partis-bcr 1.0.11.post1.dev1__cp312-cp312-manylinux1_x86_64.whl → 1.0.11.post1.dev3__cp312-cp312-manylinux1_x86_64.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 (652) 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.dev3.data}/scripts/partis-test.py +6 -0
  5. {partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.11.post1.dev3.dist-info}/METADATA +1 -1
  6. {partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.11.post1.dev3.dist-info}/RECORD +652 -125
  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. test/paired/new-results/test/simu/igh+igl/igl.yaml +1 -0
  635. test/paired/new-results/test/simu/igh.yaml +1 -0
  636. test/paired/new-results/test/simu/igk.yaml +1 -0
  637. test/paired/new-results/test/simu/igl.yaml +1 -0
  638. test/paired/new-results/test/simu/meta.yaml +1 -0
  639. test/paired/new-results/test.log +227 -33
  640. test/test.py +6 -0
  641. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev3.data}/scripts/cf-alleles.py +0 -0
  642. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev3.data}/scripts/cf-germlines.py +0 -0
  643. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev3.data}/scripts/compare-plotdirs.py +0 -0
  644. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev3.data}/scripts/extract-pairing-info.py +0 -0
  645. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev3.data}/scripts/gctree-run.py +0 -0
  646. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev3.data}/scripts/get-naive-probabilities.py +0 -0
  647. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev3.data}/scripts/parse-output.py +0 -0
  648. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev3.data}/scripts/split-loci.py +0 -0
  649. {partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.11.post1.dev3.dist-info}/WHEEL +0 -0
  650. {partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.11.post1.dev3.dist-info}/entry_points.txt +0 -0
  651. {partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.11.post1.dev3.dist-info}/licenses/COPYING +0 -0
  652. {partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.11.post1.dev3.dist-info}/top_level.txt +0 -0
test/new-results/test/parameters/data/hmm/hmms/IGHV3-11_star_04.yaml ADDED
@@ -0,0 +1,4484 @@
1
+ !!python/object:python.hmmwriter.HMM
2
+ extras:
3
+ gene_prob: 0.08695652173913043
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+ overall_mute_freq: 0.08760869565217394
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+ per_gene_mute_freq: 0.10461488451671755
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+ name: IGHV3-11_star_04
7
+ states:
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+ - !!python/object:python.hmmwriter.State
9
+ emissions: null
10
+ extras: {}
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+ name: init
12
+ transitions:
13
+ IGHV3-11_star_04_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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+ IGHV3-11_star_04_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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+ probs:
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+ A: 0.03333333333333333
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+ C: 0.9
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+ G: 0.03333333333333333
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+ T: 0.03333333333333333
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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: IGHV3-11_star_04_0
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+ transitions:
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+ IGHV3-11_star_04_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: 0.9
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+ C: 0.03333333333333333
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+ G: 0.03333333333333333
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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: A
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+ name: IGHV3-11_star_04_1
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+ transitions:
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+ IGHV3-11_star_04_2: 1.0
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+ - !!python/object:python.hmmwriter.State
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+ emissions:
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+ A: 0.03333333333333333
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+ track: nukes
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+ ambiguous_emission_prob: 0.25
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+ germline: G
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+ name: IGHV3-11_star_04_2
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+ transitions:
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+ IGHV3-11_star_04_3: 1.0
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+ - !!python/object:python.hmmwriter.State
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+ emissions:
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+ germline: G
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+ name: IGHV3-11_star_04_3
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+ transitions:
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+ IGHV3-11_star_04_4: 1.0
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+ - !!python/object:python.hmmwriter.State
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+ emissions:
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+ G: 0.03333333333333333
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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: IGHV3-11_star_04_4
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+ transitions:
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+ IGHV3-11_star_04_5: 1.0
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+ - !!python/object:python.hmmwriter.State
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+ emissions:
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+ A: 0.03333333333333333
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+ C: 0.03333333333333333
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+ track: nukes
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+ germline: G
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+ name: IGHV3-11_star_04_5
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+ transitions:
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+ IGHV3-11_star_04_6: 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: IGHV3-11_star_04_6
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+ transitions:
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+ IGHV3-11_star_04_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: IGHV3-11_star_04_7
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+ transitions:
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+ IGHV3-11_star_04_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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+ extras:
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+ ambiguous_emission_prob: 0.25
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+ germline: G
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+ name: IGHV3-11_star_04_8
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+ transitions:
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+ IGHV3-11_star_04_9: 1.0
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+ - !!python/object:python.hmmwriter.State
167
+ emissions:
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+ germline: C
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+ name: IGHV3-11_star_04_9
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+ transitions:
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+ IGHV3-11_star_04_10: 1.0
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+ - !!python/object:python.hmmwriter.State
182
+ emissions:
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+ ambiguous_char: N
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+ ambiguous_emission_prob: 0.25
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+ germline: T
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+ name: IGHV3-11_star_04_10
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+ transitions:
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+ IGHV3-11_star_04_11: 1.0
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+ - !!python/object:python.hmmwriter.State
197
+ emissions:
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+ ambiguous_emission_prob: 0.25
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+ germline: G
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+ name: IGHV3-11_star_04_11
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+ transitions:
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+ IGHV3-11_star_04_12: 1.0
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+ - !!python/object:python.hmmwriter.State
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+ emissions:
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+ G: 0.9
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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: G
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+ name: IGHV3-11_star_04_12
224
+ transitions:
225
+ IGHV3-11_star_04_13: 1.0
226
+ - !!python/object:python.hmmwriter.State
227
+ emissions:
228
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+ A: 0.03333333333333333
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+ ambiguous_emission_prob: 0.25
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+ germline: T
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+ name: IGHV3-11_star_04_13
239
+ transitions:
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+ IGHV3-11_star_04_14: 1.0
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+ - !!python/object:python.hmmwriter.State
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+ emissions:
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+ germline: G
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+ name: IGHV3-11_star_04_14
254
+ transitions:
255
+ IGHV3-11_star_04_15: 1.0
256
+ - !!python/object:python.hmmwriter.State
257
+ emissions:
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+ name: IGHV3-11_star_04_15
269
+ transitions:
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+ IGHV3-11_star_04_16: 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: IGHV3-11_star_04_16
284
+ transitions:
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+ IGHV3-11_star_04_17: 1.0
286
+ - !!python/object:python.hmmwriter.State
287
+ emissions:
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+ IGHV3-11_star_04_18: 1.0
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+ - !!python/object:python.hmmwriter.State
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+ emissions:
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315
+ IGHV3-11_star_04_19: 1.0
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+ - !!python/object:python.hmmwriter.State
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+ - !!python/object:python.hmmwriter.State
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1748
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1749
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1750
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1751
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1752
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1753
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1754
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1755
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1756
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1757
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1758
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1759
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1760
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1761
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1762
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1763
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1764
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1765
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1766
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1767
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1768
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1769
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1770
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1771
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1772
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1773
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1774
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1775
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1776
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1777
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1778
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1779
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1780
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1781
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1782
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1783
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1784
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1785
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1786
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1787
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1788
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1789
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1790
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1791
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1792
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1793
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1794
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1795
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1796
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1797
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1798
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1799
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1800
+ IGHV3-11_star_04_118: 1.0
1801
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1802
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1803
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1804
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1805
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1806
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1807
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1808
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1809
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1810
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1811
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1812
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1813
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1814
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1815
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1816
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1817
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1818
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1819
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1820
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1821
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1822
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1823
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1824
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1825
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1826
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1827
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1828
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1829
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1830
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1831
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1832
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1833
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1834
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1835
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1836
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1837
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1838
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1839
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1840
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1841
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1842
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1843
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1844
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1845
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1846
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1847
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1848
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1849
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1850
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1851
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1852
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1853
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1854
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1855
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1856
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1857
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1858
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1859
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1860
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1861
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1862
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1863
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1864
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1865
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1866
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1867
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1868
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1869
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1870
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1871
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1872
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1873
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1874
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1875
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1876
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1877
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1878
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1879
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1880
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1881
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1882
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1883
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1884
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1885
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1886
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1887
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1888
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1889
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1890
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1891
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1892
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1893
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1894
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1895
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1896
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1897
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1898
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1899
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1900
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1901
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1902
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1903
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1904
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1905
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1906
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1907
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1908
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1909
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1910
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1911
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1912
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1913
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1914
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1915
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1916
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1917
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1918
+ name: IGHV3-11_star_04_125
1919
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1920
+ IGHV3-11_star_04_126: 1.0
1921
+ - !!python/object:python.hmmwriter.State
1922
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1923
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1924
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1925
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1926
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1927
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1928
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1929
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1930
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1931
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1932
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1933
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1934
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1935
+ IGHV3-11_star_04_127: 1.0
1936
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1937
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1938
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1939
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1940
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1941
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1942
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1943
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1944
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1945
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1946
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1947
+ germline: A
1948
+ name: IGHV3-11_star_04_127
1949
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1950
+ IGHV3-11_star_04_128: 1.0
1951
+ - !!python/object:python.hmmwriter.State
1952
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1953
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1954
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1955
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1956
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1957
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1958
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1959
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1960
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1961
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1962
+ germline: G
1963
+ name: IGHV3-11_star_04_128
1964
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1965
+ IGHV3-11_star_04_129: 1.0
1966
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1967
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1968
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1969
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1970
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1971
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1972
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1973
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1974
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1975
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1976
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1977
+ germline: G
1978
+ name: IGHV3-11_star_04_129
1979
+ transitions:
1980
+ IGHV3-11_star_04_130: 1.0
1981
+ - !!python/object:python.hmmwriter.State
1982
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1983
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1984
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1985
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1986
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1987
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1988
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1989
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1990
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1991
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1992
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1993
+ name: IGHV3-11_star_04_130
1994
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1995
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1996
+ - !!python/object:python.hmmwriter.State
1997
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1998
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1999
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2000
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2001
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2002
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2003
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2004
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2005
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2006
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2007
+ germline: G
2008
+ name: IGHV3-11_star_04_131
2009
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2010
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2011
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2012
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2013
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2014
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2015
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2016
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2017
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2018
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2019
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2020
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2021
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2022
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2023
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2024
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2025
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2026
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2027
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2028
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2029
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2030
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2031
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2032
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2033
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2034
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2035
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2036
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2037
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2038
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2039
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2040
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2041
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2042
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2043
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2044
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2045
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2046
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2047
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2048
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2049
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2050
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2051
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2052
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2053
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2054
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2055
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2056
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2057
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2058
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2059
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2060
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2061
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2062
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2063
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2064
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2065
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2066
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2067
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2068
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2069
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2070
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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
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2084
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2085
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2086
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2087
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2088
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2089
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2090
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2091
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2092
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2093
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2094
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2095
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2096
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2097
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2098
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2099
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2100
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2101
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2102
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2103
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2104
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2105
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2106
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2107
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2108
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2109
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2110
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2111
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2112
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2113
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2114
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2115
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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
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2124
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2125
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2126
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2127
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2128
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2129
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2130
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2131
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2132
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2133
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2134
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2135
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2136
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2137
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2138
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2139
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2140
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2141
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2142
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2143
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2144
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2145
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2146
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2147
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2148
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2150
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2151
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2152
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2153
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2154
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2155
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2156
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2157
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2158
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2159
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2160
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2161
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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
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2169
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2170
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2171
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2172
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2173
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2174
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2175
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2176
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2177
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2178
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2180
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2181
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2182
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2183
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2184
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2185
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2186
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2187
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2188
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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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2201
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2202
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2203
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2204
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2205
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2206
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2207
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2208
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2209
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2210
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2211
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2212
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2213
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2214
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2216
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2217
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2218
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2219
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2220
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2221
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2222
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2223
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2224
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2225
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2226
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2227
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2228
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2229
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2230
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2231
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2232
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2233
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2234
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2235
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2236
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2237
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2238
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2239
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2240
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2241
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2242
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2243
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2244
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2245
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2246
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2247
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2248
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2249
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2250
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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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2261
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2262
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2263
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2264
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2265
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2266
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2267
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2268
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2269
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2270
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2271
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2272
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2273
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2274
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2276
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2277
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2278
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2279
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2280
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2281
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2282
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2283
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2285
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2286
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2287
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2288
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2289
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2291
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2292
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2293
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2294
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2295
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2296
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2297
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2300
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2301
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2302
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2303
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2304
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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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2315
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2316
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2318
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2319
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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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2336
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2337
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2534
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2549
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2564
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2579
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2609
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2624
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2626
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2641
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2717
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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
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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
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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
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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
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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
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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
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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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3400
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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
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3466
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3467
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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
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3479
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3480
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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
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3494
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3495
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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
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3509
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3510
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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
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3524
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3525
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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
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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
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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
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3614
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3615
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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
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3629
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3630
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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
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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
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3659
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3660
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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
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3674
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3675
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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
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3689
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3690
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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
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3704
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3705
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3706
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3707
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3708
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3709
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3710
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3711
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3712
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3713
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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
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3719
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3720
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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
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3734
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3735
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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
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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
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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
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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
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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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3806
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3807
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3808
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3809
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3810
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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
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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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3836
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3837
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3838
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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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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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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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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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3866
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3868
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3869
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3870
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3871
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3872
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3875
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3876
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3879
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3881
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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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3890
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3896
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3898
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3899
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3901
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3902
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3908
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3909
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3911
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3913
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3914
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3916
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3917
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3923
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3926
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3928
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3929
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3931
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3932
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3935
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3936
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3938
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3939
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3941
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3943
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3944
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3946
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3947
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3953
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3956
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3959
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3961
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3962
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3965
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3971
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3973
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3974
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3976
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3977
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3980
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3992
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4004
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4007
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4022
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4034
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4037
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4049
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4052
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4061
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4064
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4067
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4232
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4260
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4320
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4322
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