Mercurial > repos > artbio > repenrich2
changeset 6:388a47ca4199 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit a9af1284d644055565b6cf3401569694218ab8e9
| author | artbio |
|---|---|
| date | Mon, 22 Apr 2024 10:31:50 +0000 |
| parents | 08e50af788f7 |
| children | 61e0404f0d76 |
| files | RepEnrich2.py macros.xml repenrich2.xml test-data/chrY_paired_class_fraction_counts.tab test-data/chrY_paired_family_fraction_counts.tab test-data/chrY_paired_fraction_counts.tab test-data/chrY_single_class_fraction_counts.tab test-data/chrY_single_family_fraction_counts.tab test-data/chrY_single_fraction_counts.tab |
| diffstat | 9 files changed, 338 insertions(+), 338 deletions(-) [+] |
line wrap: on
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--- a/RepEnrich2.py Sun Apr 21 21:52:40 2024 +0000 +++ b/RepEnrich2.py Mon Apr 22 10:31:50 2024 +0000 @@ -197,14 +197,14 @@ # print class-, family- and fraction-repeats counts to files with open("class_fraction_counts.tsv", 'w') as fout: for key in sorted(classfractionalcounts): - fout.write(f"{key}\t{classfractionalcounts[key]}\n") + fout.write(f"{key}\t{round(classfractionalcounts[key], 2)}\n") with open("family_fraction_counts.tsv", 'w') as fout: for key in sorted(familyfractionalcounts): - fout.write(f"{key}\t{familyfractionalcounts[key]}\n") + fout.write(f"{key}\t{round(familyfractionalcounts[key], 2)}\n") with open("fraction_counts.tsv", 'w') as fout: for key in sorted(fractionalcounts): fout.write(f"{key}\t{repeat_ref[key]['class']}\t" f"{repeat_ref[key]['family']}\t" - f"{fractionalcounts[key]}\n") + f"{round(fractionalcounts[key], 2)}\n")
--- a/macros.xml Sun Apr 21 21:52:40 2024 +0000 +++ b/macros.xml Mon Apr 22 10:31:50 2024 +0000 @@ -1,6 +1,6 @@ <macros> <token name="@TOOL_VERSION@">2.31.1</token> - <token name="@VERSION_SUFFIX@">5</token> + <token name="@VERSION_SUFFIX@">6</token> <token name="@PROFILE@">23.0</token> <xml name="repenrich_requirements">
--- a/repenrich2.xml Sun Apr 21 21:52:40 2024 +0000 +++ b/repenrich2.xml Mon Apr 22 10:31:50 2024 +0000 @@ -38,16 +38,16 @@ bowtie2 -x $index_path -p \${GALAXY_SLOTS:-4} input.fastq | samtools sort -@ "\${GALAXY_SLOTS:-4}" -T tmp -O bam -o aligned.bam 2>&1 && samtools view -@ "\${GALAXY_SLOTS:-4}" -F 4 -b -q 38 aligned.bam -o unique.bam && - samtools view -@ "\${GALAXY_SLOTS:-4}" -h -F 4 -b aligned.bam \ - | samtools view -@ "\${GALAXY_SLOTS:-4}" -U -b -q 38 - \ - | bedtools bamtofastq -i /dev/stdin -fq multimap.fastq && + samtools view -@ "\${GALAXY_SLOTS:-4}" -F 4 -b aligned.bam + | samtools view -@ "\${GALAXY_SLOTS:-4}" -U filt_aligned.bam -bq 38 - > /dev/null && + bedtools bamtofastq -i filt_aligned.bam -fq multimap.fastq && #else: bowtie2 -x $index_path -p \${GALAXY_SLOTS:-4} -1 input.fastq -2 input_2.fastq | samtools sort -@ "\${GALAXY_SLOTS:-4}" -T tmp -O bam -o aligned.bam 2>&1 && samtools view -@ "\${GALAXY_SLOTS:-4}" -f 3 -b -q 38 aligned.bam -o unique.bam && - samtools view -@ "\${GALAXY_SLOTS:-4}" -f 3 -b aligned.bam \ - | samtools view -@ "\${GALAXY_SLOTS:-4}" -U -b -q 38 - \ - | samtools sort -@ "\${GALAXY_SLOTS:-4}" -n - - + samtools view -@ "\${GALAXY_SLOTS:-4}" -f 3 -b aligned.bam + | samtools view -@ "\${GALAXY_SLOTS:-4}" -U filt_aligned.bam -bq 38 - > /dev/null && + samtools sort -@ "\${GALAXY_SLOTS:-4}" -T tmp -n filt_aligned.bam | bedtools bamtofastq -i /dev/stdin -fq multimap_1.fastq -fq2 multimap_2.fastq && #end if samtools index unique.bam &&
--- a/test-data/chrY_paired_class_fraction_counts.tab Sun Apr 21 21:52:40 2024 +0000 +++ b/test-data/chrY_paired_class_fraction_counts.tab Mon Apr 22 10:31:50 2024 +0000 @@ -1,6 +1,6 @@ -DNA 148.0 -LINE 195.0 -LTR 26742.0 -Low_complexity 0.0 -RC 0.0 -Simple_repeat 0.0 +DNA 194.66 +LINE 279.83 +LTR 27051.62 +Low_complexity 8.48 +RC 4.24 +Simple_repeat 161.17
--- a/test-data/chrY_paired_family_fraction_counts.tab Sun Apr 21 21:52:40 2024 +0000 +++ b/test-data/chrY_paired_family_fraction_counts.tab Mon Apr 22 10:31:50 2024 +0000 @@ -1,13 +1,13 @@ -CMC-Transib 30.0 -CR1 4.0 -Copia 25834.0 -Gypsy 857.0 -Helitron 0.0 -Jockey 105.0 -LOA 0.0 -Low_complexity 0.0 -P 32.0 -Pao 51.0 -R1 86.0 -Simple_repeat 0.0 -TcMar-Tc1 86.0 +CMC-Transib 38.48 +CR1 8.24 +Copia 25859.45 +Gypsy 1107.24 +Helitron 4.24 +Jockey 164.38 +LOA 4.24 +Low_complexity 8.48 +P 40.48 +Pao 84.93 +R1 102.97 +Simple_repeat 161.17 +TcMar-Tc1 115.69
--- a/test-data/chrY_paired_fraction_counts.tab Sun Apr 21 21:52:40 2024 +0000 +++ b/test-data/chrY_paired_fraction_counts.tab Mon Apr 22 10:31:50 2024 +0000 @@ -1,145 +1,145 @@ -A-rich Low_complexity Low_complexity 0.0 -ACCORD2_I-int LTR Gypsy 0.0 -ACCORD2_LTR LTR Gypsy 0.0 -ACCORD_I-int LTR Gypsy 0.0 -BARI1 DNA TcMar-Tc1 0.0 -BATUMI_LTR LTR Pao 0.0 -BS LINE Jockey 0.0 -BS2 LINE Jockey 58.0 -BURDOCK_I-int LTR Gypsy 0.0 -Baggins1 LINE LOA 0.0 -Bica_I-int LTR Gypsy 38.0 -Bica_LTR LTR Gypsy 0.0 -CIRCE LTR Gypsy 0.0 -Chouto_I-int LTR Gypsy 0.0 -Copia1-I_DM LTR Copia 0.0 -Copia_I-int LTR Copia 25181.0 -Copia_LTR LTR Copia 647.0 -DIVER2_I-int LTR Pao 0.0 -DIVER2_LTR LTR Pao 0.0 -DM1731_I-int LTR Copia 6.0 -DM1731_LTR LTR Copia 0.0 -DM176_I-int LTR Gypsy 0.0 -DM412 LTR Gypsy 0.0 -DM412B_LTR LTR Gypsy 0.0 -DMCR1A LINE CR1 4.0 -DMLTR5 LTR Gypsy 0.0 -DMRT1A LINE R1 0.0 -DMRT1B LINE R1 86.0 -DMRT1C LINE R1 0.0 -DNAREP1_DM RC Helitron 0.0 -DOC2_DM LINE Jockey 0.0 -DOC3_DM LINE Jockey 0.0 -FB4_DM DNA TcMar-Tc1 38.0 -FROGGER_I-int LTR Copia 0.0 -FW2_DM LINE Jockey 0.0 -G3_DM LINE Jockey 0.0 -G5A_DM LINE Jockey 0.0 -G5_DM LINE Jockey 0.0 -G6_DM LINE Jockey 0.0 -GA-rich Low_complexity Low_complexity 0.0 -GTWIN_I-int LTR Gypsy 0.0 -G_DM LINE Jockey 0.0 -Gypsy11_I-int LTR Gypsy 0.0 -Gypsy11_LTR LTR Gypsy 0.0 -Gypsy12_LTR LTR Gypsy 0.0 -Gypsy2-I_DM LTR Gypsy 2.0 -Gypsy2-LTR_DM LTR Gypsy 0.0 -Gypsy3_LTR LTR Gypsy 0.0 -Gypsy4_I-int LTR Gypsy 0.0 -Gypsy5_I-int LTR Gypsy 0.0 -Gypsy6A_LTR LTR Gypsy 0.0 -Gypsy6_I-int LTR Gypsy 26.0 -Gypsy8_I-int LTR Gypsy 0.0 -Gypsy8_LTR LTR Gypsy 0.0 -Gypsy9_I-int LTR Gypsy 0.0 -Gypsy_I-int LTR Gypsy 32.0 -Gypsy_LTR LTR Gypsy 1.0 -HELENA_RT LINE Jockey 0.0 -HETA LINE Jockey 24.0 -HMSBEAGLE_I-int LTR Gypsy 2.0 -IDEFIX_I-int LTR Gypsy 4.0 -IDEFIX_LTR LTR Gypsy 0.0 -Invader1_I-int LTR Gypsy 0.0 -Invader1_LTR LTR Gypsy 0.0 -Invader2_I-int LTR Gypsy 0.0 -Invader4_I-int LTR Gypsy 0.0 -Invader4_LTR LTR Gypsy 0.0 -Invader5_I-int LTR Gypsy 0.0 -Invader5_LTR LTR Gypsy 0.0 -Invader6_I-int LTR Gypsy 0.0 -Invader6_LTR LTR Gypsy 0.0 -MAX_I-int LTR Pao 49.0 -MAX_LTR LTR Pao 2.0 -MDG1_I-int LTR Gypsy 0.0 -MDG1_LTR LTR Gypsy 0.0 -MDG3_I-int LTR Gypsy 152.0 -MDG3_LTR LTR Gypsy 0.0 -MICROPIA_I-int LTR Gypsy 0.0 -MICROPIA_LTR LTR Gypsy 0.0 -Mariner2_DM DNA TcMar-Tc1 0.0 -NINJA_I-int LTR Pao 0.0 -NOMAD_I-int LTR Gypsy 0.0 -PROTOP_A DNA P 32.0 -PROTOP_B DNA P 0.0 -QUASIMODO2-I_DM LTR Gypsy 42.0 -QUASIMODO2-LTR_DM LTR Gypsy 0.0 -QUASIMODO_I-int LTR Gypsy 10.0 -QUASIMODO_LTR LTR Gypsy 2.0 -R1_DM LINE R1 0.0 -ROOA_I-int LTR Pao 0.0 -ROOA_LTR LTR Pao 0.0 -ROVER-I_DM LTR Gypsy 381.0 -ROVER-LTR_DM LTR Gypsy 2.0 -S2_DM DNA TcMar-Tc1 0.0 -STALKER4_I-int LTR Gypsy 77.0 -STALKER4_LTR LTR Gypsy 4.0 -S_DM DNA TcMar-Tc1 48.0 -Stalker2_I-int LTR Gypsy 80.0 -Stalker2_LTR LTR Gypsy 2.0 -TART-A LINE Jockey 4.0 -TART_B1 LINE Jockey 19.0 -TC1-2_DM DNA TcMar-Tc1 0.0 -TC1_DM DNA TcMar-Tc1 0.0 -TLD2 LTR Gypsy 0.0 -TRANSIB1 DNA CMC-Transib 0.0 -TRANSIB2 DNA CMC-Transib 30.0 -ZAM_I-int LTR Gypsy 0.0 -_AACACA_n Simple_repeat Simple_repeat 0.0 -_AAT_n Simple_repeat Simple_repeat 0.0 -_ACAATAG_n Simple_repeat Simple_repeat 0.0 -_ACC_n Simple_repeat Simple_repeat 0.0 -_AGAGAAG_n Simple_repeat Simple_repeat 0.0 -_AGAGA_n Simple_repeat Simple_repeat 0.0 -_ATAAT_n Simple_repeat Simple_repeat 0.0 -_ATATATT_n Simple_repeat Simple_repeat 0.0 -_ATATTAT_n Simple_repeat Simple_repeat 0.0 -_ATTTTT_n Simple_repeat Simple_repeat 0.0 -_ATT_n Simple_repeat Simple_repeat 0.0 -_AT_n Simple_repeat Simple_repeat 0.0 -_A_n Simple_repeat Simple_repeat 0.0 -_CATA_n Simple_repeat Simple_repeat 0.0 -_CTTTT_n Simple_repeat Simple_repeat 0.0 -_GAGAA_n Simple_repeat Simple_repeat 0.0 -_GCCTTT_n Simple_repeat Simple_repeat 0.0 -_TAATAT_n Simple_repeat Simple_repeat 0.0 -_TAATA_n Simple_repeat Simple_repeat 0.0 -_TATAAAA_n Simple_repeat Simple_repeat 0.0 -_TATAA_n Simple_repeat Simple_repeat 0.0 -_TATCATG_n Simple_repeat Simple_repeat 0.0 -_TA_n Simple_repeat Simple_repeat 0.0 -_TGTTG_n Simple_repeat Simple_repeat 0.0 -_TTATATA_n Simple_repeat Simple_repeat 0.0 -_TTATAT_n Simple_repeat Simple_repeat 0.0 -_TTATA_n Simple_repeat Simple_repeat 0.0 -_TTA_n Simple_repeat Simple_repeat 0.0 -_TTCTT_n Simple_repeat Simple_repeat 0.0 -_TTC_n Simple_repeat Simple_repeat 0.0 -_TTTAT_n Simple_repeat Simple_repeat 0.0 -_TTTA_n Simple_repeat Simple_repeat 0.0 -_TTTC_n Simple_repeat Simple_repeat 0.0 -_TTTGA_n Simple_repeat Simple_repeat 0.0 -_TTTTAG_n Simple_repeat Simple_repeat 0.0 -_TTTTCTT_n Simple_repeat Simple_repeat 0.0 -_TTTTC_n Simple_repeat Simple_repeat 0.0 -_T_n Simple_repeat Simple_repeat 0.0 +A-rich Low_complexity Low_complexity 4.24 +ACCORD2_I-int LTR Gypsy 4.24 +ACCORD2_LTR LTR Gypsy 4.24 +ACCORD_I-int LTR Gypsy 4.24 +BARI1 DNA TcMar-Tc1 4.24 +BATUMI_LTR LTR Pao 4.24 +BS LINE Jockey 4.24 +BS2 LINE Jockey 62.24 +BURDOCK_I-int LTR Gypsy 4.24 +Baggins1 LINE LOA 4.24 +Bica_I-int LTR Gypsy 42.24 +Bica_LTR LTR Gypsy 4.24 +CIRCE LTR Gypsy 4.24 +Chouto_I-int LTR Gypsy 4.24 +Copia1-I_DM LTR Copia 4.24 +Copia_I-int LTR Copia 25185.24 +Copia_LTR LTR Copia 651.24 +DIVER2_I-int LTR Pao 4.24 +DIVER2_LTR LTR Pao 4.24 +DM1731_I-int LTR Copia 10.24 +DM1731_LTR LTR Copia 4.24 +DM176_I-int LTR Gypsy 4.24 +DM412 LTR Gypsy 4.24 +DM412B_LTR LTR Gypsy 4.24 +DMCR1A LINE CR1 8.24 +DMLTR5 LTR Gypsy 4.24 +DMRT1A LINE R1 4.24 +DMRT1B LINE R1 90.24 +DMRT1C LINE R1 4.24 +DNAREP1_DM RC Helitron 4.24 +DOC2_DM LINE Jockey 4.24 +DOC3_DM LINE Jockey 4.24 +FB4_DM DNA TcMar-Tc1 42.24 +FROGGER_I-int LTR Copia 4.24 +FW2_DM LINE Jockey 4.24 +G3_DM LINE Jockey 4.24 +G5A_DM LINE Jockey 4.24 +G5_DM LINE Jockey 4.24 +G6_DM LINE Jockey 4.24 +GA-rich Low_complexity Low_complexity 4.24 +GTWIN_I-int LTR Gypsy 4.24 +G_DM LINE Jockey 4.24 +Gypsy11_I-int LTR Gypsy 4.24 +Gypsy11_LTR LTR Gypsy 4.24 +Gypsy12_LTR LTR Gypsy 4.24 +Gypsy2-I_DM LTR Gypsy 6.24 +Gypsy2-LTR_DM LTR Gypsy 4.24 +Gypsy3_LTR LTR Gypsy 4.24 +Gypsy4_I-int LTR Gypsy 4.24 +Gypsy5_I-int LTR Gypsy 4.24 +Gypsy6A_LTR LTR Gypsy 4.24 +Gypsy6_I-int LTR Gypsy 30.24 +Gypsy8_I-int LTR Gypsy 4.24 +Gypsy8_LTR LTR Gypsy 4.24 +Gypsy9_I-int LTR Gypsy 4.24 +Gypsy_I-int LTR Gypsy 36.24 +Gypsy_LTR LTR Gypsy 5.24 +HELENA_RT LINE Jockey 4.24 +HETA LINE Jockey 28.24 +HMSBEAGLE_I-int LTR Gypsy 6.24 +IDEFIX_I-int LTR Gypsy 8.24 +IDEFIX_LTR LTR Gypsy 4.24 +Invader1_I-int LTR Gypsy 4.24 +Invader1_LTR LTR Gypsy 4.24 +Invader2_I-int LTR Gypsy 4.24 +Invader4_I-int LTR Gypsy 4.24 +Invader4_LTR LTR Gypsy 4.24 +Invader5_I-int LTR Gypsy 4.24 +Invader5_LTR LTR Gypsy 4.24 +Invader6_I-int LTR Gypsy 4.24 +Invader6_LTR LTR Gypsy 4.24 +MAX_I-int LTR Pao 53.24 +MAX_LTR LTR Pao 6.24 +MDG1_I-int LTR Gypsy 4.24 +MDG1_LTR LTR Gypsy 4.24 +MDG3_I-int LTR Gypsy 156.24 +MDG3_LTR LTR Gypsy 4.24 +MICROPIA_I-int LTR Gypsy 4.24 +MICROPIA_LTR LTR Gypsy 4.24 +Mariner2_DM DNA TcMar-Tc1 4.24 +NINJA_I-int LTR Pao 4.24 +NOMAD_I-int LTR Gypsy 4.24 +PROTOP_A DNA P 36.24 +PROTOP_B DNA P 4.24 +QUASIMODO2-I_DM LTR Gypsy 46.24 +QUASIMODO2-LTR_DM LTR Gypsy 4.24 +QUASIMODO_I-int LTR Gypsy 14.24 +QUASIMODO_LTR LTR Gypsy 6.24 +R1_DM LINE R1 4.24 +ROOA_I-int LTR Pao 4.24 +ROOA_LTR LTR Pao 4.24 +ROVER-I_DM LTR Gypsy 385.24 +ROVER-LTR_DM LTR Gypsy 6.24 +S2_DM DNA TcMar-Tc1 4.24 +STALKER4_I-int LTR Gypsy 81.24 +STALKER4_LTR LTR Gypsy 8.24 +S_DM DNA TcMar-Tc1 52.24 +Stalker2_I-int LTR Gypsy 84.24 +Stalker2_LTR LTR Gypsy 6.24 +TART-A LINE Jockey 8.24 +TART_B1 LINE Jockey 23.24 +TC1-2_DM DNA TcMar-Tc1 4.24 +TC1_DM DNA TcMar-Tc1 4.24 +TLD2 LTR Gypsy 4.24 +TRANSIB1 DNA CMC-Transib 4.24 +TRANSIB2 DNA CMC-Transib 34.24 +ZAM_I-int LTR Gypsy 4.24 +_AACACA_n Simple_repeat Simple_repeat 4.24 +_AAT_n Simple_repeat Simple_repeat 4.24 +_ACAATAG_n Simple_repeat Simple_repeat 4.24 +_ACC_n Simple_repeat Simple_repeat 4.24 +_AGAGAAG_n Simple_repeat Simple_repeat 4.24 +_AGAGA_n Simple_repeat Simple_repeat 4.24 +_ATAAT_n Simple_repeat Simple_repeat 4.24 +_ATATATT_n Simple_repeat Simple_repeat 4.24 +_ATATTAT_n Simple_repeat Simple_repeat 4.24 +_ATTTTT_n Simple_repeat Simple_repeat 4.24 +_ATT_n Simple_repeat Simple_repeat 4.24 +_AT_n Simple_repeat Simple_repeat 4.24 +_A_n Simple_repeat Simple_repeat 4.24 +_CATA_n Simple_repeat Simple_repeat 4.24 +_CTTTT_n Simple_repeat Simple_repeat 4.24 +_GAGAA_n Simple_repeat Simple_repeat 4.24 +_GCCTTT_n Simple_repeat Simple_repeat 4.24 +_TAATAT_n Simple_repeat Simple_repeat 4.24 +_TAATA_n Simple_repeat Simple_repeat 4.24 +_TATAAAA_n Simple_repeat Simple_repeat 4.24 +_TATAA_n Simple_repeat Simple_repeat 4.24 +_TATCATG_n Simple_repeat Simple_repeat 4.24 +_TA_n Simple_repeat Simple_repeat 4.24 +_TGTTG_n Simple_repeat Simple_repeat 4.24 +_TTATATA_n Simple_repeat Simple_repeat 4.24 +_TTATAT_n Simple_repeat Simple_repeat 4.24 +_TTATA_n Simple_repeat Simple_repeat 4.24 +_TTA_n Simple_repeat Simple_repeat 4.24 +_TTCTT_n Simple_repeat Simple_repeat 4.24 +_TTC_n Simple_repeat Simple_repeat 4.24 +_TTTAT_n Simple_repeat Simple_repeat 4.24 +_TTTA_n Simple_repeat Simple_repeat 4.24 +_TTTC_n Simple_repeat Simple_repeat 4.24 +_TTTGA_n Simple_repeat Simple_repeat 4.24 +_TTTTAG_n Simple_repeat Simple_repeat 4.24 +_TTTTCTT_n Simple_repeat Simple_repeat 4.24 +_TTTTC_n Simple_repeat Simple_repeat 4.24 +_T_n Simple_repeat Simple_repeat 4.24
--- a/test-data/chrY_single_class_fraction_counts.tab Sun Apr 21 21:52:40 2024 +0000 +++ b/test-data/chrY_single_class_fraction_counts.tab Mon Apr 22 10:31:50 2024 +0000 @@ -1,6 +1,6 @@ -DNA 70.0 -LINE 90.0 -LTR 13210.0 -Low_complexity 0.0 -RC 0.0 -Simple_repeat 0.0 +DNA 121.89 +LINE 184.34 +LTR 13554.36 +Low_complexity 9.43 +RC 4.72 +Simple_repeat 179.26
--- a/test-data/chrY_single_family_fraction_counts.tab Sun Apr 21 21:52:40 2024 +0000 +++ b/test-data/chrY_single_family_fraction_counts.tab Mon Apr 22 10:31:50 2024 +0000 @@ -1,13 +1,13 @@ -CMC-Transib 12.0 -CR1 2.0 -Copia 12789.0 -Gypsy 392.0 -Helitron 0.0 -Jockey 53.0 -LOA 0.0 -Low_complexity 0.0 -P 18.0 -Pao 29.0 -R1 35.0 -Simple_repeat 0.0 -TcMar-Tc1 40.0 +CMC-Transib 21.43 +CR1 6.72 +Copia 12817.3 +Gypsy 670.32 +Helitron 4.72 +Jockey 119.04 +LOA 4.72 +Low_complexity 9.43 +P 27.43 +Pao 66.74 +R1 53.87 +Simple_repeat 179.26 +TcMar-Tc1 73.02
--- a/test-data/chrY_single_fraction_counts.tab Sun Apr 21 21:52:40 2024 +0000 +++ b/test-data/chrY_single_fraction_counts.tab Mon Apr 22 10:31:50 2024 +0000 @@ -1,145 +1,145 @@ -A-rich Low_complexity Low_complexity 0.0 -ACCORD2_I-int LTR Gypsy 0.0 -ACCORD2_LTR LTR Gypsy 0.0 -ACCORD_I-int LTR Gypsy 0.0 -BARI1 DNA TcMar-Tc1 0.0 -BATUMI_LTR LTR Pao 0.0 -BS LINE Jockey 0.0 -BS2 LINE Jockey 29.0 -BURDOCK_I-int LTR Gypsy 0.0 -Baggins1 LINE LOA 0.0 -Bica_I-int LTR Gypsy 19.0 -Bica_LTR LTR Gypsy 0.0 -CIRCE LTR Gypsy 0.0 -Chouto_I-int LTR Gypsy 0.0 -Copia1-I_DM LTR Copia 0.0 -Copia_I-int LTR Copia 12652.0 -Copia_LTR LTR Copia 134.0 -DIVER2_I-int LTR Pao 1.0 -DIVER2_LTR LTR Pao 0.0 -DM1731_I-int LTR Copia 3.0 -DM1731_LTR LTR Copia 0.0 -DM176_I-int LTR Gypsy 0.0 -DM412 LTR Gypsy 0.0 -DM412B_LTR LTR Gypsy 0.0 -DMCR1A LINE CR1 2.0 -DMLTR5 LTR Gypsy 0.0 -DMRT1A LINE R1 0.0 -DMRT1B LINE R1 35.0 -DMRT1C LINE R1 0.0 -DNAREP1_DM RC Helitron 0.0 -DOC2_DM LINE Jockey 0.0 -DOC3_DM LINE Jockey 0.0 -FB4_DM DNA TcMar-Tc1 15.0 -FROGGER_I-int LTR Copia 0.0 -FW2_DM LINE Jockey 0.0 -G3_DM LINE Jockey 0.0 -G5A_DM LINE Jockey 0.0 -G5_DM LINE Jockey 0.0 -G6_DM LINE Jockey 0.0 -GA-rich Low_complexity Low_complexity 0.0 -GTWIN_I-int LTR Gypsy 0.0 -G_DM LINE Jockey 0.0 -Gypsy11_I-int LTR Gypsy 0.0 -Gypsy11_LTR LTR Gypsy 0.0 -Gypsy12_LTR LTR Gypsy 0.0 -Gypsy2-I_DM LTR Gypsy 1.0 -Gypsy2-LTR_DM LTR Gypsy 0.0 -Gypsy3_LTR LTR Gypsy 0.0 -Gypsy4_I-int LTR Gypsy 0.0 -Gypsy5_I-int LTR Gypsy 0.0 -Gypsy6A_LTR LTR Gypsy 0.0 -Gypsy6_I-int LTR Gypsy 12.0 -Gypsy8_I-int LTR Gypsy 0.0 -Gypsy8_LTR LTR Gypsy 0.0 -Gypsy9_I-int LTR Gypsy 0.0 -Gypsy_I-int LTR Gypsy 15.0 -Gypsy_LTR LTR Gypsy 0.0 -HELENA_RT LINE Jockey 0.0 -HETA LINE Jockey 12.0 -HMSBEAGLE_I-int LTR Gypsy 1.0 -IDEFIX_I-int LTR Gypsy 0.0 -IDEFIX_LTR LTR Gypsy 0.0 -Invader1_I-int LTR Gypsy 0.0 -Invader1_LTR LTR Gypsy 0.0 -Invader2_I-int LTR Gypsy 0.0 -Invader4_I-int LTR Gypsy 0.0 -Invader4_LTR LTR Gypsy 0.0 -Invader5_I-int LTR Gypsy 0.0 -Invader5_LTR LTR Gypsy 0.0 -Invader6_I-int LTR Gypsy 0.0 -Invader6_LTR LTR Gypsy 0.0 -MAX_I-int LTR Pao 27.0 -MAX_LTR LTR Pao 1.0 -MDG1_I-int LTR Gypsy 0.0 -MDG1_LTR LTR Gypsy 0.0 -MDG3_I-int LTR Gypsy 70.0 -MDG3_LTR LTR Gypsy 0.0 -MICROPIA_I-int LTR Gypsy 0.0 -MICROPIA_LTR LTR Gypsy 0.0 -Mariner2_DM DNA TcMar-Tc1 0.0 -NINJA_I-int LTR Pao 0.0 -NOMAD_I-int LTR Gypsy 0.0 -PROTOP_A DNA P 18.0 -PROTOP_B DNA P 0.0 -QUASIMODO2-I_DM LTR Gypsy 19.0 -QUASIMODO2-LTR_DM LTR Gypsy 0.0 -QUASIMODO_I-int LTR Gypsy 3.0 -QUASIMODO_LTR LTR Gypsy 1.0 -R1_DM LINE R1 0.0 -ROOA_I-int LTR Pao 0.0 -ROOA_LTR LTR Pao 0.0 -ROVER-I_DM LTR Gypsy 188.0 -ROVER-LTR_DM LTR Gypsy 1.0 -S2_DM DNA TcMar-Tc1 0.0 -STALKER4_I-int LTR Gypsy 28.0 -STALKER4_LTR LTR Gypsy 0.0 -S_DM DNA TcMar-Tc1 25.0 -Stalker2_I-int LTR Gypsy 32.0 -Stalker2_LTR LTR Gypsy 2.0 -TART-A LINE Jockey 2.0 -TART_B1 LINE Jockey 10.0 -TC1-2_DM DNA TcMar-Tc1 0.0 -TC1_DM DNA TcMar-Tc1 0.0 -TLD2 LTR Gypsy 0.0 -TRANSIB1 DNA CMC-Transib 0.0 -TRANSIB2 DNA CMC-Transib 12.0 -ZAM_I-int LTR Gypsy 0.0 -_AACACA_n Simple_repeat Simple_repeat 0.0 -_AAT_n Simple_repeat Simple_repeat 0.0 -_ACAATAG_n Simple_repeat Simple_repeat 0.0 -_ACC_n Simple_repeat Simple_repeat 0.0 -_AGAGAAG_n Simple_repeat Simple_repeat 0.0 -_AGAGA_n Simple_repeat Simple_repeat 0.0 -_ATAAT_n Simple_repeat Simple_repeat 0.0 -_ATATATT_n Simple_repeat Simple_repeat 0.0 -_ATATTAT_n Simple_repeat Simple_repeat 0.0 -_ATTTTT_n Simple_repeat Simple_repeat 0.0 -_ATT_n Simple_repeat Simple_repeat 0.0 -_AT_n Simple_repeat Simple_repeat 0.0 -_A_n Simple_repeat Simple_repeat 0.0 -_CATA_n Simple_repeat Simple_repeat 0.0 -_CTTTT_n Simple_repeat Simple_repeat 0.0 -_GAGAA_n Simple_repeat Simple_repeat 0.0 -_GCCTTT_n Simple_repeat Simple_repeat 0.0 -_TAATAT_n Simple_repeat Simple_repeat 0.0 -_TAATA_n Simple_repeat Simple_repeat 0.0 -_TATAAAA_n Simple_repeat Simple_repeat 0.0 -_TATAA_n Simple_repeat Simple_repeat 0.0 -_TATCATG_n Simple_repeat Simple_repeat 0.0 -_TA_n Simple_repeat Simple_repeat 0.0 -_TGTTG_n Simple_repeat Simple_repeat 0.0 -_TTATATA_n Simple_repeat Simple_repeat 0.0 -_TTATAT_n Simple_repeat Simple_repeat 0.0 -_TTATA_n Simple_repeat Simple_repeat 0.0 -_TTA_n Simple_repeat Simple_repeat 0.0 -_TTCTT_n Simple_repeat Simple_repeat 0.0 -_TTC_n Simple_repeat Simple_repeat 0.0 -_TTTAT_n Simple_repeat Simple_repeat 0.0 -_TTTA_n Simple_repeat Simple_repeat 0.0 -_TTTC_n Simple_repeat Simple_repeat 0.0 -_TTTGA_n Simple_repeat Simple_repeat 0.0 -_TTTTAG_n Simple_repeat Simple_repeat 0.0 -_TTTTCTT_n Simple_repeat Simple_repeat 0.0 -_TTTTC_n Simple_repeat Simple_repeat 0.0 -_T_n Simple_repeat Simple_repeat 0.0 +A-rich Low_complexity Low_complexity 4.72 +ACCORD2_I-int LTR Gypsy 4.72 +ACCORD2_LTR LTR Gypsy 4.72 +ACCORD_I-int LTR Gypsy 4.72 +BARI1 DNA TcMar-Tc1 4.72 +BATUMI_LTR LTR Pao 4.72 +BS LINE Jockey 4.72 +BS2 LINE Jockey 33.72 +BURDOCK_I-int LTR Gypsy 4.72 +Baggins1 LINE LOA 4.72 +Bica_I-int LTR Gypsy 23.72 +Bica_LTR LTR Gypsy 4.72 +CIRCE LTR Gypsy 4.72 +Chouto_I-int LTR Gypsy 4.72 +Copia1-I_DM LTR Copia 4.72 +Copia_I-int LTR Copia 12656.72 +Copia_LTR LTR Copia 138.72 +DIVER2_I-int LTR Pao 5.72 +DIVER2_LTR LTR Pao 4.72 +DM1731_I-int LTR Copia 7.72 +DM1731_LTR LTR Copia 4.72 +DM176_I-int LTR Gypsy 4.72 +DM412 LTR Gypsy 4.72 +DM412B_LTR LTR Gypsy 4.72 +DMCR1A LINE CR1 6.72 +DMLTR5 LTR Gypsy 4.72 +DMRT1A LINE R1 4.72 +DMRT1B LINE R1 39.72 +DMRT1C LINE R1 4.72 +DNAREP1_DM RC Helitron 4.72 +DOC2_DM LINE Jockey 4.72 +DOC3_DM LINE Jockey 4.72 +FB4_DM DNA TcMar-Tc1 19.72 +FROGGER_I-int LTR Copia 4.72 +FW2_DM LINE Jockey 4.72 +G3_DM LINE Jockey 4.72 +G5A_DM LINE Jockey 4.72 +G5_DM LINE Jockey 4.72 +G6_DM LINE Jockey 4.72 +GA-rich Low_complexity Low_complexity 4.72 +GTWIN_I-int LTR Gypsy 4.72 +G_DM LINE Jockey 4.72 +Gypsy11_I-int LTR Gypsy 4.72 +Gypsy11_LTR LTR Gypsy 4.72 +Gypsy12_LTR LTR Gypsy 4.72 +Gypsy2-I_DM LTR Gypsy 5.72 +Gypsy2-LTR_DM LTR Gypsy 4.72 +Gypsy3_LTR LTR Gypsy 4.72 +Gypsy4_I-int LTR Gypsy 4.72 +Gypsy5_I-int LTR Gypsy 4.72 +Gypsy6A_LTR LTR Gypsy 4.72 +Gypsy6_I-int LTR Gypsy 16.72 +Gypsy8_I-int LTR Gypsy 4.72 +Gypsy8_LTR LTR Gypsy 4.72 +Gypsy9_I-int LTR Gypsy 4.72 +Gypsy_I-int LTR Gypsy 19.72 +Gypsy_LTR LTR Gypsy 4.72 +HELENA_RT LINE Jockey 4.72 +HETA LINE Jockey 16.72 +HMSBEAGLE_I-int LTR Gypsy 5.72 +IDEFIX_I-int LTR Gypsy 4.72 +IDEFIX_LTR LTR Gypsy 4.72 +Invader1_I-int LTR Gypsy 4.72 +Invader1_LTR LTR Gypsy 4.72 +Invader2_I-int LTR Gypsy 4.72 +Invader4_I-int LTR Gypsy 4.72 +Invader4_LTR LTR Gypsy 4.72 +Invader5_I-int LTR Gypsy 4.72 +Invader5_LTR LTR Gypsy 4.72 +Invader6_I-int LTR Gypsy 4.72 +Invader6_LTR LTR Gypsy 4.72 +MAX_I-int LTR Pao 31.72 +MAX_LTR LTR Pao 5.72 +MDG1_I-int LTR Gypsy 4.72 +MDG1_LTR LTR Gypsy 4.72 +MDG3_I-int LTR Gypsy 74.72 +MDG3_LTR LTR Gypsy 4.72 +MICROPIA_I-int LTR Gypsy 4.72 +MICROPIA_LTR LTR Gypsy 4.72 +Mariner2_DM DNA TcMar-Tc1 4.72 +NINJA_I-int LTR Pao 4.72 +NOMAD_I-int LTR Gypsy 4.72 +PROTOP_A DNA P 22.72 +PROTOP_B DNA P 4.72 +QUASIMODO2-I_DM LTR Gypsy 23.72 +QUASIMODO2-LTR_DM LTR Gypsy 4.72 +QUASIMODO_I-int LTR Gypsy 7.72 +QUASIMODO_LTR LTR Gypsy 5.72 +R1_DM LINE R1 4.72 +ROOA_I-int LTR Pao 4.72 +ROOA_LTR LTR Pao 4.72 +ROVER-I_DM LTR Gypsy 192.72 +ROVER-LTR_DM LTR Gypsy 5.72 +S2_DM DNA TcMar-Tc1 4.72 +STALKER4_I-int LTR Gypsy 32.72 +STALKER4_LTR LTR Gypsy 4.72 +S_DM DNA TcMar-Tc1 29.72 +Stalker2_I-int LTR Gypsy 36.72 +Stalker2_LTR LTR Gypsy 6.72 +TART-A LINE Jockey 6.72 +TART_B1 LINE Jockey 14.72 +TC1-2_DM DNA TcMar-Tc1 4.72 +TC1_DM DNA TcMar-Tc1 4.72 +TLD2 LTR Gypsy 4.72 +TRANSIB1 DNA CMC-Transib 4.72 +TRANSIB2 DNA CMC-Transib 16.72 +ZAM_I-int LTR Gypsy 4.72 +_AACACA_n Simple_repeat Simple_repeat 4.72 +_AAT_n Simple_repeat Simple_repeat 4.72 +_ACAATAG_n Simple_repeat Simple_repeat 4.72 +_ACC_n Simple_repeat Simple_repeat 4.72 +_AGAGAAG_n Simple_repeat Simple_repeat 4.72 +_AGAGA_n Simple_repeat Simple_repeat 4.72 +_ATAAT_n Simple_repeat Simple_repeat 4.72 +_ATATATT_n Simple_repeat Simple_repeat 4.72 +_ATATTAT_n Simple_repeat Simple_repeat 4.72 +_ATTTTT_n Simple_repeat Simple_repeat 4.72 +_ATT_n Simple_repeat Simple_repeat 4.72 +_AT_n Simple_repeat Simple_repeat 4.72 +_A_n Simple_repeat Simple_repeat 4.72 +_CATA_n Simple_repeat Simple_repeat 4.72 +_CTTTT_n Simple_repeat Simple_repeat 4.72 +_GAGAA_n Simple_repeat Simple_repeat 4.72 +_GCCTTT_n Simple_repeat Simple_repeat 4.72 +_TAATAT_n Simple_repeat Simple_repeat 4.72 +_TAATA_n Simple_repeat Simple_repeat 4.72 +_TATAAAA_n Simple_repeat Simple_repeat 4.72 +_TATAA_n Simple_repeat Simple_repeat 4.72 +_TATCATG_n Simple_repeat Simple_repeat 4.72 +_TA_n Simple_repeat Simple_repeat 4.72 +_TGTTG_n Simple_repeat Simple_repeat 4.72 +_TTATATA_n Simple_repeat Simple_repeat 4.72 +_TTATAT_n Simple_repeat Simple_repeat 4.72 +_TTATA_n Simple_repeat Simple_repeat 4.72 +_TTA_n Simple_repeat Simple_repeat 4.72 +_TTCTT_n Simple_repeat Simple_repeat 4.72 +_TTC_n Simple_repeat Simple_repeat 4.72 +_TTTAT_n Simple_repeat Simple_repeat 4.72 +_TTTA_n Simple_repeat Simple_repeat 4.72 +_TTTC_n Simple_repeat Simple_repeat 4.72 +_TTTGA_n Simple_repeat Simple_repeat 4.72 +_TTTTAG_n Simple_repeat Simple_repeat 4.72 +_TTTTCTT_n Simple_repeat Simple_repeat 4.72 +_TTTTC_n Simple_repeat Simple_repeat 4.72 +_T_n Simple_repeat Simple_repeat 4.72