Index of /pub/users/ac19/Home_files/Lustre_Backup/TraDIS_Scripts_Carla
Name
Last modified
Size
Description
Parent Directory
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typhi_tradis.R
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tradis_gene_insert_sites
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tradis_essentiality_Modified_Cdiff6.R
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tradis_essentiality.R
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tradis_analysis
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tagBAM.py
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sortbam.o
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sortbam.e
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sortBAM.sh
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scripts/
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runTradis.sh
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runTradis.o
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runTradis.e
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runSmalt.sh
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runSmalt.o
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runSmalt.e
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runPicard.py
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removeTag.sh
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removeTag.py
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log_4
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job_name.o
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job_name.e
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filterFastQ.sh
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filterFastQ.py
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filterFastQ.o
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filterFastQ.e
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err_4
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entED_diff.R
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convertSmalt.sh
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convertSmalt.o
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convertSmalt.e
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checkSAM.sh
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checkSAM.py
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bamcheck.sh
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bamcheck.o
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bamcheck.e
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Ty2_baseline.fixed.tab
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TraDIS_plot_summary.pl
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Second_test/
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Rplots.pdf
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Pseudomonas_aeruginosa_UCBPP-PA14_v1.index.smi
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Pseudomonas_aeruginosa_UCBPP-PA14_v1.index.sma
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Pseudomonas_aeruginosa_UCBPP-PA14_v1.gff
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Pseudomonas_aeruginosa_UCBPP-PA14_v1.fa
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Pseudomonas_aeruginosa_UCBPP-PA14_v1.embl
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LMN24_9876#90_merged.bam.insertion.csv
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LMN24_9876#90_merged.bam.corrected.bam.bai
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LMN24_9876#90_merged.bam.corrected.bam
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LMN24_9876#90_merged.bam.Pseudomonas_aeruginosa_UCBPP-PA14_v1.insert_site_plot.gz
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LMN24_9876#90_merged.bam.Pseudomonas_aeruginosa_UCBPP-PA14_v1.insert_site_plot.csv
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LMN24_9876#90_merged.bam
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LMN23_9876#82_merged.bam.insertion.csv
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LMN23_9876#82_merged.bam.corrected.bam.bai
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LMN23_9876#82_merged.bam.corrected.bam
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LMN23_9876#82_merged.bam.Pseudomonas_aeruginosa_UCBPP-PA14_v1.insert_site_plot.gz
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LMN23_9876#82_merged.bam.Pseudomonas_aeruginosa_UCBPP-PA14_v1.insert_site_plot.csvLMN21_9876#66_merged.bam.Pseudomonas_aeruginosa_UCBPP-PA14_v1.insert_site_plot.csv.output.csv
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LMN23_9876#82_merged.bam.Pseudomonas_aeruginosa_UCBPP-PA14_v1.insert_site_plot.csv
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LMN23_9876#82_merged.bam
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LMN22_9876#74_vs_LMN24_9876#90_merged_PA14.csv
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LMN22_9876#74_merged.bam.insertion.csv
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LMN22_9876#74_merged.bam.corrected.bam.bai
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LMN22_9876#74_merged.bam.corrected.bam
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LMN22_9876#74_merged.bam.Pseudomonas_aeruginosa_UCBPP-PA14_v1.insert_site_plot.gz
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LMN22_9876#74_merged.bam.Pseudomonas_aeruginosa_UCBPP-PA14_v1.insert_site_plot.csv
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LMN22_9876#74_merged.bam
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LMN21_9876#74_merged.bam.insertion.csv
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LMN21_9876#74_merged.bam.corrected.bam.bai
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LMN21_9876#74_merged.bam.corrected.bam
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LMN21_9876#66_merged.bam.insertion.csv
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LMN21_9876#66_merged.bam.corrected.bam.bai
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LMN21_9876#66_merged.bam.corrected.bam
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LMN21_9876#66_merged.bam.Pseudomonas_aeruginosa_UCBPP-PA14_v1.insert_site_plot.gz
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LMN21_9876#66_merged.bam.Pseudomonas_aeruginosa_UCBPP-PA14_v1.insert_site_plot.csv
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LMN21_9876#66_merged.bam
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LMN8_9876#57_merged.bam.insertion.csv
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LMN8_9876#57_merged.bam.corrected.bam.bai
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LMN8_9876#57_merged.bam.corrected.bam
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LMN8_9876#57_merged.bam.Pseudomonas_aeruginosa_UCBPP-PA14_v1.insert_site_plot.gz
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LMN8_9876#57_merged.bam.Pseudomonas_aeruginosa_UCBPP-PA14_v1.insert_site_plot.csvLMN5_9876#33_merged.bam.Pseudomonas_aeruginosa_UCBPP-PA14_v1.insert_site_plot.csv.output.csv
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LMN8_9876#57_merged.bam.Pseudomonas_aeruginosa_UCBPP-PA14_v1.insert_site_plot.csv
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LMN8_9876#57_merged.bam
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LMN7_9876#49_merged.bam.insertion.csv
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LMN7_9876#49_merged.bam.corrected.bam.bai
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LMN7_9876#49_merged.bam.corrected.bam
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LMN7_9876#49_merged.bam.Pseudomonas_aeruginosa_UCBPP-PA14_v1.insert_site_plot.gz
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LMN7_9876#49_merged.bam.Pseudomonas_aeruginosa_UCBPP-PA14_v1.insert_site_plot.csvLMN5_9876#33_merged.bam.Pseudomonas_aeruginosa_UCBPP-PA14_v1.insert_site_plot.csv.output.csv
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LMN7_9876#49_merged.bam.Pseudomonas_aeruginosa_UCBPP-PA14_v1.insert_site_plot.csv
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LMN7_9876#49_merged.bam
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LMN6_9876#41_merged.bam.insertion.csv
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LMN6_9876#41_merged.bam.corrected.bam.bai
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LMN6_9876#41_merged.bam.corrected.bam
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LMN6_9876#41_merged.bam.Pseudomonas_aeruginosa_UCBPP-PA14_v1.insert_site_plot.gz
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LMN6_9876#41_merged.bam.Pseudomonas_aeruginosa_UCBPP-PA14_v1.insert_site_plot.csv
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LMN6_9876#41_merged.bam
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LMN5_9876#33_merged.bam.insertion.csv
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LMN5_9876#33_merged.bam.corrected.bam.bai
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LMN5_9876#33_merged.bam.corrected.bam
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LMN5_9876#33_merged.bam.Pseudomonas_aeruginosa_UCBPP-PA14_v1.insert_site_plot.gz
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LMN5_9876#33_merged.bam.Pseudomonas_aeruginosa_UCBPP-PA14_v1.insert_site_plot.csv
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LMN5_9876#33_merged.bam
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LMN4_9876#25_merged.csv
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LMN4_9876#25_merged.bam.insertion.csv
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LMN4_9876#25_merged.bam.corrected.bam.bai
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LMN4_9876#25_merged.bam.corrected.bam
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LMN4_9876#25_merged.bam.Pseudomonas_aeruginosa_UCBPP-PA14_v1.insert_site_plot.gz
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LMN4_9876#25_merged.bam.Pseudomonas_aeruginosa_UCBPP-PA14_v1.insert_site_plot.csv
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LMN4_9876#25_merged.bam
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LMN3_9876#17_merged.csv
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LMN3_9876#17_merged.bam.insertion.csv
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LMN3_9876#17_merged.bam.corrected.bam.bai
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LMN3_9876#17_merged.bam.corrected.bam
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LMN3_9876#17_merged.bam.Pseudomonas_aeruginosa_UCBPP-PA14_v1.insert_site_plot.gz
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LMN3_9876#17_merged.bam.Pseudomonas_aeruginosa_UCBPP-PA14_v1.insert_site_plot.csvLMN1_9876#1_merged.bam.Pseudomonas_aeruginosa_UCBPP-PA14_v1.insert_site_plot.csv.output.pdf
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LMN3_9876#17_merged.bam.Pseudomonas_aeruginosa_UCBPP-PA14_v1.insert_site_plot.csvLMN1_9876#1_merged.bam.Pseudomonas_aeruginosa_UCBPP-PA14_v1.insert_site_plot.csv.output.csv
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LMN3_9876#17_merged.bam.Pseudomonas_aeruginosa_UCBPP-PA14_v1.insert_site_plot.csv
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LMN3_9876#17_merged.bam
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LMN2_9876#9_merged.bam.insertion.csv
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LMN2_9876#9_merged.bam.corrected.bam.bai
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LMN2_9876#9_merged.bam.corrected.bam
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LMN2_9876#9_merged.bam.Pseudomonas_aeruginosa_UCBPP-PA14_v1.insert_site_plot.gz
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LMN2_9876#9_merged.bam.Pseudomonas_aeruginosa_UCBPP-PA14_v1.insert_site_plot.csv
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LMN2_9876#9_merged.bam
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LMN1_9876#1_merged.bam.insertion.csv
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LMN1_9876#1_merged.bam.corrected.bam.bai
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LMN1_9876#1_merged.bam.corrected.bam
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LMN1_9876#1_merged.bam.Pseudomonas_aeruginosa_UCBPP-PA14_v1.insert_site_plot.gz
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LMN1_9876#1_merged.bam.Pseudomonas_aeruginosa_UCBPP-PA14_v1.insert_site_plot.csv
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LMN1_9876#1_merged.bam
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First_test/
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521350.se.markdup.bam.bai
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521350.se.markdup.bam
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9876_2#90_1.tag.fastq
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9876_2#90_1.notag.fastq.mapped.bam.sort.bam.insertion.csv
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9876_2#90_1.notag.fastq.mapped.bam.sort.bam.corrected.bam.bai
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9876_2#82_1.notag.fastq.mapped.bam.sort.bam
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9876_2#74_1.notag.fastq.mapped.bam.sort.bam.insertion.csv
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9876_2#74_1.notag.fastq.mapped.bam.sort.bam.corrected.bam.bai
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9876_2#74_1.notag.fastq.mapped.bam.sort.bam.Pseudomonas_aeruginosa_UCBPP-PA14_v1.insert_site_plot.gz
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9876_2#74_1.notag.fastq.mapped.bam.sort.bam
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9876_2#41_1.notag.fastq.mapped.bam.sort.bam
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2020-09-28 14:53
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2020-09-28 14:53
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2020-09-28 14:53
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2020-09-28 14:53
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2020-09-28 14:53
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2020-09-28 14:53
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2020-09-28 14:53
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2020-09-28 14:53
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2020-09-28 14:53
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2020-09-28 14:53
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2020-09-28 14:53
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2020-09-28 14:53
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2020-09-28 14:53
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2020-09-28 14:53
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2020-09-28 14:53
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2020-09-28 14:53
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2020-09-28 14:53
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2020-09-28 14:53
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2020-09-28 14:53
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2020-09-28 14:53
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2020-09-28 14:53
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2020-09-28 14:53
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2020-09-28 14:53
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2020-09-28 14:53
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2020-09-28 14:53
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2020-09-28 14:53
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2020-09-28 14:53
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2020-09-28 14:53
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2020-09-28 14:53
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2020-09-28 14:53
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2020-09-28 14:53
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2020-09-28 14:53
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2020-09-28 14:53
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2020-09-28 14:53
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