176
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3177
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3178
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3179
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3180
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3181
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3182
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3183
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3184
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3185
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3186
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3187
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3188
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3189
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3190
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3191
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3192
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3193
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3194
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3195
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3196
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3197
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3198
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3199
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3200
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3201
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3202
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3203
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3204
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3205
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3206
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3207
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3208
+ name: IGHV4-61_star_01_211
3209
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3210
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3211
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3212
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3213
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3214
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3215
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3216
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3217
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3218
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3219
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3220
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3221
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3222
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3223
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3224
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3225
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3226
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3227
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3228
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3229
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3230
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3231
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3232
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3233
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3234
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3235
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3236
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3237
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3238
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3239
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3240
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3241
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3242
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3243
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3244
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3245
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3246
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3247
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3248
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3249
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3250
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3251
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3252
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3253
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3254
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3255
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3256
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3257
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3258
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3259
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3260
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3261
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3262
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3263
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3264
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3265
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3266
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3267
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3268
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3269
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3270
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3271
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3272
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3273
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3274
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3275
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3276
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3277
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3278
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3279
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3280
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3281
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3282
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3283
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3284
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3285
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3286
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3287
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3288
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3289
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3290
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3291
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3292
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3293
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3294
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3295
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3296
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3297
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3298
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3299
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3300
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3301
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3302
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3303
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3304
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3305
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3306
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3307
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3308
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3309
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3310
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3311
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3312
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3313
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3314
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3315
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3316
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3317
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3318
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3319
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3320
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3321
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3322
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3323
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3324
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3325
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3326
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3327
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3328
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3329
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3330
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3331
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3332
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3333
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3334
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3335
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3336
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3337
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3338
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3339
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3340
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3341
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3342
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3343
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3344
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3345
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3346
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3347
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3348
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3349
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3350
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3351
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3352
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3353
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3354
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3355
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3356
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3357
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3358
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3359
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3360
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3361
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3362
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3363
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3364
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3365
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3366
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3367
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3368
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3369
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3370
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3371
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3372
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3373
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3374
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3375
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3376
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3377
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3378
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3379
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3380
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3381
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3382
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3383
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3384
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3385
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3386
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3387
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3388
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3389
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3390
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3391
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3392
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3393
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3394
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3395
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3396
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3397
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3398
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3399
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3401
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3402
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3403
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3404
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3405
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3406
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3407
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3408
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3409
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3410
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3411
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3412
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3413
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3414
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3415
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3416
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3417
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3418
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3419
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3420
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3421
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3422
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3423
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3424
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3425
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3426
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3427
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3428
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3429
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3430
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3431
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3432
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3433
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3434
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3435
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3436
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3437
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3438
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3439
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3440
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3441
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3442
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3443
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3444
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3445
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3446
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3447
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3448
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3449
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3450
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3451
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3452
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3453
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3454
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3455
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3456
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3457
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3458
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3459
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3460
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3461
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3462
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3463
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3464
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3465
+ IGHV4-61_star_01_229: 1.0
3466
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3467
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3468
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3469
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3470
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3471
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3472
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3473
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3474
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3475
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3476
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3477
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3478
+ name: IGHV4-61_star_01_229
3479
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3480
+ IGHV4-61_star_01_230: 1.0
3481
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3482
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3483
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3484
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3485
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3486
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3487
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3488
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3489
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3490
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3491
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3492
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3493
+ name: IGHV4-61_star_01_230
3494
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3495
+ IGHV4-61_star_01_231: 1.0
3496
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3497
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3498
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3499
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3500
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3501
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3502
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3503
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3504
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3505
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3506
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3507
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3508
+ name: IGHV4-61_star_01_231
3509
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3510
+ IGHV4-61_star_01_232: 1.0
3511
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3512
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3513
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3514
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3515
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3516
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3517
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3518
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3519
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3520
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3521
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3522
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3523
+ name: IGHV4-61_star_01_232
3524
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3525
+ IGHV4-61_star_01_233: 1.0
3526
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3527
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3528
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3529
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3530
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3531
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3532
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3533
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3534
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3535
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3536
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3537
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3538
+ name: IGHV4-61_star_01_233
3539
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3540
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3541
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3542
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3543
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3544
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3545
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3546
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3547
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3548
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3549
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3550
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3551
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3552
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3553
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3554
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3555
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3556
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3557
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3558
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3559
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3560
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3561
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3562
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3563
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3564
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3565
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3566
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3567
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3568
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3569
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3570
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3571
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3572
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3573
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3574
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3575
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3576
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3577
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3578
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3579
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3580
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3581
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3582
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3583
+ name: IGHV4-61_star_01_236
3584
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3585
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3586
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3587
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3588
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3589
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3590
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3591
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3592
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3593
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3594
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3595
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3596
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3597
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3598
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3599
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3600
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3601
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3602
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3603
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3604
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3605
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3606
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3607
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3608
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3609
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3610
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3611
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3612
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3613
+ name: IGHV4-61_star_01_238
3614
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3615
+ IGHV4-61_star_01_239: 1.0
3616
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3617
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3618
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3619
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3620
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3621
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3622
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3623
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3624
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3625
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3626
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3627
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3628
+ name: IGHV4-61_star_01_239
3629
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3630
+ IGHV4-61_star_01_240: 1.0
3631
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3632
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3633
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3634
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3635
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3636
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3637
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3638
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3639
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3640
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3641
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3642
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3643
+ name: IGHV4-61_star_01_240
3644
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3645
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3646
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3647
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3648
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3649
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3650
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3651
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3652
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3653
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3654
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3655
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3656
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3657
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3658
+ name: IGHV4-61_star_01_241
3659
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3660
+ IGHV4-61_star_01_242: 1.0
3661
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3662
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3663
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3664
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3665
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3666
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3667
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3668
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3669
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3670
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3671
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3672
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3673
+ name: IGHV4-61_star_01_242
3674
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3675
+ IGHV4-61_star_01_243: 1.0
3676
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3677
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3678
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3679
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3680
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3681
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3682
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3683
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3684
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3685
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3686
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3687
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3688
+ name: IGHV4-61_star_01_243
3689
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3690
+ IGHV4-61_star_01_244: 1.0
3691
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3692
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3693
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3694
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3695
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3696
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3697
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3698
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3699
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3700
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3701
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3702
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3703
+ name: IGHV4-61_star_01_244
3704
+ transitions:
3705
+ IGHV4-61_star_01_245: 1.0
3706
+ - !!python/object:python.hmmwriter.State
3707
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3708
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3709
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3710
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3711
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3712
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3713
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3714
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3715
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3716
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3717
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3718
+ name: IGHV4-61_star_01_245
3719
+ transitions:
3720
+ IGHV4-61_star_01_246: 1.0
3721
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3722
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3723
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3724
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3725
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3726
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3727
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3728
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3729
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3730
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3731
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3732
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3733
+ name: IGHV4-61_star_01_246
3734
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3735
+ IGHV4-61_star_01_247: 1.0
3736
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3737
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3738
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3739
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3740
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3741
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3742
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3743
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3744
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3745
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3746
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3747
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3748
+ name: IGHV4-61_star_01_247
3749
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3750
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3751
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3752
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3753
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3754
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3755
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3756
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3757
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3758
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3759
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3760
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3761
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3762
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3763
+ name: IGHV4-61_star_01_248
3764
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3765
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3766
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3767
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3768
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3769
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3770
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3771
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3772
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3773
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3774
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3775
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3776
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3777
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3778
+ name: IGHV4-61_star_01_249
3779
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3780
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3781
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3782
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3783
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3784
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3785
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3786
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3787
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3788
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3789
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3790
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3791
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3792
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3793
+ name: IGHV4-61_star_01_250
3794
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3795
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3796
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3797
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3798
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3799
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3800
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3801
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3802
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3803
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3804
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3805
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3806
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3807
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3808
+ name: IGHV4-61_star_01_251
3809
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3810
+ IGHV4-61_star_01_252: 1.0
3811
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3812
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3813
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3814
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3815
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3816
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3817
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3818
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3819
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3820
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3821
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3822
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3823
+ name: IGHV4-61_star_01_252
3824
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3825
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3826
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3827
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3828
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3829
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3830
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3831
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3832
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3833
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3834
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3835
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3836
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3837
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3838
+ name: IGHV4-61_star_01_253
3839
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3840
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3841
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3842
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3843
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3844
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3845
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3846
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3847
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3848
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3849
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3850
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3851
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3852
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3853
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3854
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3855
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3856
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3857
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3858
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3859
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3860
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3861
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3862
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3863
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3864
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3865
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3866
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3867
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3868
+ name: IGHV4-61_star_01_255
3869
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3870
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3871
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3872
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3873
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3874
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3875
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3876
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3877
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3878
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3879
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3880
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3881
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3882
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3883
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3884
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3885
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3886
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3887
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3888
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3889
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3890
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3891
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3892
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3893
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3894
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3895
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3896
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3897
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3898
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3899
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3900
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3901
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3902
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3903
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3904
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3905
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3906
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3907
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3908
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3909
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3910
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3911
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3912
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3913
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3914
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3915
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3916
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3917
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3918
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3919
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3920
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3921
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3922
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3923
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3924
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3925
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3926
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3927
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3928
+ name: IGHV4-61_star_01_259
3929
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3930
+ IGHV4-61_star_01_260: 1.0
3931
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3932
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3933
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3934
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3935
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3936
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3937
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3938
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3939
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3940
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3941
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3942
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3943
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3944
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3945
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3946
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3947
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3948
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3949
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3950
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3951
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3952
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3953
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3954
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3955
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3956
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3957
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3958
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3959
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3960
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3961
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3962
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3963
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3964
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3965
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3966
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3967
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3968
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3969
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3970
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3971
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3972
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3973
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3974
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3975
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3976
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3977
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3978
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3979
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3980
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3981
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3982
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3983
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3984
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3985
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3986
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3987
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3988
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3989
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3990
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3991
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3992
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3993
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3994
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3995
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3996
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3997
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3998
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3999
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4000
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4001
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4002
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4003
+ name: IGHV4-61_star_01_264
4004
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4005
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4006
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4007
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4008
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4009
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4010
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4011
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4012
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4013
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4014
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4015
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4016
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4017
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4018
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4019
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4020
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4021
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4022
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4023
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4024
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4025
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4026
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4027
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4028
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4029
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4030
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4031
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4032
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4033
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4050
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4065
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4275
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4397
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4509
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