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notes: This a model from the article: Monte Carlo analysis of an ODE Model of the Sea Urchin Endomesoderm Network. Kühn C, Wierling C, Kühn A, Klipp E, Panopoulou G, Lehrach H, Poustka AJ. BMC Syst Biol. 2009 Aug 23;3:83. 19698179 , Abstract: BACKGROUND: Gene Regulatory Networks (GRNs) control the differentiation, specification and function of cells at the genomic level. The levels of interactions within large GRNs are of enormous depth and complexity. Details about many GRNs are emerging, but in most cases it is unknown to what extent they control a given process, i.e. the grade of completeness is uncertain. This uncertainty stems from limited experimental data, which is the main bottleneck for creating detailed dynamical models of cellular processes. Parameter estimation for each node is often infeasible for very large GRNs. We propose a method, based on random parameter estimations through Monte-Carlo simulations to measure completeness grades of GRNs. RESULTS: We developed a heuristic to assess the completeness of large GRNs, using ODE simulations under different conditions and randomly sampled parameter sets to detect parameter-invariant effects of perturbations. To test this heuristic, we constructed the first ODE model of the whole sea urchin endomesoderm GRN, one of the best studied large GRNs. We find that nearly 48% of the parameter-invariant effects correspond with experimental data, which is 65% of the expected optimal agreement obtained from a submodel for which kinetic parameters were estimated and used for simulations. Randomized versions of the model reproduce only 23.5% of the experimental data. CONCLUSION: The method described in this paper enables an evaluation of network topologies of GRNs without requiring any parameter values. The benefit of this method is exemplified in the first mathematical analysis of the complete Endomesoderm Network Model. The predictions we provide deliver candidate nodes in the network that are likely to be erroneous or miss u…
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155817
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155805
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536452
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537188
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539615
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147501
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535782
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147489
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535779
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536870
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538262
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538261
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535752
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133877
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536383
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133865
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535053
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537223
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539638
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148590
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148578
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535848
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540248
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534981
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536064
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536239
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536185
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537029
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539011
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539009
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536052
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536743
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141869
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535371
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537131
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539577
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145655
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535641
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537596
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539928
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159813
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159800
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536434
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536866
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538250
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538249
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133697
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536374
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133685
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535044
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537779
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540051
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165685
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165673
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536617
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535833
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537014
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538945
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538944
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538943
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538941
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536125
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536131
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141172
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536713
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141160
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535341
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537407
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539762
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154462
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154450
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536272
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536491
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537845
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540101
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167801
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167789
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536683
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537479
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539859
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156637
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156625
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536335
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535764
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536776
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535305
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537728
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540017
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164050
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164038
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536566
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537830
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540091
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167320
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167308
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536668
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537437
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539818
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539817
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539816
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539814
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155331
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155319
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535524
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535368
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535902
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537766
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540042
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165252
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535941
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165240
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537097
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539554
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144572
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144560
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535569
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535338
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536031
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537577
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539915
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536413
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536635
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536993
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538843
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538841
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140149
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140137
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535296
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537826
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540088
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536662
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167176
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536049
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167164
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535113
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535635
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537425
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539778
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539777
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539776
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539774
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155043
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536692
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155031
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535500
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537187
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539614
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535773
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147453
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147438
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537107
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539561
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144909
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144897
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535590
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540247
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537410
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539764
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154585
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154560
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536275
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154547
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536161
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536554
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536980
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536016
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535887
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139386
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535269
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538768
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538767
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538766
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538765
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538764
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538762
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139398
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536019
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537137
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539581
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145860
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145848
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535656
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537776
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540049
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165576
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536614
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536524
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540230
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537595
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159751
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537298
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539689
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536028
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537218
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539635
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148434
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535839
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535116
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537406
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154414
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154402
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536269
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537478
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539858
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536332
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535572
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156577
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536822
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538040
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538038
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538037
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538035
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131667
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536455
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131655
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535455
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536476
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537124
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535626
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145427
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145415
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540260
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536894
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538393
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538392
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538391
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538390
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535695
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535755
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135142
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135129
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535101
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537247
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539655
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149336
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535899
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535185
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537314
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539700
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151499
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536055
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536938
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538581
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538580
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538579
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538578
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538577
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538576
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538575
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538574
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535863
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535791
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535893
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537940
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540165
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536197
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170820
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537155
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539593
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146425
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146413
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535689
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537053
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539445
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539444
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539443
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539441
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143124
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536787
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540252
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537038
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539063
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539062
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539061
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539059
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536155
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142363
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536764
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142351
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535389
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537869
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540117
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168557
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536707
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535830
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536137
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537533
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539886
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157793
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157781
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536371
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537971
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540185
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536793
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171837
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536245
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171824
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535329
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537142
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539584
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146005
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145993
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535662
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537040
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539072
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539071
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539069
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539067
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537563
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536401
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537266
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537332
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152077
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152065
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537892
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540132
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535077
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537520
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539877
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157345
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537790
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537661
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539971
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537215
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536659
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534962
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537253
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539659
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149528
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535914
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535137
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540211
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540250
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540274
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540249
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540231
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540232
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173100
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540273
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535995
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537551
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539898
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158358
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536389
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537808
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540072
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536644
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536515
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536932
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137011
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538553
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536858
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538218
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538217
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538216
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538215
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536359
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536578
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536404
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537313
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536686
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536815
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538010
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538008
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538007
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538005
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131486
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536368
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131474
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535440
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538001
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540205
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536808
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172800
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172787
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537359
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539730
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152934
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152922
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535956
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537163
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539598
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146677
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535701
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146665
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535665
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146653
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535704
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536114
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536846
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535578
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538160
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538159
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538158
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538157
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538156
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538155
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132644
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535005
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132656
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537148
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539588
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146185
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146173
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540284
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537935
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540162
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170688
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170676
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536773
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535428
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536689
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535737
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536233
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536833
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535548
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131993
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534975
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538095
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538103
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538098
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538088
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538106
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538101
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538091
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538104
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538094
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538086
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538089
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538092
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538097
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538100
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132005
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536305
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537179
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539609
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147221
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535767
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147209
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535647
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147197
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537922
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540153
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536758
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536173
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170241
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537625
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536900
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536449
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535632
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540276
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537697
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539995
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537805
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537995
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537181
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147257
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537610
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160234
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537166
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539600
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537515
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539874
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157201
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536353
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536999
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140451
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535314
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537508
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539867
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536344
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156973
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535584
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156961
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537946
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540169
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536779
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171025
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536203
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171013
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535659
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536761
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537649
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539963
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536485
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161498
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161486
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536924
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136591
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535161
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136603
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536512
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538514
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538513
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538512
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538511
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538510
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537751
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540032
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164759
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535878
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540214
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540259
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173582
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537671
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539978
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162209
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536509
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537539
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539890
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157985
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157973
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536794
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535323
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540243
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535386
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536085
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535620
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536749
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537898
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540136
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536734
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169481
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169469
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537526
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539881
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536362
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157552
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157540
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536863
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538236
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538235
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538234
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538233
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133529
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133517
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535038
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537667
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539975
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536503
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162075
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535821
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162063
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536942
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535872
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538603
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538592
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538602
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538601
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538594
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538599
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538600
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538593
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538595
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538596
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538597
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538598
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535842
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540239
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536825
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538052
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538050
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538049
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538047
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131741
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535461
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537844
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540100
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167753
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536070
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167741
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537652
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539965
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536488
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161594
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161582
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536004
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537914
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540148
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170011
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169999
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536752
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537617
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539942
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160487
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160475
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535908
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537727
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540016
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536563
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164002
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163990
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540268
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537436
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539813
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539812
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539811
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539809
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155295
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536797
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155283
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537205
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539626
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148025
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535815
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148013
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535818
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537173
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539605
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147003
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146991
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535731
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535512
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536881
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535593
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535725
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538312
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538315
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538309
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538307
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538311
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538314
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538308
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538306
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538310
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538313
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538316
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538305
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134387
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535074
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537794
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540063
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166166
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166154
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536632
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536923
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538509
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538508
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538507
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538506
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535806
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535158
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537902
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540140
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169613
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537677
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539982
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162401
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537104
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539559
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144812
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144800
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535134
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537386
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153789
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153777
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536209
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537083
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539545
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144149
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144137
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537581
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159318
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536419
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537284
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539680
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150541
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150529
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537635
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539954
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161064
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161052
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535422
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535485
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537025
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538993
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538992
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538991
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538990
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538988
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141652
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536079
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141664
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537812
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166731
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537446
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536302
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536948
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538615
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538613
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538610
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137759
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536557
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537775
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537071
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539520
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539519
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539517
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143825
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143813
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537841
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536677
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167657
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167645
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536906
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135709
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538442
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538441
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538440
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538439
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538438
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537433
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539802
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539799
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155223
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155211
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537616
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539941
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160439
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160427
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540267
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537118
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145235
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145222
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537233
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539645
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148914
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148902
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535869
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536966
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535242
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538698
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538697
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538696
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538695
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538693
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138713
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536596
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540258
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537793
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540062
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166118
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166106
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537421
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539771
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536293
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536227
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154886
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536284
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537758
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540037
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165011
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164999
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537868
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540116
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536704
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168521
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536111
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168509
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537676
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539981
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162365
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162353
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537103
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539558
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144764
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144752
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537385
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153729
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536206
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537938
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540164
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170772
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537283
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539679
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150481
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536194
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537743
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536876
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538291
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538284
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538283
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538281
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537229
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539642
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537331
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537709
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540004
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163412
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535071
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537214
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148302
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148290
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536947
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538608
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538607
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538606
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137698
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536212
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537659
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539970
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161822
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537953
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540174
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171255
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537761
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540039
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165107
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165095
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537049
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539426
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536781
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535410
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537836
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540095
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167513
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167500
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536674
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536251
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537605
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539934
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160102
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160090
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536443
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538000
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172751
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172739
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537251
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539658
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149492
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149480
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535911
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537197
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147779
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147767
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537232
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539644
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148866
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148854
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535653
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536058
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537574
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539913
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159090
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159078
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537757
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540036
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164963
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164951
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536990
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538824
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538825
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538823
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538822
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538819
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538821
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538820
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538817
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538831
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538829
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538830
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538828
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538827
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536140
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535086
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537457
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539843
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155914
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155902
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536873
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538274
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538273
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134022
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134010
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535059
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536915
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538483
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538482
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136215
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136203
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535143
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537374
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539740
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153404
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153391
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535380
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537416
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154766
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154754
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537854
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540107
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168089
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168077
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537134
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539579
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145764
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145752
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536869
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538260
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538259
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538258
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538257
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538256
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538255
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133793
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535050
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133805
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537017
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141316
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536719
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538961
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538960
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538959
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538958
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538957
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538955
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141304
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535347
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535875
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537884
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540127
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169049
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169037
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536314
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537512
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539872
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157117
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157105
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536350
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537950
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540172
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171170
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171158
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536782
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534984
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537355
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539727
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152789
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152777
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536146
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537871
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540118
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168617
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536112
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168605
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535602
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535095
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537604
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539933
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160054
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160042
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535227
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537032
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536224
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141978
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535377
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141990
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539020
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539023
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539026
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539029
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539019
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539022
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539025
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539028
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539031
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539021
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539024
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539027
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539030
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539017
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536152
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537530
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539884
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157697
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157685
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537977
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540189
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536796
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172040
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536254
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172028
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537785
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540056
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165877
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165865
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536623
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536001
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537413
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539766
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154682
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154669
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537392
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539752
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153981
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153969
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536221
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537263
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539666
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149866
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149854
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537373
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153355
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153343
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537569
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539910
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158946
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158934
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537338
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539716
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152270
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152258
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537731
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540019
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164146
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164134
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536569
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534999
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537440
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539828
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539827
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539826
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539824
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155404
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536802
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535530
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537818
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540082
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166936
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166924
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536656
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535677
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537598
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539929
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159860
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159848
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537323
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539706
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151788
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151776
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537409
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539763
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154511
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154499
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537511
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539869
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157069
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157057
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537557
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539902
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158562
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158550
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535299
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537319
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539703
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537158
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539595
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146521
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146509
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535359
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540209
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173004
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537239
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539650
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535968
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149107
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149095
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536995
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538850
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538849
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538848
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538847
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538846
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538844
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536073
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140197
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140185
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535302
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536338
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537341
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539718
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536287
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152366
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536119
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152354
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536116
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535200
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537974
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540187
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171941
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535509
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535263
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537670
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539977
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536506
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162173
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162161
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540240
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537566
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539908
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158850
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158838
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537269
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539670
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150059
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150047
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537379
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539743
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153548
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153536
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537749
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540031
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164723
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164711
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537895
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540134
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536731
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169385
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169373
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537191
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539617
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147598
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147586
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535776
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147573
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537620
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539944
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160583
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160571
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536458
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537337
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539715
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152222
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152210
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540236
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536839
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132318
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534990
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132330
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536320
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538138
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538137
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538136
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538135
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538134
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538133
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538132
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538130
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536941
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538591
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538590
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538589
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538588
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535947
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137470
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137458
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535194
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537928
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540157
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170446
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170434
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537056
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539459
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539458
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539457
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539456
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539455
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539453
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143245
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535425
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536230
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143257
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536790
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537554
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539900
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158466
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158454
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535152
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536025
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536191
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537287
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539682
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150637
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150625
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536806
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535107
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536299
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537172
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539604
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146955
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146943
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535728
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537043
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539390
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539388
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539082
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539081
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539080
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539078
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142555
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535398
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142567
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537464
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539848
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156155
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156143
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537988
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540196
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172379
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172367
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535011
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537713
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540007
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163568
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163556
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536551
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540254
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537347
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539722
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152546
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152534
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536128
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537901
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540139
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169577
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169565
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535998
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536437
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536951
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538625
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538624
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538619
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538623
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538621
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538627
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538620
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538626
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538622
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538628
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137867
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535212
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537700
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536809
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536905
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537011
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537518
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539876
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540222
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537644
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537094
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537877
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536115
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537007
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538902
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538894
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538689
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538688
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538687
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537823
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540287
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537706
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537196
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537067
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536902
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537737
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540278
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537010
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537329
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537475
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537658
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536891
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538678
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536887
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537035
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537908
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536872
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537851
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537133
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537772
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537655
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537262
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537439
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537919
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536855
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133177
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537310
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536926
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537799
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537034
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536158
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537907
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537109
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537224
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537932
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537740
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537176
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539607
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147100
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147088
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537211
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539630
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148205
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148193
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537074
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539531
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539530
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539529
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539527
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143897
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143885
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535491
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537059
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143401
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535431
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539477
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539476
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539475
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539474
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539473
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539472
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539471
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539469
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143413
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537992
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540199
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172511
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172499
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536824
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538046
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538044
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538043
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538041
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131705
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131693
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535458
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536896
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535758
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535104
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538399
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538398
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538397
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538396
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538395
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538394
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135202
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537619
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539943
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160535
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160523
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537584
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539920
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159426
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159414
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536422
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536854
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133079
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538195
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538204
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538198
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538202
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538196
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538200
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538199
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538201
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538203
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538197
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133067
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535020
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537482
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539862
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156733
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156721
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537767
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540043
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165300
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165288
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536605
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535236
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537833
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540093
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167416
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167404
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536671
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537157
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539594
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146473
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146461
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536215
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537796
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540064
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166214
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166202
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537238
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539649
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149071
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149059
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149047
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537388
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539749
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153837
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153825
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537973
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540186
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171889
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171876
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535518
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537085
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539546
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144197
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144185
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536842
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538144
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538143
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538142
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538141
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132464
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132451
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534996
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536996
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536236
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140270
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538859
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538858
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538857
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538856
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538855
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538854
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538853
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538851
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140258
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540280
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535449
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535686
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537931
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540159
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170543
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170530
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537565
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539907
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158802
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158790
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536647
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536879
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538304
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538303
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134350
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134338
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537334
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539713
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152126
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152114
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536981
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139458
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535272
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538777
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538776
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538775
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538774
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538773
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538772
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538771
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538769
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139470
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537814
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540078
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166792
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166780
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537175
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539606
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147051
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147039
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537073
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539524
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539522
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143861
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143849
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535488
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540213
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540246
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540256
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540251
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540253
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540229
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540237
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540224
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173245
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540245
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540238
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537058
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143329
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536791
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539467
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539466
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539465
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539464
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539463
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539462
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539460
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537881
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540125
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168953
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168941
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537553
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158418
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158406
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537140
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539583
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145956
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537991
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540198
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172475
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172463
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537125
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539573
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145487
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145463
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540261
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537248
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539656
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149396
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149384
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535905
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537956
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540176
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171356
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537764
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fast: false
reversible: false
name: mRNA_M_Sm30_degradation

540041
type: LocalParameter
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165204
type: SpeciesReference
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species: 536811

165192
type: SpeciesReference
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535320
type: Species
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name: GENE_P_Ets1

540220
type: Event
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event assignment: 174148
event assignment: 174160
trigger: 174015
event assignment: 174063
event assignment: 174075
event assignment: 174136
use values from trigger time: true
event assignment: 174051
event assignment: 174172
name: e11
event assignment: 174111
event assignment: 174099
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event assignment: 174087
event assignment: 174124

174015
type: Trigger
persistant: true
initial value: true

540241
type: Parameter
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value: 1.0
name: E_Gcad_S1

540286
type: Parameter
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value: 0.0
name: M_cB_S2

540285
type: Parameter
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value: 1.0
name: M_cB_S1

540242
type: Parameter
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value: 0.0
name: E_Gcad_S2

537583
type: Reaction
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product: 159378
reactant: 159366
fast: false
reversible: false
name: mRNA_E_Pmar1_translation

539919
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159378
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species: 535680

159366
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537286
type: Reaction
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modifier: 150601
product: 150589
reactant: 150577
fast: false
reversible: false
name: PROTEIN_M_UMADelta_degradation

539681
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150589
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150577
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536897
type: Reaction
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modifier: 135300
modifier: 135287
product: 135275
reactant: 135263
fast: false
reversible: false
name: GENE_E_SuTx_transcription

538403
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538402
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538401
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538400
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135275
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135263
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species: 535107

536939
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product: 137396
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modifier: 137408
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137396
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137384
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538587
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538586
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538585
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538584
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538583
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538582
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537839
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reactant: 167597
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reversible: false
name: mRNA_P_Delta_degradation

540097
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167609
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167597
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537481
type: Reaction
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fast: false
reversible: false
name: mRNA_E_Erg_translation

539860
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156685
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156673
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537352
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name: PROTEIN_P_GroTCF_accociation

539725
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152704
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152692
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152680
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537941
type: Reaction
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fast: false
reversible: false
name: mRNA_P_Sm30_degradation

540166
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170880
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species: 536811

170868
type: SpeciesReference
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537710
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fast: false
reversible: false
name: mRNA_M_Gcm_degradation

540005
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163472
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species: 536811

163460
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537235
type: Reaction
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name: PROTEIN_M_Gcm_degradation

539647
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148963
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148951
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537302
type: Reaction
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reversible: false
name: PROTEIN_M_frizzled_a_inactivation

539692
type: LocalParameter
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151137
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536034
type: Species
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name: PROTEIN_M_frizzled_i

151125
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535479
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initial amount: NaN
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name: PRE_M_SoxB1

536848
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modifier: 132742
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fast: false
reversible: false
name: GENE_E_Ets1_transcription

538164
type: LocalParameter
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538163
type: LocalParameter
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538162
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538161
type: LocalParameter
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535743
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name: PROTEIN_E_UbiqEts1

132730
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132718
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535008
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name: GENE_E_Ets1

535308
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name: GENE_P_Dpt

537937
type: Reaction
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reversible: false
name: mRNA_P_Pmar1_translation

540163
type: LocalParameter
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170736
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species: 536194

170724
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537143
type: Reaction
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name: PROTEIN_E_Notch_inactivation

539585
type: LocalParameter
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146053
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146041
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537536
type: Reaction
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product: 157889
reactant: 157877
fast: false
reversible: false
name: mRNA_E_Gelsolin_degradation

539888
type: LocalParameter
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157889
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species: 536811

157877
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537041
type: Reaction
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modifier: 142519
product: 142507
reactant: 142495
fast: false
reversible: false
name: GENE_P_Pks_transcription

539077
type: LocalParameter
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539076
type: LocalParameter
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539075
type: LocalParameter
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539073
type: LocalParameter
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142507
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species: 536770

142495
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species: 535395

535395
type: Species
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boundary condition: true
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initial concentration: 0.0
initial amount: NaN
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name: GENE_P_Pks

536878
type: Reaction
reactant: 134241
modifier: 134301
fast: false
name: GENE_E_MspL_transcription
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kinetic law: 134326
product: 134253
modifier: 134277
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modifier: 134289
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134241
type: SpeciesReference
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species: 535068

538295
type: LocalParameter
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538302
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538293
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538300
type: LocalParameter
value: 1.0

538301
type: LocalParameter
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538296
type: LocalParameter
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538299
type: LocalParameter
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538294
type: LocalParameter
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538297
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538298
type: LocalParameter
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134253
type: SpeciesReference
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species: 536398

537419
type: Reaction
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product: 154862
reactant: 154850
fast: false
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name: PROTEIN_P_frizzled_a_inactivation

539770
type: LocalParameter
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154862
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536290
type: Species
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name: PROTEIN_P_frizzled_i

154850
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species: 536287

537857
type: Reaction
kinetic law: 168209
modifier: 168197
product: 168185
reactant: 168173
fast: false
reversible: false
name: mRNA_P_Eve_degradation

540109
type: LocalParameter
value: 0.119

168185
type: SpeciesReference
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species: 536811

168173
type: SpeciesReference
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species: 536695

536695
type: Species
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boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 534968
name: mRNA_P_Eve

537521
type: Reaction
kinetic law: 157429
modifier: 157417
product: 157405
reactant: 157393
fast: false
reversible: false
name: mRNA_E_FvMo_degradation

539878
type: LocalParameter
value: 0.119

157405
type: SpeciesReference
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species: 536811

157393
type: SpeciesReference
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species: 536359

535788
type: Species
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initial concentration: 0.0
initial amount: NaN
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name: PROTEIN_E_z13

537662
type: Reaction
kinetic law: 161955
modifier: 161943
product: 161931
reactant: 161919
fast: false
reversible: false
name: mRNA_M_Delta_degradation

539972
type: LocalParameter
value: 0.119

161931
type: SpeciesReference
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species: 536811

161919
type: SpeciesReference
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species: 536500

537139
type: Reaction
kinetic law: 145932
modifier: 145920
product: 145908
reactant: 145896
fast: false
reversible: false
name: PROTEIN_E_Not_degradation

539582
type: LocalParameter
value: 0.3

145908
type: SpeciesReference
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species: 536811

145896
type: SpeciesReference
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species: 535659

537254
type: Reaction
kinetic law: 149612
modifier: 149600
product: 149588
reactant: 149576
fast: false
reversible: false
name: PROTEIN_M_Notch_activation

539660
type: LocalParameter
value: 0.683876854591

149588
type: SpeciesReference
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species: 535917

149576
type: SpeciesReference
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species: 535920

537692
type: Reaction
kinetic law: 162919
modifier: 162907
product: 162895
reactant: 162883
fast: false
reversible: false
name: mRNA_M_FoxN23_degradation

539992
type: LocalParameter
value: 0.119

162895
type: SpeciesReference
stoichiometry: 1.0
species: 536811

162883
type: SpeciesReference
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species: 536530

536530
type: Species
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boundary condition: false
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initial concentration: 0.0
initial amount: NaN
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name: mRNA_M_FoxN23

537320
type: Reaction
kinetic law: 151728
modifier: 151716
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reactant: 151692
fast: false
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name: PROTEIN_P_Delta_degradation

539704
type: LocalParameter
value: 0.3

151704
type: SpeciesReference
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species: 536811

151692
type: SpeciesReference
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species: 536064

535350
type: Species
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boundary condition: true
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initial amount: NaN
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name: GENE_P_Gcad

537517
type: Reaction
kinetic law: 157285
modifier: 157273
product: 157261
reactant: 157249
fast: false
reversible: false
name: mRNA_E_FoxN23_translation

539875
type: LocalParameter
value: 2.0

157261
type: SpeciesReference
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species: 535593

157249
type: SpeciesReference
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species: 536811

537955
type: Reaction
kinetic law: 171343
modifier: 171330
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reactant: 171304
fast: false
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name: mRNA_P_SoxC_translation

540175
type: LocalParameter
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171317
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species: 536212

171304
type: SpeciesReference
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537589
type: Reaction
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modifier: 159583
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fast: false
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name: mRNA_E_Sm30_translation

539923
type: LocalParameter
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159571
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species: 535686

159559
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536933
type: Reaction
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reactant: 137108
fast: false
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name: GENE_M_FoxN23_transcription

538561
type: LocalParameter
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538560
type: LocalParameter
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137120
type: SpeciesReference
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species: 536530

137108
type: SpeciesReference
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535179
type: Species
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name: GENE_M_FoxN23

540219
type: Event
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event assignment: 173991
delay: 173979
trigger: 173967
use values from trigger time: true
name: e8

540281
type: Parameter
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value: 1.0
name: P_UbiqHesC_S1

540282
type: Parameter
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value: 0.0
name: P_UbiqHesC_S2

173967
type: Trigger
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537358
type: Reaction
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name: PROTEIN_P_Hnf6_degradation

539729
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152886
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152874
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535149
type: Species
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name: GENE_M_Delta

537838
type: Reaction
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name: mRNA_P_CyP_translation

540096
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167561
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species: 536061

167549
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536816
type: Reaction
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name: E_Notch_Hill_Kinetic

538016
type: LocalParameter
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538014
type: LocalParameter
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538013
type: LocalParameter
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538011
type: LocalParameter
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131522
type: SpeciesReference
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species: 536404

131510
type: SpeciesReference
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535443
type: Species
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name: PRE_E_Notch

537607
type: Reaction
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fast: false
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name: mRNA_E_SuTx_translation

539935
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160150
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160138
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535734
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name: PROTEIN_E_UbiqAlx1

537316
type: Reaction
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name: PROTEIN_P_CAPK_degradation

539701
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151559
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species: 536811

151547
type: SpeciesReference
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537199
type: Reaction
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name: PROTEIN_M_Bra_degradation

539622
type: LocalParameter
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147827
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147815
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536920
type: Reaction
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fast: false
reversible: false
name: GENE_M_Dpt_transcription

538501
type: LocalParameter
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538500
type: LocalParameter
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538499
type: LocalParameter
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538498
type: LocalParameter
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136423
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136411
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species: 535152

537301
type: Reaction
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name: PROTEIN_M_frizzled_a_activation

539691
type: LocalParameter
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151089
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151077
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536479
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name: mRNA_M_Alx1

537149
type: Reaction
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reactant: 146221
fast: false
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name: PROTEIN_E_Pks_degradation

539589
type: LocalParameter
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146233
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146221
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537535
type: Reaction
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reactant: 157829
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name: mRNA_E_Gcm_translation

539887
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157841
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157829
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535407
type: Species
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name: GENE_P_Sm50

537376
type: Reaction
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reactant: 153440
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name: PROTEIN_P_Otx_degradation

539741
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153452
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153440
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537418
type: Reaction
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name: PROTEIN_P_frizzled_a_activation

539769
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154814
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154802
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537151
type: Reaction
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reactant: 146269
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name: PROTEIN_E_Pmar1_degradation

539590
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146281
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146269
type: SpeciesReference
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536834
type: Reaction
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kinetic law: 132186
fast: false
reversible: false
name: GENE_E_Bra_transcription
reactant: 132114
modifier: 132174
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modifier: 132138
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132126
type: SpeciesReference
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538118
type: LocalParameter
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538116
type: LocalParameter
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538115
type: LocalParameter
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538113
type: LocalParameter
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538112
type: LocalParameter
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538110
type: LocalParameter
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538109
type: LocalParameter
value: 1.0

538107
type: LocalParameter
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132114
type: SpeciesReference
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species: 534978

534978
type: Species
constant: true
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has only substance units: false
initial concentration: 0.0
initial amount: NaN
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name: GENE_E_Bra

540272
type: Parameter
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value: 0.0
name: P_UbiqSoxC_S2

537443
type: Reaction
kinetic law: 155501
modifier: 155489
product: 155477
reactant: 155465
fast: false
reversible: false
name: mRNA_E_Alx1_degradation

539834
type: LocalParameter
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155477
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species: 536811

155465
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537923
type: Reaction
kinetic law: 170326
modifier: 170314
product: 170302
reactant: 170289
fast: false
reversible: false
name: mRNA_P_Nrl_degradation

540154
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170302
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species: 536811

170289
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species: 536761

537626
type: Reaction
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modifier: 160787
product: 160775
reactant: 160763
fast: false
reversible: false
name: mRNA_E_VEGFR_degradation

539948
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160775
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species: 536811

160763
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536467
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initial concentration: 0.0
initial amount: NaN
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name: mRNA_E_VEGFR

540277
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537698
type: Reaction
kinetic law: 163112
modifier: 163100
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reactant: 163075
fast: false
reversible: false
name: mRNA_M_FvMo_degradation

539996
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163088
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163075
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537886
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reactant: 169085
fast: false
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name: mRNA_P_Gcad_translation

540128
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169097
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169085
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537806
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name: mRNA_M_VEGFR_degradation

540071
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166551
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166539
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537182
type: Reaction
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modifier: 147330
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name: PROTEIN_E_Wnt8_degradation

539611
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147318
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147306
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537167
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name: PROTEIN_E_TBr_degradation

539601
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146810
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146798
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537998
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reversible: false
name: mRNA_P_cB_translation

540203
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172703
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172691
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537613
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name: mRNA_E_Tel_translation

539939
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160343
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160331
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540264
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537911
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reversible: false
name: mRNA_P_Lim_degradation

540146
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169915
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169903
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537545
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fast: false
reversible: false
name: mRNA_E_Hnf6_degradation

539894
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158178
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species: 536811

158166
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537983
type: Reaction
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reversible: false
name: mRNA_P_UbiqHnf6_translation

540193
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172232
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species: 536263

536263
type: Species
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name: PROTEIN_P_UbiqHnf6

172220
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species: 536811

537686
type: Reaction
kinetic law: 162727
modifier: 162715
product: 162703
reactant: 162691
fast: false
reversible: false
name: mRNA_M_FoxA_degradation

539988
type: LocalParameter
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162703
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species: 536811

162691
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537113
type: Reaction
kinetic law: 145125
modifier: 145113
product: 145101
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name: PROTEIN_E_GSK3_i_activation

539565
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145101
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145089
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537395
type: Reaction
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fast: false
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name: PROTEIN_P_Tel_degradation

539754
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154077
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154065
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537293
type: Reaction
kinetic law: 150869
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fast: false
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name: PROTEIN_M_VEGFSignal_accociation

539686
type: LocalParameter
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150856
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150844
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150832
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150820
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537590
type: Reaction
kinetic law: 159643
modifier: 159631
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name: mRNA_E_Sm50_degradation

539924
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159619
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159607
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537461
type: Reaction
kinetic law: 156083
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name: mRNA_E_CyP_degradation

539846
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156059
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species: 536811

156047
type: SpeciesReference
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species: 536317

536317
type: Species
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name: mRNA_E_CyP

537503
type: Reaction
kinetic law: 156853
modifier: 156841
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name: mRNA_E_Eve_degradation

539864
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156829
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156817
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536341
type: Species
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name: mRNA_E_Eve

537278
type: Reaction
kinetic law: 150373
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name: PROTEIN_M_SuH_degradation

539676
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150349
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150337
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537344
type: Reaction
kinetic law: 152474
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name: PROTEIN_P_GataC_degradation

539720
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152450
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species: 536811

152438
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537719
type: Reaction
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fast: false
reversible: false
name: mRNA_M_Hex_degradation

540011
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163761
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species: 536811

163749
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537673
type: Reaction
kinetic law: 162293
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reactant: 162257
fast: false
reversible: false
name: mRNA_M_Endo16_translation

539979
type: LocalParameter
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162269
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species: 535827

535827
type: Species
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has only substance units: false
initial concentration: 0.0
initial amount: NaN
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name: PROTEIN_M_Endo16

162257
type: SpeciesReference
stoichiometry: 1.0
species: 536811

W3 CDTF: Fri Jan 15 16:34:00 GMT 2010

537100
type: Reaction
kinetic law: 144692
modifier: 144680
product: 144668
reactant: 144656
fast: false
reversible: false
name: PROTEIN_E_Erg_degradation

539556
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144668
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species: 536811

144656
type: SpeciesReference
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537979
type: Reaction
kinetic law: 172112
modifier: 172100
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fast: false
reversible: false
name: mRNA_P_UbiqHesC_degradation

540190
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172088
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172076
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537280
type: Reaction
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modifier: 150409
product: 150397
reactant: 150385
fast: false
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name: PROTEIN_M_SuTx_degradation

539677
type: LocalParameter
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150397
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species: 536811

150385
type: SpeciesReference
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species: 535962

535962
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name: PROTEIN_M_SuTx

536957
type: Reaction
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product: 138218
kinetic law: 138290
reversible: false
modifier: 138254
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reactant: 138206
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138218
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species: 536575

538652
type: LocalParameter
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538658
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538654
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538655
type: LocalParameter
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538649
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538656
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538650
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538651
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538657
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538653
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138206
type: SpeciesReference
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species: 535224

535224
type: Species
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name: GENE_M_MspL

535218
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name: GENE_M_Lim

536987
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kinetic law: 139858
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139785
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538809
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538803
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538804
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538805
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538808
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538811
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538806
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538801
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538807
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538810
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139773
type: SpeciesReference
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540271
type: Parameter
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537442
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reactant: 155428
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name: P_cB_Hill_Kinetic

539833
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539832
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539831
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539829
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155441
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155428
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535533
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name: PRE_P_cB

537325
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name: PROTEIN_P_Dri_degradation

539707
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151836
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151824
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536827
type: Reaction
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name: E_VEGF_Hill_Kinetic

538058
type: LocalParameter
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538056
type: LocalParameter
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538055
type: LocalParameter
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538053
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131777
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131765
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537916
type: Reaction
kinetic law: 170085
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fast: false
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name: mRNA_P_Msp130_translation

540149
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170060
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170048
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537559
type: Reaction
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539903
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158610
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158598
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537242
type: Reaction
kinetic law: 149228
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name: PROTEIN_M_Hex_degradation

539652
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149204
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149192
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537089
type: Reaction
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name: PROTEIN_E_Delta_activation

539549
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144341
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144329
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536975
type: Reaction
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kinetic law: 139242
name: GENE_M_SoxC_transcription

536013
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name: PROTEIN_M_UbiqSoxC

139182
type: SpeciesReference
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535260
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name: GENE_M_SoxC

139194
type: SpeciesReference
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538749
type: LocalParameter
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538748
type: LocalParameter
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538747
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538746
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538745
type: LocalParameter
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538743
type: LocalParameter
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540263
type: Parameter
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540228
type: Parameter
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name: E_SoxB1_S2

537002
type: Reaction
fast: false
modifier: 140547
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reactant: 140511
kinetic law: 140571
product: 140523
name: GENE_P_Erg_transcription
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140511
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535317
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name: GENE_P_Erg

538879
type: LocalParameter
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538878
type: LocalParameter
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538877
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538876
type: LocalParameter
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538875
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538873
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140523
type: SpeciesReference
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537467
type: Reaction
kinetic law: 156276
modifier: 156264
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reactant: 156240
fast: false
reversible: false
name: mRNA_E_Dpt_degradation

539850
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156252
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156240
type: SpeciesReference
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537509
type: Reaction
kinetic law: 157045
modifier: 157033
product: 157021
reactant: 157009
fast: false
reversible: false
name: mRNA_E_FoxA_degradation

539868
type: LocalParameter
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157021
type: SpeciesReference
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157009
type: SpeciesReference
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537947
type: Reaction
kinetic law: 171098
modifier: 171085
product: 171073
reactant: 171061
fast: false
reversible: false
name: mRNA_P_Snail_degradation

540170
type: LocalParameter
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171073
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171061
type: SpeciesReference
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537716
type: Reaction
kinetic law: 163688
modifier: 163676
product: 163664
reactant: 163652
fast: false
reversible: false
name: mRNA_M_HesC_degradation

540009
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163664
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163652
type: SpeciesReference
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species: 536554

537904
type: Reaction
kinetic law: 169698
modifier: 169686
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reactant: 169662
fast: false
reversible: false
name: mRNA_P_Hox_translation

540141
type: LocalParameter
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169674
type: SpeciesReference
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species: 536155

169662
type: SpeciesReference
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species: 536811

537077
type: Reaction
kinetic law: 143981
product: 143969
reactant: 143957
fast: false
reversible: false
name: M_cB_Hill_Kinetic

539541
type: LocalParameter
value: 10.0

539540
type: LocalParameter
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539539
type: LocalParameter
value: 11.0

539537
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143969
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species: 536650

143957
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species: 535497

535497
type: Species
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initial concentration: 0.0
initial amount: NaN
in compartment: 534968
name: PRE_M_cB

535473
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has only substance units: false
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in compartment: 534968
name: PRE_M_Notch

537308
type: Reaction
kinetic law: 151342
modifier: 151330
product: 151318
reactant: 151305
fast: false
reversible: false
name: PROTEIN_P_Alx1_degradation

539696
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151318
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151305
type: SpeciesReference
stoichiometry: 1.0
species: 536043

W3 CDTF: Wed Aug 31 20:46:06 BST 2011

537637
type: Reaction
kinetic law: 161136
modifier: 161124
product: 161112
reactant: 161100
fast: false
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539955
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161112
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161100
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536912
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538476
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538472
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136083
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136071
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537193
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535254
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537527
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539882
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537668
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162111
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537368
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536908
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538451
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538447
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536851
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538177
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538175
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538174
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538173
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540269
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173774
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537206
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148061
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540227
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537832
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167356
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537466
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156203
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537601
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539931
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159957
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159945
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536968
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538702
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538706
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536882
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538471
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537782
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537680
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537026
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538995
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141725
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537449
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155671
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155659
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540208
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537842
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167693
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537778
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165637
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537013
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537880
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539807
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539804
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155259
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155247
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536936
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137240
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537203
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537763
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165143
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537691
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162847
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537119
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536992
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537679
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537106
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144860
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144848
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537781
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537856
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168125
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537136
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537952
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537853
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537265
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537122
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ORG:
  orgname: EMBL-EBI
n:
  given: Vijayalakshmi
  family: Chelliah