Mercurial > repos > artbio > repenrich2
changeset 8:567549a49eb2 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit b3b166a8e991f49227e4888b8065b57cec0ba949
| author | artbio |
|---|---|
| date | Thu, 25 Apr 2024 09:06:48 +0000 |
| parents | 61e0404f0d76 |
| children | 2b61c6407efb |
| files | RepEnrich2.py macros.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 | 8 files changed, 331 insertions(+), 330 deletions(-) [+] |
line wrap: on
line diff
--- a/RepEnrich2.py Tue Apr 23 21:44:44 2024 +0000 +++ b/RepEnrich2.py Thu Apr 25 09:06:48 2024 +0000 @@ -110,7 +110,7 @@ write to files to save memory ''' metagenome, fastqfile = args - b_opt = "-k 1 -p 1 --quiet --no-hd" + b_opt = "-k 1 -p 1 --quiet --no-hd --no-unal" command = shlex.split(f"bowtie2 {b_opt} -x {metagenome} {fastqfile}") bowtie_align = subprocess.run(command, check=True, capture_output=True, text=True).stdout @@ -148,6 +148,7 @@ repeats_by_reads[read].append(repname) for repname in repeats_by_reads: repeats_by_reads[repname] = list(set(repeats_by_reads[repname])) + # this repeats_by_reads dictionary is far too big # 3 dictionnaries and 1 pointer variable to be populated fractionalcounts = defaultdict(float)
--- a/macros.xml Tue Apr 23 21:44:44 2024 +0000 +++ b/macros.xml Thu Apr 25 09:06:48 2024 +0000 @@ -1,6 +1,6 @@ <macros> <token name="@TOOL_VERSION@">2.31.1</token> - <token name="@VERSION_SUFFIX@">7</token> + <token name="@VERSION_SUFFIX@">8</token> <token name="@PROFILE@">23.0</token> <xml name="repenrich_requirements">
--- a/test-data/chrY_paired_class_fraction_counts.tab Tue Apr 23 21:44:44 2024 +0000 +++ b/test-data/chrY_paired_class_fraction_counts.tab Thu Apr 25 09:06:48 2024 +0000 @@ -1,6 +1,6 @@ -DNA 194.66 -LINE 279.83 -LTR 27051.62 -Low_complexity 8.48 -RC 4.24 -Simple_repeat 161.17 +DNA 184.0 +LINE 227.0 +LTR 27179.0 +Low_complexity 0.67 +RC 0.0 +Simple_repeat 90.33
--- a/test-data/chrY_paired_family_fraction_counts.tab Tue Apr 23 21:44:44 2024 +0000 +++ b/test-data/chrY_paired_family_fraction_counts.tab Thu Apr 25 09:06:48 2024 +0000 @@ -1,13 +1,13 @@ -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 +CMC-Transib 30.0 +CR1 4.0 +Copia 25880.0 +Gypsy 1238.0 +Helitron 0.0 +Jockey 107.0 +LOA 0.0 +Low_complexity 0.67 +P 60.0 +Pao 61.0 +R1 116.0 +Simple_repeat 90.33 +TcMar-Tc1 94.0
--- a/test-data/chrY_paired_fraction_counts.tab Tue Apr 23 21:44:44 2024 +0000 +++ b/test-data/chrY_paired_fraction_counts.tab Thu Apr 25 09:06:48 2024 +0000 @@ -1,145 +1,145 @@ -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-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 49.0 +Bica_LTR LTR Gypsy 1.0 +CIRCE LTR Gypsy 0.0 +Chouto_I-int LTR Gypsy 1.5 +Copia1-I_DM LTR Copia 0.0 +Copia_I-int LTR Copia 25220.0 +Copia_LTR LTR Copia 652.0 +DIVER2_I-int LTR Pao 1.0 +DIVER2_LTR LTR Pao 2.0 +DM1731_I-int LTR Copia 8.0 +DM1731_LTR LTR Copia 0.0 +DM176_I-int LTR Gypsy 0.0 +DM412 LTR Gypsy 12.5 +DM412B_LTR LTR Gypsy 0.0 +DMCR1A LINE CR1 4.0 +DMLTR5 LTR Gypsy 0.0 +DMRT1A LINE R1 0.0 +DMRT1B LINE R1 116.0 +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 41.0 +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 0.67 +GTWIN_I-int LTR Gypsy 12.5 +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 4.0 +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 1.0 +Gypsy6_I-int LTR Gypsy 31.0 +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 8.0 +IDEFIX_LTR LTR Gypsy 2.0 +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 56.0 +MAX_LTR LTR Pao 2.0 +MDG1_I-int LTR Gypsy 0.0 +MDG1_LTR LTR Gypsy 0.0 +MDG3_I-int LTR Gypsy 156.5 +MDG3_LTR LTR Gypsy 2.5 +MICROPIA_I-int LTR Gypsy 51.0 +MICROPIA_LTR LTR Gypsy 2.0 +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 50.0 +PROTOP_B DNA P 10.0 +QUASIMODO2-I_DM LTR Gypsy 43.0 +QUASIMODO2-LTR_DM LTR Gypsy 0.0 +QUASIMODO_I-int LTR Gypsy 108.0 +QUASIMODO_LTR LTR Gypsy 23.0 +R1_DM LINE R1 0.0 +ROOA_I-int LTR Pao 0.0 +ROOA_LTR LTR Pao 0.0 +ROVER-I_DM LTR Gypsy 414.0 +ROVER-LTR_DM LTR Gypsy 6.0 +S2_DM DNA TcMar-Tc1 0.0 +STALKER4_I-int LTR Gypsy 143.5 +STALKER4_LTR LTR Gypsy 25.0 +S_DM DNA TcMar-Tc1 53.0 +Stalker2_I-int LTR Gypsy 103.0 +Stalker2_LTR LTR Gypsy 3.0 +TART-A LINE Jockey 4.0 +TART_B1 LINE Jockey 21.0 +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 2.17 +_AGAGA_n Simple_repeat Simple_repeat 43.0 +_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 45.17 +_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/test-data/chrY_single_class_fraction_counts.tab Tue Apr 23 21:44:44 2024 +0000 +++ b/test-data/chrY_single_class_fraction_counts.tab Thu Apr 25 09:06:48 2024 +0000 @@ -1,6 +1,6 @@ -DNA 121.89 -LINE 184.34 -LTR 13554.36 -Low_complexity 9.43 -RC 4.72 -Simple_repeat 179.26 +DNA 109.0 +LINE 129.0 +LTR 13705.0 +Low_complexity 0.0 +RC 0.0 +Simple_repeat 91.0
--- a/test-data/chrY_single_family_fraction_counts.tab Tue Apr 23 21:44:44 2024 +0000 +++ b/test-data/chrY_single_family_fraction_counts.tab Thu Apr 25 09:06:48 2024 +0000 @@ -1,13 +1,13 @@ -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 +CMC-Transib 15.0 +CR1 2.0 +Copia 12865.0 +Gypsy 805.0 +Helitron 0.0 +Jockey 54.0 +LOA 0.0 +Low_complexity 0.0 +P 44.0 +Pao 35.0 +R1 73.0 +Simple_repeat 91.0 +TcMar-Tc1 50.0
--- a/test-data/chrY_single_fraction_counts.tab Tue Apr 23 21:44:44 2024 +0000 +++ b/test-data/chrY_single_fraction_counts.tab Thu Apr 25 09:06:48 2024 +0000 @@ -1,145 +1,145 @@ -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 +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 31.0 +Bica_LTR LTR Gypsy 0.0 +CIRCE LTR Gypsy 0.0 +Chouto_I-int LTR Gypsy 1.5 +Copia1-I_DM LTR Copia 0.0 +Copia_I-int LTR Copia 12703.0 +Copia_LTR LTR Copia 157.0 +DIVER2_I-int LTR Pao 1.0 +DIVER2_LTR LTR Pao 2.0 +DM1731_I-int LTR Copia 5.0 +DM1731_LTR LTR Copia 0.0 +DM176_I-int LTR Gypsy 0.0 +DM412 LTR Gypsy 12.5 +DM412B_LTR LTR Gypsy 0.0 +DMCR1A LINE CR1 2.0 +DMLTR5 LTR Gypsy 0.0 +DMRT1A LINE R1 0.0 +DMRT1B LINE R1 73.0 +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 22.0 +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 12.5 +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 3.0 +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 18.0 +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 16.0 +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 6.0 +IDEFIX_LTR LTR Gypsy 2.0 +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 31.0 +MAX_LTR LTR Pao 1.0 +MDG1_I-int LTR Gypsy 0.0 +MDG1_LTR LTR Gypsy 0.0 +MDG3_I-int LTR Gypsy 80.0 +MDG3_LTR LTR Gypsy 3.0 +MICROPIA_I-int LTR Gypsy 51.0 +MICROPIA_LTR LTR Gypsy 2.0 +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 37.5 +PROTOP_B DNA P 6.5 +QUASIMODO2-I_DM LTR Gypsy 22.0 +QUASIMODO2-LTR_DM LTR Gypsy 0.0 +QUASIMODO_I-int LTR Gypsy 100.0 +QUASIMODO_LTR LTR Gypsy 24.0 +R1_DM LINE R1 0.0 +ROOA_I-int LTR Pao 0.0 +ROOA_LTR LTR Pao 0.0 +ROVER-I_DM LTR Gypsy 224.0 +ROVER-LTR_DM LTR Gypsy 5.0 +S2_DM DNA TcMar-Tc1 0.0 +STALKER4_I-int LTR Gypsy 107.0 +STALKER4_LTR LTR Gypsy 23.0 +S_DM DNA TcMar-Tc1 28.0 +Stalker2_I-int LTR Gypsy 58.5 +Stalker2_LTR LTR Gypsy 2.0 +TART-A LINE Jockey 2.0 +TART_B1 LINE Jockey 11.0 +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 15.0 +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 2.5 +_AGAGA_n Simple_repeat Simple_repeat 43.0 +_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 45.5 +_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