) ( ( ) ) ) ( ( _______)_ .-'---------| ( C|/\/\/\/\/| '-./\/\/\/\/| '_________' '-------' <<< Cleaning Genome >>> ) ( ( ) ) ) ( ( _______)_ .-'---------| ( C|/\/\/\/\/| '-./\/\/\/\/| '_________' '-------' <<< Getting RepeatMasker Sequences for 7227 and Saving as Fasta >>> ) ( ( ) ) ) ( ( _______)_ .-'---------| ( C|/\/\/\/\/| '-./\/\/\/\/| '_________' '-------' <<< Running Initial Mask with Known Repeats >>> RepeatMasker version 4.2.4 Search Engine: NCBI/RMBLAST [ 2.17.1+ ] Using FamDB: /opt/conda/envs/bioenv/share/famdb-3.0.0 Title : Dfam Version : 4.0 Date : 2026-05-22 Families : 43,193 Species/Taxa Search: Drosophila melanogaster [NCBI Taxonomy ID: 7227] Lineage: root;cellular organisms;Eukaryota;Opisthokonta;Metazoa; Eumetazoa;Bilateria;Protostomia;Ecdysozoa;Panarthropoda; Arthropoda;Mandibulata;Pancrustacea;Hexapoda;Insecta; Dicondylia;Pterygota ;Neoptera;Endopterygota; Diptera;Brachycera;Muscomorpha;Eremoneura;Cyclorrhapha; Schizophora;Acalyptratae;Ephydroidea;Drosophilidae; Drosophilinae;Drosophilini;Drosophila Including only curated families: 390/390 families in ancestor taxa; 9/9 lineage-specific families analyzing file /workspace/genomes/GCF_000001215.4/GCF_000001215.4_Release_6_plus_ISO1_MT_genomic.fna.prep identifying Simple Repeats in batch 1 of 2476 identifying matches to 7227 sequences in batch 1 of 2476 identifying Simple Repeats in batch 2 of 2476 .... identifying Simple Repeats in batch 2475 of 2476 identifying Simple Repeats in batch 2476 of 2476 identifying matches to 7227 sequences in batch 2476 of 2476 identifying Simple Repeats in batch 2476 of 2476 ProcessRepeats: Adjudicating alignments ............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................... ProcessRepeats: Masking sequences ProcessRepeats: Generating table output done ) ( ( ) ) ) ( ( _______)_ .-'---------| ( C|/\/\/\/\/| '-./\/\/\/\/| '_________' '-------' <<< Detecting Novel Repeats >>> Building database GCF_000001215.4: Reading /workspace/analysis/GCF_000001215.4/earlgray_out/GCF_000001215.4_EarlGrey/GCF_000001215.4_RepeatMasker/GCF_000001215.4_Release_6_plus_ISO1_MT_genomic.fna.prep.masked... Number of sequences (bp) added to database: 1870 ( 143726002 bp ) Samplable genome size (contigs >= 40 kb): 138612213 bp Capping at round 5 (-genomeSampleSizeMax 81000000) RepeatModeler Version 2.0.7 =========================== Using output directory = /workspace/analysis/GCF_000001215.4/earlgray_out/GCF_000001215.4_EarlGrey/GCF_000001215.4_RepeatModeler/RM_232123.TueAug42120492026 Search Engine = rmblast 2.17.1+ Threads = 4 Dependencies: TRF 4.10, RECON 1.10, RepeatScout 1.0.7, RepeatMasker 4.2.4, RepeatAfterMe 0.0.7 LTR Structural Analysis: Disabled [use -LTRStruct to enable] Random Number Seed: 1785878449 Database = /workspace/analysis/GCF_000001215.4/earlgray_out/GCF_000001215.4_EarlGrey/GCF_000001215.4_Database/GCF_000001215.4 . - Sequences = 1870 - Bases = 143726002 - N50 = 28110227 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 29940745-32079331 | [ 1 ] 27802159-29940744 | [ 1 ] 25663573-27802158 | [ ] 23524987-25663572 | [ 2 ] 21386402-23524987 | [ 1 ] 19247816-21386401 | [ ] 17109230-19247815 | [ ] 14970644-17109229 | [ ] 12832058-14970643 | [ ] 10693473-12832058 | [ ] 8554887-10693472 | [ ] 6416301-8554886 | [ ] 4277715-6416300 | [ ] 2139129-4277714 | [ 1 ] 544-2139129 |************************************************** [ 1864 ] Storage Throughput = excellent ( 2752.34 MB/s ) Ready to start the sampling process. INFO: The runtime of RepeatModeler heavily depends on the quality of the assembly and the repetitive content of the sequences. It is not imperative that RepeatModeler completes all rounds in order to obtain useful results. At the completion of each round, the files ( consensi.fa, and families.stk ) found in: /workspace/analysis/GCF_000001215.4/earlgray_out/GCF_000001215.4_EarlGrey/GCF_000001215.4_RepeatModeler/RM_232123.TueAug42120492026/ will contain all results produced thus far. These files may be manually copied and run through RepeatClassifier should the program be terminated early. RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 51149737 bp ( 40004460 non ambiguous ) - Num Contigs Represented = 151 - Sequence extraction : 00:00:27 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: Running build_lmer_table ( l = 14, min = 10 ).. - RepeatScout: Running RepeatScout.. : 82 raw families identified - RepeatScout: Running filtering stage.. 79 families remaining - RepeatScout: 00:01:36 (hh:mm:ss) Elapsed Time - Collecting repeat instances... - Refining 75 families... 00:00:32 (hh:mm:ss) Elapsed Time - Redundant Families and Large Satellite Filtering.. : 0 satellite(s), 24 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time Round Time: 00:02:39 (hh:mm:ss) Elapsed Time : 51 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:07 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... 78 Tandem Repeats Masked - TRFMask time 00:00:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... -- Collecting 180 ranges... 180 repeats masked totaling 62783 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 12773255 bp Num Contigs Represented = 33 Non ambiguous bp: Initial: 10029017 bp After Masking: 9941963 bp Masked: 0.87 % -- Input Database Coverage: 12773255 bp out of 143726002 bp ( 8.89 % ) Sampling Time: 00:00:26 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 57291 0% completed, 00:14:02 (hh:mm:ss) est. time remaining. 1% completed, 00:6:59 (hh:mm:ss) est. time remaining. 1% completed, 00:8:21 (hh:mm:ss) est. time remaining. .... 99% completed, 00:0:00 (hh:mm:ss) est. time remaining. 100% completed, 00:0:00 (hh:mm:ss) est. time remaining. Comparison Time: 00:10:16 (hh:mm:ss) Elapsed Time, 621 HSPs Collected - RECON: Running imagespread.. imagespread: NOTE: this is a compatibility shim. imagespread was merged into eledef in RECON 1.09. RECON Elapsed: 00:00:00 (hh:mm:ss) Elapsed Time - RECON: Running initial definition of elements ( eledef ).. RECON Elapsed: 00:00:00 (hh:mm:ss) Elapsed Time - RECON: Running re-definition of elements ( eleredef ).. RECON Elapsed: 00:00:00 (hh:mm:ss) Elapsed Time - RECON: Running re-definition of edges ( edgeredef ).. RECON Elapsed: 00:00:00 (hh:mm:ss) Elapsed Time - RECON: Running family definition ( famdef ).. RECON Elapsed: 00:00:00 (hh:mm:ss) Elapsed Time - Obtaining element sequences Number of families returned by RECON: 290 Processing families with greater than 15 elements Instance Gathering: 00:00:00 (hh:mm:ss) Elapsed Time Refining 1 families Family Refinement: 00:00:03 (hh:mm:ss) Elapsed Time Round Time: 00:10:46 (hh:mm:ss) Elapsed Time : 1 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:21 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... 208 Tandem Repeats Masked - TRFMask time 00:00:26 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... -- Collecting 887 ranges... 886 repeats masked totaling 435744 bp(s). - TE Masking time 00:00:27 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 38416482 bp Num Contigs Represented = 126 Non ambiguous bp: Initial: 30014529 bp After Masking: 29508888 bp Masked: 1.68 % -- Input Database Coverage: 51189737 bp out of 143726002 bp ( 35.62 % ) Sampling Time: 00:01:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 559153 0% completed, 01:54:24 (hh:mm:ss) est. time remaining. 0% completed, 01:49:50 (hh:mm:ss) est. time remaining. ... 99% completed, 00:0:00 (hh:mm:ss) est. time remaining. 99% completed, 00:0:00 (hh:mm:ss) est. time remaining. 100% completed, 00:0:00 (hh:mm:ss) est. time remaining. Comparison Time: 01:26:52 (hh:mm:ss) Elapsed Time, 5281 HSPs Collected - RECON: Running imagespread.. imagespread: NOTE: this is a compatibility shim. imagespread was merged into eledef in RECON 1.09. RECON Elapsed: 00:00:00 (hh:mm:ss) Elapsed Time - RECON: Running initial definition of elements ( eledef ).. RECON Elapsed: 00:00:00 (hh:mm:ss) Elapsed Time - RECON: Running re-definition of elements ( eleredef ).. RECON Elapsed: 00:00:00 (hh:mm:ss) Elapsed Time - RECON: Running re-definition of edges ( edgeredef ).. RECON Elapsed: 00:00:00 (hh:mm:ss) Elapsed Time - RECON: Running family definition ( famdef ).. RECON Elapsed: 00:00:00 (hh:mm:ss) Elapsed Time - Obtaining element sequences Number of families returned by RECON: 1661 Processing families with greater than 15 elements Instance Gathering: 00:00:00 (hh:mm:ss) Elapsed Time Refining 6 families Family Refinement: 00:00:03 (hh:mm:ss) Elapsed Time Round Time: 01:28:13 (hh:mm:ss) Elapsed Time : 5 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 81000000 bp - Sequence extraction : 00:00:49 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... 527 Tandem Repeats Masked - TRFMask time 00:01:00 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... -- Collecting 1194 ranges... 1193 repeats masked totaling 384485 bp(s). - TE Masking time 00:01:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 89051406 bp Num Contigs Represented = 231 Non ambiguous bp: Initial: 69977401 bp After Masking: 69423297 bp Masked: 0.79 % -- Input Database Coverage: 140241143 bp out of 143726002 bp ( 97.58 % ) Sampling Time: 00:03:00 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2936676 0% completed, 10:5:30 (hh:mm:ss) est. time remaining. 0% completed, 10:5:07 (hh:mm:ss) est. time remaining. ... 99% completed, 00:0:00 (hh:mm:ss) est. time remaining. 100% completed, 00:0:00 (hh:mm:ss) est. time remaining. Comparison Time: 07:45:48 (hh:mm:ss) Elapsed Time, 27693 HSPs Collected - RECON: Running imagespread.. imagespread: NOTE: this is a compatibility shim. imagespread was merged into eledef in RECON 1.09. RECON Elapsed: 00:00:00 (hh:mm:ss) Elapsed Time - RECON: Running initial definition of elements ( eledef ).. RECON Elapsed: 00:00:01 (hh:mm:ss) Elapsed Time - RECON: Running re-definition of elements ( eleredef ).. RECON Elapsed: 00:00:01 (hh:mm:ss) Elapsed Time - RECON: Running re-definition of edges ( edgeredef ).. RECON Elapsed: 00:00:01 (hh:mm:ss) Elapsed Time - RECON: Running family definition ( famdef ).. RECON Elapsed: 00:00:00 (hh:mm:ss) Elapsed Time - Obtaining element sequences Number of families returned by RECON: 6155 Processing families with greater than 15 elements Instance Gathering: 00:00:00 (hh:mm:ss) Elapsed Time Refining 51 families Family Refinement: 00:00:38 (hh:mm:ss) Elapsed Time Round Time: 07:49:32 (hh:mm:ss) Elapsed Time : 44 families discovered. RepeatScout/RECON discovery complete: 101 families found # # RepeatClassifier # # Version 2.0.7 # Threads: 4 # Current Working Directory: /workspace/analysis/GCF_000001215.4/earlgray_out/GCF_000001215.4_EarlGrey/GCF_000001215.4_RepeatModeler/RM_232123.TueAug42120492026 # Protein Library: /opt/conda/envs/bioenv/share/RepeatMasker/Libraries/RepeatPeps.lib # - 18011 proteins # Consensi Library: /opt/conda/envs/bioenv/share/RepeatMasker/Libraries/RepeatMasker.lib # - 30659 consensus sequences - Looking for simple/tandem and low complexity sequences.. - Looking for similarity to known repeat proteins.. - Looking for similarity to known repeat consensi.. Classification Time: 00:01:56 (hh:mm:ss) Elapsed Time Program Time: 09:33:06 (hh:mm:ss) Elapsed Time Working directory: /workspace/analysis/GCF_000001215.4/earlgray_out/GCF_000001215.4_EarlGrey/GCF_000001215.4_RepeatModeler/RM_232123.TueAug42120492026 may be deleted unless there were problems with the run. The results have been saved to: /workspace/analysis/GCF_000001215.4/earlgray_out/GCF_000001215.4_EarlGrey/GCF_000001215.4_Database/ GCF_000001215.4-families.fa - Consensus sequences for each family identified. GCF_000001215.4-families.stk - Seed alignments for each family identified. GCF_000001215.4-rmod.log - Execution log. Useful for reproducing results. For reproducibility and maintaining the provenance of your results, it is **highly** recommended that these three files are preserved (even the *-rmod.log file). The seed alignment data is particularly important for understanding the origin of the family consensus and for submission to databases like Dfam. If further curation is performed on these families, consider keeping modified multiple sequence alignments generated as part of that effort, in addition to the improved consensus sequences derived from them. Finally, please contribute de-novo or curated families to to the Dfam open database and be a part of this growing community resource. For more information visit http://dfam.org or contact help@dfam.org. ) ( ( ) ) ) ( ( _______)_ .-'---------| ( C|/\/\/\/\/| '-./\/\/\/\/| '_________' '-------' <<< Straining TEs and Refining de novo Consensus Sequences >>> Building a new DB, current time: 08/05/2026 06:54:00 New DB name: /workspace/genomes/GCF_000001215.4/GCF_000001215.4_Release_6_plus_ISO1_MT_genomic.fna.prep New DB title: /workspace/genomes/GCF_000001215.4/GCF_000001215.4_Release_6_plus_ISO1_MT_genomic.fna.prep Sequence type: Nucleotide Keep MBits: T Maximum file size: 3000000000B Adding sequences from FASTA; added 1870 sequences in 1.61205 seconds. Splitting run 1 Initial trf check for 1 # 0 sec rnd-1_family-57.fasta 0.99009900990099 0% 1:100=0s rnd-1_family-57.fasta  .... 100 100% 101:0=0s rnd-1_family-33.fasta  # 0.75 sec rnd-1_family-33.fasta 100 100% 101:0=0s rnd-1_family-33.fasta  Trimming and sorting based on mreps, TRF, SA-SSR Removing temporary files Reclassifying repeats # # RepeatClassifier # # Version 2.0.7 # Threads: 4 # Current Working Directory: /workspace/analysis/GCF_000001215.4/earlgray_out/GCF_000001215.4_EarlGrey/GCF_000001215.4_strainer/TS_GCF_000001215.4-families.fa_2839/classify # Protein Library: /opt/conda/envs/bioenv/share/RepeatMasker/Libraries/RepeatPeps.lib # - 18011 proteins # Consensi Library: /opt/conda/envs/bioenv/share/RepeatMasker/Libraries/RepeatMasker.lib # - 30659 consensus sequences - Looking for simple/tandem and low complexity sequences.. - Looking for similarity to known repeat proteins.. - Looking for similarity to known repeat consensi.. /workspace/analysis/GCF_000001215.4/earlgray_out/GCF_000001215.4_EarlGrey/GCF_000001215.4_strainer Compiling library ) ( ( ) ) ) ( ( _______)_ .-'---------| ( C|/\/\/\/\/| '-./\/\/\/\/| '_________' '-------' <<< Identifying Repeats Using Species-Specific Library >>> RepeatMasker version 4.2.4 Search Engine: NCBI/RMBLAST [ 2.17.1+ ] Using FamDB: /opt/conda/envs/bioenv/share/famdb-3.0.0 Title : Dfam Version : 4.0 Date : 2026-05-22 Families : 43,193 Using Custom Repeat Library: /workspace/analysis/GCF_000001215.4/earlgray_out/GCF_000001215.4_EarlGrey/GCF_000001215.4_Curated_Library/GCF_000001215.4_combined_library.fasta analyzing file /workspace/genomes/GCF_000001215.4/GCF_000001215.4_Release_6_plus_ISO1_MT_genomic.fna.prep identifying Simple Repeats in batch 1 of 2476 identifying matches to GCF_000001215.4_combined_library.fasta sequences in batch 1 of 2476 ... identifying matches to GCF_000001215.4_combined_library.fasta sequences in batch 2476 of 2476 identifying Simple Repeats in batch 2476 of 2476 ProcessRepeats: Adjudicating alignments ..................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................... ProcessRepeats: Masking sequences ProcessRepeats: Generating table output done ) ( ( ) ) ) ( ( _______)_ .-'---------| ( C|/\/\/\/\/| '-./\/\/\/\/| '_________' '-------' <<< Defragmenting Repeats >>> ) ( ( ) ) ) ( ( _______)_ .-'---------| ( C|/\/\/\/\/| '-./\/\/\/\/| '_________' '-------' <<< Running LTR Finder >>> Wed Aug 5 08:24:06 2026 CPU1: running on ctg_1_sub1 Wed Aug 5 08:24:06 2026 CPU2: running on ctg_1_sub2 ... Wed Aug 5 08:27:36 2026 CPU4: running on ctg_1870_sub1 Wed Aug 5 08:34:49 2026 Job finished! Check out GCF_000001215.4_Release_6_plus_ISO1_MT_genomic.fna.prep.finder.combine.scn ) ( ( ) ) ) ( ( _______)_ .-'---------| ( C|/\/\/\/\/| '-./\/\/\/\/| '_________' '-------' <<< Generating GFF Files >>> ) ( ( ) ) ) ( ( _______)_ .-'---------| ( C|/\/\/\/\/| '-./\/\/\/\/| '_________' '-------' <<< Running RepeatCraft >>> Step 1: Reformating GFF... Parsing LTR_FINDER GFF... Step 2: Labelling short TEs... Missing mapfile, use unite size for all TEs except simple repeat, low complexity and satellite. 'ARTEFACT' is not in the mapfile. Skip filtering ARTEFACT Step 3: Labelling LTR groups... Updated LTR.gff with LTRgroup attribute to:ltrfinder_reformat.gff Step 4: Labelling TE groups...(loose mode) Progress:1/146576... ... Progress:146575/146576... Step 5: Merging GFF records by labels... Step 6: Writing stat file..Removing tmp files... Done ) ( ( ) ) ) ( ( _______)_ .-'---------| ( C|/\/\/\/\/| '-./\/\/\/\/| '_________' '-------' <<< Resolving Overlapping Repeats >>> [1] "Searching for Nested TEs. Iteration:1" [1] "Searching for Nested TEs. Iteration:2" [1] "Searching for Nested TEs. Iteration:3" [1] "Searching for Nested TEs. Iteration:4" [1] "Searching for Nested TEs. Iteration:5" [1] "Searching for Nested TEs. Iteration:6" [1] "Searching for Nested TEs. Iteration:7" [1] "Searching for Nested TEs. Iteration:8" [1] "Searching for Nested TEs. Iteration:9" ) ( ( ) ) ) ( ( _______)_ .-'---------| ( C|/\/\/\/\/| '-./\/\/\/\/| '_________' '-------' <<< Done! >>> ) ( ( ) ) ) ( ( _______)_ .-'---------| ( C|/\/\/\/\/| '-./\/\/\/\/| '_________' '-------' <<< Generating Summary Plots >>> systemfonts and textshaping have been compiled with different versions of Freetype. Because of this, textshaping will not use the font cache provided by systemfontsJoining with `by = join_by(Family)` Joining with `by = join_by(Family)` Indexing genome Splitting repeat library Reading in gff Writing chunks to disk Starting calculations Finished calculations Total run time for 134678 rows was 923.1854908466339 seconds systemfonts and textshaping have been compiled with different versions of Freetype. Because of this, textshaping will not use the font cache provided by systemfonts ) ( ( ) ) ) ( ( _______)_ .-'---------| ( C|/\/\/\/\/| '-./\/\/\/\/| '_________' '-------' <<< Tidying Directories and Organising Important Files >>> cp: warning: source file '/workspace/analysis/GCF_000001215.4/earlgray_out/GCF_000001215.4_EarlGrey/GCF_000001215.4_Curated_Library/GCF_000001215.4_combined_library.fasta' specified more than once /opt/conda/envs/bioenv/bin/earlGrey: line 378: bc: command not found /opt/conda/envs/bioenv/bin/earlGrey: line 379: bc: command not found /opt/conda/envs/bioenv/bin/earlGrey: line 380: bc: command not found ) ( ( ) ) ) ( ( _______)_ .-'---------| ( C|/\/\/\/\/| '-./\/\/\/\/| '_________' '-------' <<< Done in 00:00:00.00 >>> ) ( ( ) ) ) ( ( _______)_ .-'---------| ( C|/\/\/\/\/| '-./\/\/\/\/| '_________' '-------' <<< TE library, Summary Figures, and TE Quantifications in Standard Formats Can Be Found in /workspace/analysis/GCF_000001215.4/earlgray_out/GCF_000001215.4_EarlGrey/GCF_000001215.4_summaryFiles/ >>> |TE Classification | Coverage (bp)|Copy Number | % Genome Coverage| Genome Size| TE Family Count| |:-------------------------------------------------|-------------:|:-------------|-----------------:|-----------:|---------------:| |DNA | 1760231|3178 | 1.2247130| 143726002| 42| |DNA-nested | 4100|45 | 0.0028527| 143726002| 15| |Rolling Circle | 919697|4492 | 0.6398960| 143726002| 2| |Rolling Circle-nested | 6618|68 | 0.0046046| 143726002| 1| |Penelope | 0|0 | 0.0000000| 143726002| NA| |Penelope-nested | 0|0 | 0.0000000| 143726002| NA| |LINE | 6725150|6642 | 4.6791464| 143726002| 54| |LINE-nested | 56758|344 | 0.0394904| 143726002| 33| |SINE | 0|0 | 0.0000000| 143726002| NA| |SINE-nested | 0|0 | 0.0000000| 143726002| NA| |LTR | 16717580|15832 | 11.6315627| 143726002| 287| |LTR-nested | 103924|235 | 0.0723070| 143726002| 70| |Other (Simple Repeat, Microsatellite, RNA) | 5186784|94398 | 3.6088000| 143726002| 8959| |Other (Simple Repeat, Microsatellite, RNA)-nested | 68462|1052 | 0.0476337| 143726002| 331| |Unclassified | 2872998|7975 | 1.9989410| 143726002| 79| |Unclassified-nested | 64860|417 | 0.0451275| 143726002| 31| |Total Interspersed Repeat | 34182440|132517 | 23.7830591| 143726002| NA| |Non-Repeat | 109543562|notApplicable | 76.2169409| 143726002| NA|