#!/bin/bash
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Zoey/chr28_14282337_14282551_Racon_Corrected_Contig0.fasta tig00000001:8607-8620 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Zoey/chr29_31417182_31417395_Racon_Corrected_Contig0.fasta tig00000001:10019-10031 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Zoey/chr29_31417182_31417395_Racon_Corrected_Contig0.fasta tig00000001:5290-5308 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Zoey/chr22_41020068_41020322_Racon_Corrected_Contig0.fasta tig00000001:8325-8340 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Zoey/chr12_30160895_30161108_Racon_Corrected_Contig0.fasta tig00000001:12422-12434 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Zoey/chr12_30160895_30161108_Racon_Corrected_Contig0.fasta tig00000001:15459-15459 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Zoey/chr12_30160895_30161108_Racon_Corrected_Contig0.fasta tig00000001:19241-19240 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Zoey/chr12_30160895_30161108_Racon_Corrected_Contig1.fasta tig00000002:3927-3942 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Zoey/chrX_56417470_56417758_Racon_Corrected_Contig0.fasta tig00000001:9179-9190 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Zoey/chr9_29406962_29407240_Racon_Corrected_Contig0.fasta tig00000001:6339-6354 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Zoey/chr1_66556324_66556541_Racon_Corrected_Contig0.fasta tig00000001:10528-10544 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Zoey/chr17_35601722_35601962_Racon_Corrected_Contig0.fasta tig00000001:7651-7684 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Zoey/chr17_35601722_35601962_Racon_Corrected_Contig0.fasta tig00000001:3461-3469 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Zoey/chr17_35601722_35601962_Racon_Corrected_Contig1.fasta tig00000002:8728-8744 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Zoey/chr21_42853678_42853896_Racon_Corrected_Contig0.fasta tig00000001:7240-7239 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Zoey/chr21_42853678_42853896_Racon_Corrected_Contig0.fasta tig00000001:4190-4191 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Zoey/chr21_42853678_42853896_Racon_Corrected_Contig1.fasta tig00000002:7299-7316 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Zoey/chr1_100923051_100923325_Racon_Corrected_Contig0.fasta tig00000001:8926-8925 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Zoey/chr1_100923051_100923325_Racon_Corrected_Contig0.fasta tig00000001:2803-2815 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Zoey/chr25_45486737_45486951_Racon_Corrected_Contig0.fasta tig00000001:10888-10901 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Zoey/chr8_13531038_13531254_Racon_Corrected_Contig0.fasta tig00000001:5074-5082 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Zoey/chr8_13531038_13531254_Racon_Corrected_Contig0.fasta tig00000001:4037-4049 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Zoey/chr9_44472500_44472754_Racon_Corrected_Contig0.fasta tig00000001:9060-9067 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Zoey/chr3_16544788_16545105_Racon_Corrected_Contig0.fasta ctg1:12353-12367 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Zoey/chr8_15866401_15866629_Racon_Corrected_Contig0.fasta tig00000001:369-376 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Zoey/chr8_15866401_15866629_Racon_Corrected_Contig0.fasta tig00000001:8027-8039 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Zoey/chr1_45084016_45084230_Racon_Corrected_Contig0.fasta tig00000001:11294-11307 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Zoey/chr7_50858850_50859110_Racon_Corrected_Contig0.fasta tig00000001:10574-10589 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Zoey/chr22_37743686_37743889_Racon_Corrected_Contig0.fasta tig00000001:4876-4875 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Zoey/chr22_37743686_37743889_Racon_Corrected_Contig0.fasta tig00000001:10733-10748 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Zoey/chr1_33772064_33772279_Racon_Corrected_Contig1.fasta tig00000002:8926-8940 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Zoey/chr22_54124481_54124748_Racon_Corrected_Contig0.fasta tig00000001:2948-2964 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Zoey/chr22_54124481_54124748_Racon_Corrected_Contig0.fasta tig00000001:10983-10994 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Zoey/chr17_27583906_27584120_Racon_Corrected_Contig0.fasta tig00000001:8398-8411 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Zoey/chr32_21027992_21028205_Racon_Corrected_Contig0.fasta tig00000001:2853-2853 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Zoey/chr32_21027992_21028205_Racon_Corrected_Contig0.fasta tig00000001:6790-6791 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Zoey/chr15_60509532_60509745_Racon_Corrected_Contig0.fasta ctg1:9569-9572 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Zoey/chr27_15988745_15989145_Racon_Corrected_Contig0.fasta tig00000001:7299-7298 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Zoey/chr27_15988745_15989145_Racon_Corrected_Contig0.fasta tig00000001:7299-7298 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Zoey/chr27_15988745_15989145_Racon_Corrected_Contig0.fasta tig00000001:8191-8190 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Zoey/chr12_49183551_49183820_Racon_Corrected_Contig0.fasta tig00000001:9048-9061 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Zoey/chr10_48277677_48277891_Racon_Corrected_Contig0.fasta tig00000001:10480-10493 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Zoey/chr33_30836627_30836890_Racon_Corrected_Contig0.fasta tig00000001:9055-9071 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Zoey/chr32_26587612_26587827_Racon_Corrected_Contig0.fasta tig00000001:6364-6378 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Zoey/chr4_47622158_47622683_Racon_Corrected_Contig0.fasta tig00000001:9883-9898 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Zoey/chr14_35081794_35082011_Racon_Corrected_Contig0.fasta tig00000001:10063-10078 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Zoey/chr16_30109531_30109744_Racon_Corrected_Contig0.fasta tig00000001:7377-7389 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Zoey/chr8_73448087_73448340_Racon_Corrected_Contig1.fasta tig00000002:11314-11313 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Zoey/chr8_73448087_73448340_Racon_Corrected_Contig1.fasta tig00000002:15262-15261 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Zoey/chr8_73448087_73448340_Racon_Corrected_Contig1.fasta tig00000002:12243-12242 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Zoey/chr8_73448087_73448340_Racon_Corrected_Contig1.fasta tig00000002:15262-15261 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Zoey/chr8_73448087_73448340_Racon_Corrected_Contig1.fasta tig00000002:13714-13715 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Zoey/chr8_73448087_73448340_Racon_Corrected_Contig1.fasta tig00000002:15500-15499 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Zoey/chr8_73448087_73448340_Racon_Corrected_Contig1.fasta tig00000002:10327-10327 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Zoey/chr8_73448087_73448340_Racon_Corrected_Contig1.fasta tig00000002:15480-15479 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Zoey/chr8_73448087_73448340_Racon_Corrected_Contig1.fasta tig00000002:2703-2703 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Zoey/chr8_73448087_73448340_Racon_Corrected_Contig1.fasta tig00000002:509-508 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Zoey/chr8_73448087_73448340_Racon_Corrected_Contig3.fasta tig00000004:4154-4154 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Zoey/chr8_73448087_73448340_Racon_Corrected_Contig3.fasta tig00000004:6192-6191 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Zoey/chr8_73448087_73448340_Racon_Corrected_Contig4.fasta tig00000005:11192-11194 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Zoey/chr11_14497198_14497482_Racon_Corrected_Contig0.fasta tig00000001:10279-10292 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Zoey/chr22_38912212_38912426_Racon_Corrected_Contig0.fasta tig00000001:9997-10005 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Zoey/chr10_61064496_61064711_Racon_Corrected_Contig0.fasta tig00000001:10935-10948 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Zoey/chr10_61064496_61064711_Racon_Corrected_Contig0.fasta tig00000001:4737-4750 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Zoey/chr28_11546183_11546397_Racon_Corrected_Contig0.fasta tig00000001:8840-8853 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Zoey/chr1_108061098_108061326_Racon_Corrected_Contig0.fasta tig00000001:9126-9129 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Zoey/chr1_108061098_108061326_Racon_Corrected_Contig0.fasta tig00000001:13746-13760 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Zoey/chrX_97860193_97860401_Racon_Corrected_Contig0.fasta tig00000001:9558-9572 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Zoey/chr10_22964069_22965722_Racon_Corrected_Contig0.fasta tig00000001:11603-11617 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Zoey/chr22_53615275_53615485_Racon_Corrected_Contig0.fasta tig00000001:9111-9119 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Zoey/chr11_26893362_26893579_Racon_Corrected_Contig0.fasta tig00000001:869-875 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Zoey/chr11_26893362_26893579_Racon_Corrected_Contig0.fasta tig00000001:13698-13697 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Zoey/chr37_18627181_18627817_Racon_Corrected_Contig0.fasta tig00000001:5690-5689 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Zoey/chr19_12559888_12560128_Racon_Corrected_Contig0.fasta tig00000001:2747-2761 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Zoey/chr19_12559888_12560128_Racon_Corrected_Contig0.fasta tig00000001:12958-12974 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Zoey/chr38_3592982_3593212_Racon_Corrected_Contig1.fasta tig00000002:7778-7794 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Zoey/chr36_29962917_29963161_Racon_Corrected_Contig0.fasta tig00000001:5717-5730 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Zoey/chr25_2301759_2301989_Racon_Corrected_Contig0.fasta tig00000001:4358-4372 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Zoey/chr34_5679215_5679422_Racon_Corrected_Contig0.fasta tig00000001:7102-7115 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Ros/chr31_6637671_6637888_Racon_Corrected_Contig0.fasta tig00000001:1837-1836 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Ros/chr31_6637671_6637888_Racon_Corrected_Contig0.fasta tig00000001:14129-14142 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Ros/chr31_6637671_6637888_Racon_Corrected_Contig0.fasta tig00000001:15779-15779 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Ros/chr31_6637671_6637888_Racon_Corrected_Contig0.fasta tig00000001:22962-22977 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Ros/chr12_8208049_8208254_Racon_Corrected_Contig0.fasta tig00000001:14852-14856 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Ros/chr28_11546183_11546398_Racon_Corrected_Contig0.fasta tig00000001:21076-21089 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Ros/chr3_37001209_37001425_Racon_Corrected_Contig0.fasta tig00000001:16477-16492 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Ros/chr3_37001209_37001425_Racon_Corrected_Contig0.fasta tig00000001:25339-25354 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Ros/chr12_64227007_64227224_Racon_Corrected_Contig0.fasta tig00000001:17651-17661 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Ros/chr28_8197193_8197407_Racon_Corrected_Contig0.fasta tig00000001:24791-24804 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Ros/chr23_27162228_27162446_Racon_Corrected_Contig0.fasta tig00000001:16298-16315 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Ros/chr23_27162228_27162446_Racon_Corrected_Contig0.fasta tig00000001:24983-24999 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Ros/chr12_59663216_59663432_Racon_Corrected_Contig0.fasta tig00000001:12094-12094 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Ros/chr12_59663216_59663432_Racon_Corrected_Contig0.fasta tig00000001:11563-11579 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Ros/chrX_72287909_72288124_Racon_Corrected_Contig0.fasta tig00000001:17845-17856 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Ros/chr36_19200859_19201120_Racon_Corrected_Contig0.fasta ctg1:12404-12417 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Ros/chr36_19200859_19201120_Racon_Corrected_Contig0.fasta ctg1:28000-28001 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Ros/chr32_3354989_3355204_Racon_Corrected_Contig0.fasta tig00000001:20528-20543 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Ros/chr32_3354989_3355204_Racon_Corrected_Contig0.fasta tig00000001:23241-23252 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Ros/chr32_3354989_3355204_Racon_Corrected_Contig1.fasta tig00000002:18982-18996 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Ros/chr8_49711349_49711564_Racon_Corrected_Contig0.fasta ctg1:7752-7766 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Ros/chr8_49711349_49711564_Racon_Corrected_Contig0.fasta ctg1:1369-1370 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Ros/chr8_49711349_49711564_Racon_Corrected_Contig0.fasta ctg1:2645-2648 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Ros/chr8_49711349_49711564_Racon_Corrected_Contig0.fasta ctg1:7767-7766 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Ros/chr21_21009197_21009397_Racon_Corrected_Contig0.fasta ctg1:13180-13195 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Ros/chr8_73448122_73448340_Racon_Corrected_Contig0.fasta tig00000001:5981-5994 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Ros/chr8_73448122_73448340_Racon_Corrected_Contig0.fasta tig00000001:17988-17990 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Ros/chr17_35601732_35601949_Racon_Corrected_Contig0.fasta tig00000001:14921-14937 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Ros/chr6_44720778_44720997_Racon_Corrected_Contig0.fasta tig00000001:12736-12752 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Ros/chr25_15560814_15561027_Racon_Corrected_Contig0.fasta tig00000001:19975-19980 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Ros/chr15_1203110_1203324_Racon_Corrected_Contig0.fasta tig00000001:7453-7457 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Ros/chr15_1203110_1203324_Racon_Corrected_Contig0.fasta tig00000001:24243-24256 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Ros/chr17_27583906_27584120_Racon_Corrected_Contig0.fasta tig00000001:14638-14651 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Ros/chr4_66318438_66318655_Racon_Corrected_Contig0.fasta tig00000001:21507-21522 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Ros/chr32_21027992_21028205_Racon_Corrected_Contig0.fasta tig00000001:16677-16677 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Ros/chr32_21027992_21028205_Racon_Corrected_Contig0.fasta tig00000001:20627-20628 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Ros/chr32_21027992_21028205_Racon_Corrected_Contig1.fasta tig00000002:15545-15558 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Ros/chr25_12267668_12267881_Racon_Corrected_Contig0.fasta tig00000001:14536-14547 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Ros/chr25_12267668_12267881_Racon_Corrected_Contig0.fasta tig00000001:21589-21589 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Ros/chr25_12267668_12267881_Racon_Corrected_Contig0.fasta tig00000001:34410-34419 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Ros/chr6_40495504_40495718_Racon_Corrected_Contig0.fasta tig00000001:18164-18177 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Ros/chr32_26587596_26587812_Racon_Corrected_Contig0.fasta tig00000001:21022-21036 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Ros/chr4_7689988_7690204_Racon_Corrected_Contig0.fasta tig00000001:25064-25078 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Ros/chr25_2301789_2302004_Racon_Corrected_Contig0.fasta tig00000001:18167-18181 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Ros/chr11_26893362_26893580_Racon_Corrected_Contig0.fasta ctg1:7734-7740 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Ros/chr11_26893362_26893580_Racon_Corrected_Contig0.fasta ctg1:20665-20664 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Ros/chr6_16972422_16972639_Racon_Corrected_Contig0.fasta tig00000001:21224-21239 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Ros/chr6_16972422_16972639_Racon_Corrected_Contig0.fasta tig00000001:25528-25542 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Ros/chr38_10004118_10004333_Racon_Corrected_Contig0.fasta tig00000001:15526-15540 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Ros/chr13_15707862_15708081_Racon_Corrected_Contig0.fasta tig00000001:16057-16074 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Ros/chr22_54124535_54124748_Racon_Corrected_Contig0.fasta tig00000001:9413-9429 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Ros/chr22_54124535_54124748_Racon_Corrected_Contig0.fasta tig00000001:17482-17493 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Ros/chr22_38912212_38912426_Racon_Corrected_Contig0.fasta tig00000001:14534-14543 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Ros/chr1_108061126_108061338_Racon_Corrected_Contig0.fasta tig00000001:20792-20795 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Ros/chr1_108061126_108061338_Racon_Corrected_Contig0.fasta tig00000001:25432-25446 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Ros/chr1_108061126_108061338_Racon_Corrected_Contig0.fasta tig00000001:29924-29924 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Ros/chr5_69944487_69944704_Racon_Corrected_Contig0.fasta ctg1:15883-15898 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Ros/chr5_69944487_69944704_Racon_Corrected_Contig0.fasta ctg1:27979-27978 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Ros/chr7_34021465_34021682_Racon_Corrected_Contig0.fasta tig00000001:24554-24555 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Ros/chr8_62058732_62058946_Racon_Corrected_Contig0.fasta tig00000001:8450-8450 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Ros/chr10_31704401_31704617_Racon_Corrected_Contig0.fasta tig00000001:11319-11319 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Ros/chr10_31704401_31704617_Racon_Corrected_Contig1.fasta tig00000002:21636-21651 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Ros/chr1_116562128_116562345_Racon_Corrected_Contig0.fasta tig00000001:16132-16146 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Ros/chr38_15164181_15164394_Racon_Corrected_Contig0.fasta tig00000001:29308-29310 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Ros/chr38_15164181_15164394_Racon_Corrected_Contig0.fasta tig00000001:21344-21343 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Ros/chr18_39992834_39993048_Racon_Corrected_Contig0.fasta ctg1:22666-22678 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Ros/chr17_21903729_21903951_Racon_Corrected_Contig0.fasta tig00000001:21873-21872 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Ros/chr17_21903729_21903951_Racon_Corrected_Contig0.fasta tig00000001:31447-31446 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Ros/chr2_39229519_39229738_Racon_Corrected_Contig0.fasta ctg1:11667-11674 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Ros/chr25_27977691_27977910_Racon_Corrected_Contig0.fasta tig00000001:11777-11785 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Ros/chr25_27977691_27977910_Racon_Corrected_Contig0.fasta tig00000001:26417-26432 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Ros/chr25_27977691_27977910_Racon_Corrected_Contig1.fasta tig00000002:17214-17232 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Ros/chr21_30106661_30107685_Racon_Corrected_Contig0.fasta tig00000001:2867-2866 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Ros/chr21_30106661_30107685_Racon_Corrected_Contig0.fasta tig00000001:7695-7694 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Ros/chr21_30106661_30107685_Racon_Corrected_Contig0.fasta tig00000001:9039-9038 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr3_37001209_37001425_Racon_Corrected_Contig0.fasta tig00000001:16654-16669 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr3_37001209_37001425_Racon_Corrected_Contig0.fasta tig00000001:25526-25541 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr3_37001209_37001425_Racon_Corrected_Contig1.fasta tig00000002:17173-17174 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr1_49336513_49336715_Racon_Corrected_Contig0.fasta tig00000001:1124-1126 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr1_49336513_49336715_Racon_Corrected_Contig0.fasta tig00000001:1192-1196 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr1_49336513_49336715_Racon_Corrected_Contig0.fasta tig00000001:15359-15361 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr21_39631217_39631434_Racon_Corrected_Contig0.fasta tig00000001:12849-12858 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr16_2661324_2661530_Racon_Corrected_Contig0.fasta tig00000001:17884-17889 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr27_41428680_41428896_Racon_Corrected_Contig0.fasta tig00000001:19812-19827 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr22_37743669_37743882_Racon_Corrected_Contig0.fasta tig00000001:20913-20922 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr22_37743669_37743882_Racon_Corrected_Contig1.fasta tig00000002:15401-15417 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr11_14497196_14497412_Racon_Corrected_Contig0.fasta tig00000001:16298-16308 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr18_49079185_49079385_Racon_Corrected_Contig0.fasta tig00000001:26516-26521 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr17_34674836_34675053_Racon_Corrected_Contig0.fasta tig00000001:15847-15856 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr11_42183972_42184187_Racon_Corrected_Contig0.fasta tig00000001:13731-13744 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr12_59663216_59663432_Racon_Corrected_Contig0.fasta tig00000001:19419-19432 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr12_59663216_59663432_Racon_Corrected_Contig0.fasta tig00000001:17594-17594 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr12_59663216_59663432_Racon_Corrected_Contig1.fasta tig00000002:14225-14225 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr12_59663216_59663432_Racon_Corrected_Contig1.fasta tig00000002:13695-13711 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr25_15560812_15561027_Racon_Corrected_Contig0.fasta tig00000001:17953-17958 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr25_15560812_15561027_Racon_Corrected_Contig0.fasta tig00000001:27531-27530 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr9_11426885_11427104_Racon_Corrected_Contig0.fasta tig00000001:6596-6611 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr10_61064495_61064711_Racon_Corrected_Contig0.fasta tig00000001:15032-15045 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr10_61064495_61064711_Racon_Corrected_Contig0.fasta tig00000001:8805-8818 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr36_30106482_30106698_Racon_Corrected_Contig0.fasta ctg1:5071-5070 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr36_30106482_30106698_Racon_Corrected_Contig0.fasta ctg1:16974-16987 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr1_108061124_108061338_Racon_Corrected_Contig0.fasta tig00000001:14746-14749 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr1_108061124_108061338_Racon_Corrected_Contig0.fasta tig00000001:19396-19410 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr1_108061124_108061338_Racon_Corrected_Contig0.fasta tig00000001:23898-23897 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr9_53808072_53808287_Racon_Corrected_Contig0.fasta tig00000001:15119-15132 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr9_53808072_53808287_Racon_Corrected_Contig0.fasta tig00000001:19926-19940 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr7_21531126_21531344_Racon_Corrected_Contig0.fasta tig00000001:12623-12639 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr8_13531038_13531254_Racon_Corrected_Contig0.fasta tig00000001:12956-12964 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr8_13531038_13531254_Racon_Corrected_Contig0.fasta tig00000001:5563-5564 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr8_13531038_13531254_Racon_Corrected_Contig0.fasta tig00000001:16828-16843 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr8_13531038_13531254_Racon_Corrected_Contig0.fasta tig00000001:11923-11935 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr8_13531038_13531254_Racon_Corrected_Contig0.fasta tig00000001:24335-24350 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr20_15418279_15418495_Racon_Corrected_Contig0.fasta tig00000001:14033-14048 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr33_30836689_30836907_Racon_Corrected_Contig0.fasta tig00000001:17830-17846 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr33_30836689_30836907_Racon_Corrected_Contig0.fasta tig00000001:30365-30371 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr33_30836689_30836907_Racon_Corrected_Contig0.fasta tig00000001:30157-30163 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr8_8085982_8086195_Racon_Corrected_Contig0.fasta tig00000001:15505-15517 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr29_31417176_31417395_Racon_Corrected_Contig0.fasta tig00000001:14519-14531 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr29_31417176_31417395_Racon_Corrected_Contig0.fasta tig00000001:9757-9776 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr4_83156171_83156387_Racon_Corrected_Contig0.fasta tig00000001:12437-12436 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr27_36868293_36868508_Racon_Corrected_Contig0.fasta tig00000001:10733-10736 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr27_36868293_36868508_Racon_Corrected_Contig0.fasta tig00000001:13209-13225 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr27_36868293_36868508_Racon_Corrected_Contig0.fasta tig00000001:31035-31034 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr27_36868293_36868508_Racon_Corrected_Contig1.fasta tig00000002:16394-16393 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chrX_106960949_106961165_Racon_Corrected_Contig0.fasta tig00000001:14765-14771 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chrX_106960949_106961165_Racon_Corrected_Contig0.fasta tig00000001:17804-17819 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr18_16670314_16670529_Racon_Corrected_Contig0.fasta tig00000001:14955-14967 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr12_30160889_30161108_Racon_Corrected_Contig0.fasta tig00000001:15574-15586 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr12_30160889_30161108_Racon_Corrected_Contig0.fasta tig00000001:18650-18651 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr12_30160889_30161108_Racon_Corrected_Contig0.fasta tig00000001:22460-22459 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr25_12267668_12267881_Racon_Corrected_Contig0.fasta tig00000001:17310-17321 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr6_40495504_40495718_Racon_Corrected_Contig0.fasta tig00000001:17650-17663 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr28_8197192_8197407_Racon_Corrected_Contig0.fasta tig00000001:17416-17429 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr32_15406830_15407046_Racon_Corrected_Contig0.fasta tig00000001:15213-15228 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr22_38912211_38912426_Racon_Corrected_Contig0.fasta tig00000001:16174-16187 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr17_29922985_29923200_Racon_Corrected_Contig0.fasta tig00000001:9302-9316 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr6_41148014_41148227_Racon_Corrected_Contig0.fasta tig00000001:11548-11554 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr30_33617415_33617632_Racon_Corrected_Contig0.fasta tig00000001:19445-19461 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr13_48456939_48457154_Racon_Corrected_Contig1.fasta tig00000002:14485-14498 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr15_46433339_46433556_Racon_Corrected_Contig0.fasta tig00000001:14912-14927 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr21_42853677_42853896_Racon_Corrected_Contig0.fasta tig00000001:2402-2416 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr21_42853677_42853896_Racon_Corrected_Contig0.fasta tig00000001:18845-18862 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr21_42853677_42853896_Racon_Corrected_Contig0.fasta tig00000001:14904-14922 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr21_42853677_42853896_Racon_Corrected_Contig0.fasta tig00000001:32614-32614 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr8_45341810_45342026_Racon_Corrected_Contig0.fasta tig00000001:15342-15356 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr8_45341810_45342026_Racon_Corrected_Contig0.fasta tig00000001:18829-18832 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr25_2301789_2302004_Racon_Corrected_Contig0.fasta tig00000001:14620-14634 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr25_2301789_2302004_Racon_Corrected_Contig1.fasta tig00000002:1924-1940 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr10_31704399_31704617_Racon_Corrected_Contig0.fasta tig00000001:16534-16549 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr10_31704399_31704617_Racon_Corrected_Contig1.fasta tig00000002:15304-15303 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr10_31704399_31704617_Racon_Corrected_Contig1.fasta tig00000002:20524-20524 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr13_62072549_62072764_Racon_Corrected_Contig0.fasta tig00000001:16975-16988 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr13_52139162_52139376_Racon_Corrected_Contig0.fasta tig00000001:11998-12012 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr13_52139162_52139376_Racon_Corrected_Contig1.fasta tig00000002:15921-15934 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr20_31990452_31990669_Racon_Corrected_Contig0.fasta tig00000001:20693-20708 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr7_34021465_34021682_Racon_Corrected_Contig0.fasta tig00000001:16215-16217 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr1_47668198_47668417_Racon_Corrected_Contig0.fasta tig00000001:15953-15965 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr1_47668198_47668417_Racon_Corrected_Contig0.fasta tig00000001:25779-25794 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr3_59142706_59142923_Racon_Corrected_Contig0.fasta tig00000001:14593-14607 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr1_116562128_116562345_Racon_Corrected_Contig0.fasta tig00000001:15739-15753 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr11_54387061_54387277_Racon_Corrected_Contig1.fasta tig00000002:17740-17754 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr25_45486736_45486951_Racon_Corrected_Contig0.fasta tig00000001:14690-14703 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr37_6766832_6767045_Racon_Corrected_Contig0.fasta tig00000001:17156-17168 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr6_4232232_4232432_Racon_Corrected_Contig0.fasta tig00000001:13247-13246 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr6_4232232_4232432_Racon_Corrected_Contig0.fasta tig00000001:14389-14390 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr6_4232232_4232432_Racon_Corrected_Contig0.fasta tig00000001:14958-14957 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr6_4232232_4232432_Racon_Corrected_Contig0.fasta tig00000001:14832-14831 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr3_72311657_72311876_Racon_Corrected_Contig0.fasta tig00000001:16678-16695 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr18_39992834_39993048_Racon_Corrected_Contig1.fasta tig00000002:10095-10107 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr17_21903729_21903951_Racon_Corrected_Contig0.fasta tig00000001:15204-15203 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr3_7203424_7203640_Racon_Corrected_Contig0.fasta tig00000001:17449-17463 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr3_7203424_7203640_Racon_Corrected_Contig0.fasta tig00000001:13351-13363 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr21_30106661_30107685_Racon_Corrected_Contig0.fasta tig00000001:2317-2316 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr20_14194421_14194636_Racon_Corrected_Contig1.fasta tig00000002:12458-12468 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr11_26893361_26893579_Racon_Corrected_Contig0.fasta tig00000001:1774-1780 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr11_26893361_26893579_Racon_Corrected_Contig0.fasta tig00000001:14921-14920 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Mischka/chr11_26893361_26893579_Racon_Corrected_Contig0.fasta tig00000001:11467-11482 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Tasha_LR/chr6_44720774_44720996_Racon_Corrected_Contig0.fasta tig00000001:8851-8867 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Tasha_LR/chr6_44720774_44720996_Racon_Corrected_Contig1.fasta tig00000002:10803-10820 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Tasha_LR/chr22_37743669_37743882_Racon_Corrected_Contig0.fasta tig00000001:11545-11544 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Tasha_LR/chr22_37743669_37743882_Racon_Corrected_Contig0.fasta tig00000001:17468-17467 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Tasha_LR/chr22_37743669_37743882_Racon_Corrected_Contig1.fasta tig00000002:12467-12483 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Tasha_LR/chr22_37743669_37743882_Racon_Corrected_Contig1.fasta tig00000002:20458-20461 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Tasha_LR/chr12_59663216_59663432_Racon_Corrected_Contig0.fasta tig00000001:10533-10532 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Tasha_LR/chr12_59663216_59663432_Racon_Corrected_Contig0.fasta tig00000001:10516-10532 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Tasha_LR/chr36_30106482_30106698_Racon_Corrected_Contig0.fasta tig00000001:1973-1972 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Tasha_LR/chr36_30106482_30106698_Racon_Corrected_Contig1.fasta tig00000002:11278-11291 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Tasha_LR/chr5_29794389_29794603_Racon_Corrected_Contig1.fasta tig00000002:13012-13024 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Tasha_LR/chr5_29794389_29794603_Racon_Corrected_Contig1.fasta tig00000002:10751-10750 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Tasha_LR/chr7_32430221_32430438_Racon_Corrected_Contig0.fasta tig00000001:12558-12557 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Tasha_LR/chr30_23930847_23931068_Racon_Corrected_Contig0.fasta tig00000001:638-643 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Tasha_LR/chr30_23930847_23931068_Racon_Corrected_Contig1.fasta tig00000002:11739-11757 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Tasha_LR/chrX_50281525_50281740_Racon_Corrected_Contig0.fasta tig00000001:10048-10052 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Tasha_LR/chrX_50281525_50281740_Racon_Corrected_Contig0.fasta tig00000001:16063-16064 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Tasha_LR/chrX_50281525_50281740_Racon_Corrected_Contig1.fasta tig00000002:8905-8919 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Tasha_LR/chr28_8197192_8197407_Racon_Corrected_Contig0.fasta tig00000001:15179-15192 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Tasha_LR/chr22_38912211_38912426_Racon_Corrected_Contig0.fasta tig00000001:11645-11658 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Tasha_LR/chr15_15924213_15924425_Racon_Corrected_Contig0.fasta tig00000001:12019-12018 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Tasha_LR/chr15_15924213_15924425_Racon_Corrected_Contig1.fasta tig00000002:8515-8530 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Tasha_LR/chr15_15924213_15924425_Racon_Corrected_Contig2.fasta tig00000003:4019-4018 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Tasha_LR/chr3_59142706_59142923_Racon_Corrected_Contig0.fasta tig00000001:8870-8885 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Tasha_LR/chr6_4232232_4232432_Racon_Corrected_Contig0.fasta tig00000001:12670-12669 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Tasha_LR/chr6_4232232_4232432_Racon_Corrected_Contig0.fasta tig00000001:12193-12192 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Tasha_LR/chr6_4232232_4232432_Racon_Corrected_Contig0.fasta tig00000001:14353-14353 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Tasha_LR/chr18_39992834_39993048_Racon_Corrected_Contig1.fasta tig00000002:13744-13756 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Tasha_LR/chr7_79081703_79081919_Racon_Corrected_Contig0.fasta tig00000001:6835-6852 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr36_163826_164043_Racon_Corrected_Contig0.fasta tig00000001:19545-19561 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr6_69994089_69994305_Racon_Corrected_Contig0.fasta tig00000001:17966-17980 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr7_23682897_23683115_Racon_Corrected_Contig0.fasta tig00000001:16920-16937 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr4_46771116_46771334_Racon_Corrected_Contig0.fasta tig00000001:14072-14085 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr3_76974680_76974889_Racon_Corrected_Contig1.fasta tig00000002:14693-14701 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr24_1726110_1726310_Racon_Corrected_Contig0.fasta tig00000001:12591-12605 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr6_32647806_32648006_Racon_Corrected_Contig0.fasta ctg1:19398-19413 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr1_49336513_49336715_Racon_Corrected_Contig0.fasta tig00000001:11269-11271 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr22_37743669_37743882_Racon_Corrected_Contig0.fasta tig00000001:13730-13729 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr4_12729446_12729661_Racon_Corrected_Contig0.fasta tig00000001:13491-13505 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr4_12729446_12729661_Racon_Corrected_Contig0.fasta tig00000001:9333-9333 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr32_6208214_6208487_Racon_Corrected_Contig0.fasta tig00000001:12392-12406 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr22_45224022_45224238_Racon_Corrected_Contig0.fasta tig00000001:14504-14519 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr17_26699888_26700088_Racon_Corrected_Contig0.fasta tig00000001:28187-28203 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr17_26699888_26700088_Racon_Corrected_Contig0.fasta tig00000001:24374-24379 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr12_59663216_59663432_Racon_Corrected_Contig0.fasta tig00000001:17611-17611 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr12_59663216_59663432_Racon_Corrected_Contig1.fasta tig00000002:20037-20052 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr12_59663216_59663432_Racon_Corrected_Contig1.fasta tig00000002:18209-18216 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr20_19157387_19157604_Racon_Corrected_Contig0.fasta tig00000001:15868-15884 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr17_42312445_42312663_Racon_Corrected_Contig0.fasta tig00000001:12623-12638 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr1_108061124_108061338_Racon_Corrected_Contig0.fasta tig00000001:12999-13002 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr1_108061124_108061338_Racon_Corrected_Contig0.fasta tig00000001:17681-17695 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr7_78317229_78317446_Racon_Corrected_Contig0.fasta tig00000001:12262-12272 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr1_108653942_108654158_Racon_Corrected_Contig0.fasta ctg1:13644-13658 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr28_10588140_10588355_Racon_Corrected_Contig0.fasta tig00000001:15092-15106 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr28_10588140_10588355_Racon_Corrected_Contig0.fasta tig00000001:11059-11073 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr20_15418279_15418495_Racon_Corrected_Contig0.fasta tig00000001:19638-19653 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr33_9086388_9086607_Racon_Corrected_Contig0.fasta tig00000001:12567-12583 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr33_9086388_9086607_Racon_Corrected_Contig1.fasta tig00000002:12556-12555 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr33_9086388_9086607_Racon_Corrected_Contig1.fasta tig00000002:9980-9994 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr18_10305594_10305813_Racon_Corrected_Contig0.fasta tig00000001:15049-15050 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr18_10305594_10305813_Racon_Corrected_Contig0.fasta tig00000001:20225-20240 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr18_10305594_10305813_Racon_Corrected_Contig1.fasta tig00000002:12228-12228 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr11_27077710_27077921_Racon_Corrected_Contig0.fasta tig00000001:16066-16082 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr31_19312763_19312977_Racon_Corrected_Contig0.fasta tig00000001:14685-14698 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr4_83156171_83156387_Racon_Corrected_Contig0.fasta tig00000001:11264-11263 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr2_51127770_51127987_Racon_Corrected_Contig0.fasta tig00000001:10154-10170 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr35_18636469_18636689_Racon_Corrected_Contig0.fasta tig00000001:15491-15506 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr5_80752327_80752543_Racon_Corrected_Contig0.fasta tig00000001:15433-15432 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr8_73448122_73448340_Racon_Corrected_Contig0.fasta tig00000001:11757-11769 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr8_73448122_73448340_Racon_Corrected_Contig0.fasta tig00000001:17814-17813 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr8_73448122_73448340_Racon_Corrected_Contig0.fasta tig00000001:19210-19213 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr8_73448122_73448340_Racon_Corrected_Contig0.fasta tig00000001:2053-2052 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr8_73448122_73448340_Racon_Corrected_Contig0.fasta tig00000001:25380-25380 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr8_73448122_73448340_Racon_Corrected_Contig1.fasta tig00000002:9342-9355 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr8_73448122_73448340_Racon_Corrected_Contig1.fasta tig00000002:21827-21829 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr8_73448122_73448340_Racon_Corrected_Contig2.fasta tig00000003:5800-5817 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr8_73448122_73448340_Racon_Corrected_Contig2.fasta tig00000003:3866-3865 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr8_73448122_73448340_Racon_Corrected_Contig2.fasta tig00000003:8656-8655 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr8_73448122_73448340_Racon_Corrected_Contig2.fasta tig00000003:7538-7553 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr8_73448122_73448340_Racon_Corrected_Contig3.fasta tig00000004:4375-4374 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr8_73448122_73448340_Racon_Corrected_Contig3.fasta tig00000004:7469-7468 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr8_73448122_73448340_Racon_Corrected_Contig3.fasta tig00000004:7470-7470 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr8_73448122_73448340_Racon_Corrected_Contig3.fasta tig00000004:3374-3373 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr8_73448122_73448340_Racon_Corrected_Contig3.fasta tig00000004:1691-1690 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr8_73448122_73448340_Racon_Corrected_Contig3.fasta tig00000004:3383-3382 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr8_73448122_73448340_Racon_Corrected_Contig3.fasta tig00000004:1691-1690 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr8_73448122_73448340_Racon_Corrected_Contig3.fasta tig00000004:4366-4365 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr8_73448122_73448340_Racon_Corrected_Contig3.fasta tig00000004:7467-7479 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr8_73448122_73448340_Racon_Corrected_Contig3.fasta tig00000004:4400-4399 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr8_73448122_73448340_Racon_Corrected_Contig3.fasta tig00000004:6962-6963 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr34_12342662_12342881_Racon_Corrected_Contig0.fasta tig00000001:14540-14547 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr34_12342662_12342881_Racon_Corrected_Contig0.fasta tig00000001:441-440 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr34_12342662_12342881_Racon_Corrected_Contig0.fasta tig00000001:422-421 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr34_12342662_12342881_Racon_Corrected_Contig1.fasta tig00000002:14787-14803 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr34_12342662_12342881_Racon_Corrected_Contig1.fasta tig00000002:28465-28464 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr34_12342662_12342881_Racon_Corrected_Contig1.fasta tig00000002:27797-27798 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr34_12342662_12342881_Racon_Corrected_Contig1.fasta tig00000002:24480-24481 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr34_12342662_12342881_Racon_Corrected_Contig1.fasta tig00000002:24945-24946 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr34_12342662_12342881_Racon_Corrected_Contig1.fasta tig00000002:28483-28482 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr34_12342662_12342881_Racon_Corrected_Contig1.fasta tig00000002:27519-27518 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr34_12342662_12342881_Racon_Corrected_Contig1.fasta tig00000002:28553-28553 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr26_14657034_14657248_Racon_Corrected_Contig0.fasta tig00000001:16497-16509 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr32_32844579_32844795_Racon_Corrected_Contig0.fasta tig00000001:17064-17079 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr32_32844579_32844795_Racon_Corrected_Contig1.fasta tig00000002:10742-10742 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr32_32844579_32844795_Racon_Corrected_Contig1.fasta tig00000002:20636-20637 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr15_1203110_1203324_Racon_Corrected_Contig0.fasta tig00000001:13045-13058 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr5_62142536_62142750_Racon_Corrected_Contig0.fasta tig00000001:15288-15302 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr2_14220059_14220274_Racon_Corrected_Contig0.fasta tig00000001:11644-11658 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr25_12267668_12267881_Racon_Corrected_Contig0.fasta tig00000001:17714-17725 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr25_12267668_12267881_Racon_Corrected_Contig0.fasta tig00000001:20934-20947 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr25_12267668_12267881_Racon_Corrected_Contig0.fasta tig00000001:26619-26625 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr25_12267668_12267881_Racon_Corrected_Contig1.fasta tig00000002:18826-18831 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr28_8197192_8197407_Racon_Corrected_Contig0.fasta tig00000001:16057-16070 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr38_9143369_9143582_Racon_Corrected_Contig0.fasta tig00000001:15826-15839 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr38_9143369_9143582_Racon_Corrected_Contig0.fasta tig00000001:10492-10508 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chrX_54952419_54952636_Racon_Corrected_Contig0.fasta tig00000001:19946-19961 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr7_69740159_69740370_Racon_Corrected_Contig0.fasta tig00000001:18508-18524 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr22_38912211_38912426_Racon_Corrected_Contig0.fasta tig00000001:16111-16124 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr30_6907109_6907325_Racon_Corrected_Contig0.fasta tig00000001:15688-15703 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr30_6907109_6907325_Racon_Corrected_Contig0.fasta tig00000001:13339-13353 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr6_70253828_70254043_Racon_Corrected_Contig0.fasta tig00000001:13121-13135 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr10_51072520_51072735_Racon_Corrected_Contig0.fasta tig00000001:19159-19164 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr15_46433339_46433556_Racon_Corrected_Contig0.fasta tig00000001:10800-10815 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr15_46433339_46433556_Racon_Corrected_Contig0.fasta tig00000001:19959-19961 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr31_8423062_8423279_Racon_Corrected_Contig0.fasta tig00000001:17626-17642 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr22_41457083_41457299_Racon_Corrected_Contig0.fasta tig00000001:17428-17443 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr32_4049783_4049996_Racon_Corrected_Contig0.fasta ctg1:2940-2945 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr32_4049783_4049996_Racon_Corrected_Contig0.fasta ctg1:14676-14688 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr27_15988745_15989144_Racon_Corrected_Contig0.fasta tig00000001:14043-14042 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr27_15988745_15989144_Racon_Corrected_Contig0.fasta tig00000001:14937-14936 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr27_15988745_15989144_Racon_Corrected_Contig0.fasta tig00000001:33130-33129 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr18_34252004_34252222_Racon_Corrected_Contig0.fasta tig00000001:16316-16332 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr18_34252004_34252222_Racon_Corrected_Contig0.fasta tig00000001:31200-31213 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr3_3460101_3460319_Racon_Corrected_Contig0.fasta ctg1:5066-5081 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr3_3460101_3460319_Racon_Corrected_Contig0.fasta ctg1:18033-18048 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr18_26995919_26996136_Racon_Corrected_Contig0.fasta tig00000001:13406-13421 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr18_26995919_26996136_Racon_Corrected_Contig0.fasta tig00000001:31095-31109 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr14_44840709_44840927_Racon_Corrected_Contig0.fasta tig00000001:14623-14640 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr14_40695628_40695839_Racon_Corrected_Contig0.fasta tig00000001:12443-12452 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr12_8208047_8208254_Racon_Corrected_Contig0.fasta tig00000001:13993-13997 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr14_52523402_52523618_Racon_Corrected_Contig0.fasta tig00000001:15473-15483 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr25_19946677_19946877_Racon_Corrected_Contig0.fasta tig00000001:10843-10854 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr7_34021465_34021682_Racon_Corrected_Contig0.fasta tig00000001:18183-18184 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr5_16511731_16511948_Racon_Corrected_Contig0.fasta tig00000001:12814-12829 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr3_32009205_32009423_Racon_Corrected_Contig0.fasta tig00000001:13332-13349 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr20_48467839_48468053_Racon_Corrected_Contig0.fasta tig00000001:12523-12538 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr20_48467839_48468053_Racon_Corrected_Contig1.fasta tig00000002:16221-16234 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr11_54387061_54387277_Racon_Corrected_Contig0.fasta tig00000001:9951-9965 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr25_45486736_45486951_Racon_Corrected_Contig0.fasta tig00000001:14778-14791 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chrX_11088742_11088956_Racon_Corrected_Contig0.fasta tig00000001:14214-14227 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr12_18624017_18624241_Racon_Corrected_Contig0.fasta tig00000001:1493-1493 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr12_18624017_18624241_Racon_Corrected_Contig0.fasta tig00000001:12541-12555 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr12_18624017_18624241_Racon_Corrected_Contig0.fasta tig00000001:18989-18991 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr12_18624017_18624241_Racon_Corrected_Contig1.fasta tig00000002:1479-1486 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr12_18624017_18624241_Racon_Corrected_Contig1.fasta tig00000002:16106-16129 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr12_18624017_18624241_Racon_Corrected_Contig1.fasta tig00000002:20305-20322 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chrX_105195944_105196160_Racon_Corrected_Contig0.fasta tig00000001:16391-16407 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr32_21197842_21198058_Racon_Corrected_Contig0.fasta tig00000001:12964-12979 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr32_21027989_21028205_Racon_Corrected_Contig0.fasta tig00000001:12116-12115 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr32_21027989_21028205_Racon_Corrected_Contig0.fasta tig00000001:16075-16076 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr17_21903729_21903951_Racon_Corrected_Contig0.fasta tig00000001:17460-17459 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr3_7203424_7203640_Racon_Corrected_Contig0.fasta tig00000001:19533-19547 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr21_30106661_30107685_Racon_Corrected_Contig0.fasta tig00000001:1508-1507 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr32_25815733_25815949_Racon_Corrected_Contig0.fasta tig00000001:22249-22266 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr32_25815733_25815949_Racon_Corrected_Contig1.fasta tig00000002:10229-10229 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr11_26893361_26893579_Racon_Corrected_Contig0.fasta tig00000001:12553-12552 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr17_32985878_32986094_Racon_Corrected_Contig0.fasta tig00000001:18380-18395 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr5_55112586_55112799_Racon_Corrected_Contig0.fasta tig00000001:17911-17923 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr17_54191264_54191480_Racon_Corrected_Contig0.fasta tig00000001:13307-13322 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr3_73548536_73548750_Racon_Corrected_Contig0.fasta tig00000001:18133-18146 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Sandy/chr25_26641310_26641525_Racon_Corrected_Contig0.fasta tig00000001:13648-13662 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Nala/chr7_77544994_77545206_Racon_Corrected_Contig0.fasta tig00000001:9148-9157 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Nala/chr8_7565359_7565575_Racon_Corrected_Contig0.fasta tig00000001:9412-9426 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Nala/chr3_37001209_37001425_Racon_Corrected_Contig0.fasta tig00000001:9701-9716 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Nala/chr3_37001209_37001425_Racon_Corrected_Contig0.fasta tig00000001:18566-18581 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Nala/chr18_49079185_49079385_Racon_Corrected_Contig0.fasta tig00000001:17703-17704 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Nala/chr17_34674836_34675053_Racon_Corrected_Contig0.fasta tig00000001:10780-10794 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Nala/chr11_42183972_42184187_Racon_Corrected_Contig0.fasta tig00000001:10627-10638 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Nala/chr12_59663216_59663432_Racon_Corrected_Contig0.fasta tig00000001:12254-12254 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Nala/chr12_59663216_59663432_Racon_Corrected_Contig0.fasta tig00000001:11722-11738 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Nala/chr10_61064495_61064711_Racon_Corrected_Contig0.fasta tig00000001:16932-16945 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Nala/chr10_61064495_61064711_Racon_Corrected_Contig0.fasta tig00000001:10703-10716 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Nala/chr16_45073261_45073463_Racon_Corrected_Contig0.fasta tig00000001:17739-17739 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Nala/chr36_30106482_30106698_Racon_Corrected_Contig0.fasta tig00000001:6335-6334 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Nala/chr36_30106482_30106698_Racon_Corrected_Contig0.fasta tig00000001:18197-18210 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Nala/chr1_108061124_108061338_Racon_Corrected_Contig0.fasta tig00000001:12764-12767 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Nala/chr1_108061124_108061338_Racon_Corrected_Contig0.fasta tig00000001:17403-17417 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Nala/chr1_108061124_108061338_Racon_Corrected_Contig0.fasta tig00000001:21897-21896 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Nala/chr9_53808072_53808287_Racon_Corrected_Contig0.fasta ctg1:10873-10886 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Nala/chr7_21531126_21531344_Racon_Corrected_Contig0.fasta tig00000001:18188-18204 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Nala/chr30_23930847_23931068_Racon_Corrected_Contig0.fasta tig00000001:14441-14442 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Nala/chr27_18176425_18176641_Racon_Corrected_Contig0.fasta tig00000001:12151-12166 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Nala/chr27_18176425_18176641_Racon_Corrected_Contig0.fasta tig00000001:7986-7985 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Nala/chr20_15418279_15418495_Racon_Corrected_Contig0.fasta tig00000001:5776-5787 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Nala/chr20_15418279_15418495_Racon_Corrected_Contig0.fasta tig00000001:9866-9883 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Nala/chr33_30836689_30836907_Racon_Corrected_Contig0.fasta tig00000001:16222-16238 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Nala/chr33_30836689_30836907_Racon_Corrected_Contig0.fasta tig00000001:28744-28750 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Nala/chr33_30836689_30836907_Racon_Corrected_Contig0.fasta tig00000001:35388-35388 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Nala/chr8_8085982_8086195_Racon_Corrected_Contig0.fasta tig00000001:15428-15440 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Nala/chr1_108449390_108449606_Racon_Corrected_Contig0.fasta tig00000001:4122-4136 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Nala/chr4_83156171_83156387_Racon_Corrected_Contig0.fasta tig00000001:10932-10940 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Nala/chr8_73448122_73448340_Racon_Corrected_Contig0.fasta tig00000001:674-673 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Nala/chr8_73448122_73448340_Racon_Corrected_Contig0.fasta tig00000001:13709-13711 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Nala/chr8_73448122_73448340_Racon_Corrected_Contig1.fasta tig00000002:11087-11087 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Nala/chr8_73448122_73448340_Racon_Corrected_Contig1.fasta tig00000002:16249-16248 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Nala/chr18_16670314_16670529_Racon_Corrected_Contig0.fasta tig00000001:15501-15515 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Nala/chr12_30160889_30161108_Racon_Corrected_Contig0.fasta tig00000001:16560-16572 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Nala/chr12_30160889_30161108_Racon_Corrected_Contig0.fasta tig00000001:19769-19770 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Nala/chr12_30160889_30161108_Racon_Corrected_Contig0.fasta tig00000001:23458-23457 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Nala/chr18_54348664_54348879_Racon_Corrected_Contig0.fasta tig00000001:13464-13478 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Nala/chr25_12267668_12267881_Racon_Corrected_Contig0.fasta tig00000001:15304-15315 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Nala/chr6_40495504_40495718_Racon_Corrected_Contig0.fasta tig00000001:12897-12903 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Nala/chr28_8197192_8197407_Racon_Corrected_Contig0.fasta tig00000001:14566-14567 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Nala/chr32_15406830_15407046_Racon_Corrected_Contig0.fasta tig00000001:14818-14833 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Nala/chr22_38912211_38912426_Racon_Corrected_Contig0.fasta tig00000001:7903-7916 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Nala/chr22_38912211_38912426_Racon_Corrected_Contig1.fasta tig00000002:845-850 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Nala/chr17_29922985_29923200_Racon_Corrected_Contig0.fasta tig00000001:9153-9167 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Nala/chr1_18064718_18064937_Racon_Corrected_Contig0.fasta tig00000001:7563-7579 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Nala/chr14_35081791_35082010_Racon_Corrected_Contig0.fasta ctg1:6743-6758 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Nala/chr27_28390586_28390802_Racon_Corrected_Contig0.fasta tig00000001:16027-16042 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Nala/chr21_42853677_42853896_Racon_Corrected_Contig0.fasta tig00000001:13564-13574 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Nala/chr21_42853677_42853896_Racon_Corrected_Contig0.fasta tig00000001:9660-9678 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Nala/chr21_42853677_42853896_Racon_Corrected_Contig0.fasta tig00000001:27366-27366 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Nala/chr8_45341810_45342026_Racon_Corrected_Contig0.fasta tig00000001:15618-15632 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Nala/chr3_48910691_48910909_Racon_Corrected_Contig0.fasta tig00000001:13197-13213 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Nala/chr25_2301789_2302004_Racon_Corrected_Contig0.fasta tig00000001:18150-18164 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Nala/chr10_31704399_31704617_Racon_Corrected_Contig0.fasta tig00000001:15948-15947 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Nala/chr10_31704399_31704617_Racon_Corrected_Contig1.fasta tig00000002:18529-18544 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Nala/chr8_61848622_61848839_Racon_Corrected_Contig0.fasta tig00000001:11971-11986 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Nala/chr8_61848622_61848839_Racon_Corrected_Contig0.fasta tig00000001:11330-11330 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Nala/chr13_62072549_62072764_Racon_Corrected_Contig0.fasta tig00000001:15954-15967 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Nala/chr13_52139162_52139376_Racon_Corrected_Contig0.fasta tig00000001:16228-16241 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Nala/chr12_15581506_15581718_Racon_Corrected_Contig0.fasta tig00000001:7974-7984 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Nala/chr12_8208047_8208254_Racon_Corrected_Contig0.fasta tig00000001:8193-8197 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Nala/chr32_3354988_3355204_Racon_Corrected_Contig0.fasta ctg1:7824-7838 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Nala/chr12_42169995_42170211_Racon_Corrected_Contig0.fasta tig00000001:9858-9864 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Nala/chr12_42169995_42170211_Racon_Corrected_Contig0.fasta tig00000001:9843-9857 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Nala/chr12_42169995_42170211_Racon_Corrected_Contig0.fasta tig00000001:15496-15502 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Nala/chr17_27583905_27584120_Racon_Corrected_Contig0.fasta tig00000001:14988-15001 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Nala/chr2_22929245_22929463_Racon_Corrected_Contig0.fasta tig00000001:9554-9570 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Nala/chr2_22929245_22929463_Racon_Corrected_Contig0.fasta tig00000001:3535-3550 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Nala/chr3_59142706_59142923_Racon_Corrected_Contig0.fasta tig00000001:10691-10706 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Nala/chr1_116562128_116562345_Racon_Corrected_Contig0.fasta ctg1:8491-8505 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Nala/chr1_116562128_116562345_Racon_Corrected_Contig0.fasta ctg1:1571-1572 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Nala/chr25_45486736_45486951_Racon_Corrected_Contig0.fasta tig00000001:15216-15229 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Nala/chr37_6766832_6767045_Racon_Corrected_Contig0.fasta tig00000001:17119-17131 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Nala/chr6_4232232_4232432_Racon_Corrected_Contig0.fasta tig00000001:13556-13555 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Nala/chr6_4232232_4232432_Racon_Corrected_Contig0.fasta tig00000001:14698-14699 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Nala/chr6_4232232_4232432_Racon_Corrected_Contig0.fasta tig00000001:15268-15267 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Nala/chr6_4232232_4232432_Racon_Corrected_Contig0.fasta tig00000001:15142-15141 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Nala/chr3_72311657_72311876_Racon_Corrected_Contig0.fasta tig00000001:8622-8639 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Nala/chr38_15164181_15164394_Racon_Corrected_Contig0.fasta tig00000001:14841-14851 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Nala/chr38_15164181_15164394_Racon_Corrected_Contig0.fasta tig00000001:20463-20462 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Nala/chr38_15164181_15164394_Racon_Corrected_Contig0.fasta tig00000001:28418-28420 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Nala/chr17_21903729_21903951_Racon_Corrected_Contig0.fasta tig00000001:17930-17929 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Nala/chr3_7203424_7203640_Racon_Corrected_Contig0.fasta tig00000001:13768-13780 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Nala/chr3_7203424_7203640_Racon_Corrected_Contig0.fasta tig00000001:9676-9690 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Nala/chr20_14194421_14194636_Racon_Corrected_Contig0.fasta tig00000001:15418-15428 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Nala/chr11_26893361_26893579_Racon_Corrected_Contig0.fasta tig00000001:3484-3490 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Nala/chr11_26893361_26893579_Racon_Corrected_Contig0.fasta tig00000001:16596-16607 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
samtools faidx /gpfs/accounts/jmkidd_root/jmkidd/blacksmi/testing_regions_for_Batcher/Nala/chr11_26893361_26893579_Racon_Corrected_Contig0.fasta tig00000001:13173-13188 >> /home/blacksmi/links/kidd-lab/matt-projects/Putative_Insertions_From_JMKidd/Regions_With_Updated_Automate/aggregated_TSDs.txt 
