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# Triesch _et al._ (2023) - Transposable elements contribute to the establishment of the glycine shuttle in Brassicaceae species
This project was mainly conducted at the [Institute of Plant Biochemistry at HHU](https://www.plant-biochemistry.hhu.de/en/).
## Contributors
- Sebastian Triesch
- https://orcid.org/0000-0001-7796-4631
- @setri100
- Alisandra K. Denton
- https://orcid.org/0000-0002-1132-0224
- Jacques W. Bouvier
- https://orcid.org/0000-0002-6617-0112
- Jan P. Buchmann
- https://orcid.org/0000-0002-6842-1229
- Vanessa Reichel-Deland
- https://orcid.org/0000-0003-2449-6402
- Ricardo Nuno Ferreira Martins Guerreiro
- Noah Busch
- Urte Schlüter
- https://orcid.org/0000-0002-9134-6511
- Benjamin Stich
- https://orcid.org/0000-0001-6791-8068
- Steven Kelly
- https://orcid.org/0000-0003-1250-7055
- Andreas P.M.Weber
- https://orcid.org/0000-0003-0970-4672
## Abstract
C3-C4 intermediate photosynthesis has evolved at least five times convergently in the Brassicaceae, despite
this family lacking _bona fide_ C4 species. The establishment of this carbon concentrating mechanism is known
to require a complex suite of ultrastructural modifications as well as changes in spatial expression patterns,
which are both thought to be underpinned by a reconfiguration of existing gene-regulatory networks. However,
to date, the mechanisms which underpin the reconfiguration of these gene networks are largely unknown.
In this study, we used a pan-genomic association approach to identify genomic features that could confer
differential gene expression toward the C3-C4 intermediate state by analysing eight C3 species and seven
C3-C4 species from five independent origins in the Brassicaceae. We found a strong correlation between
transposable element (TE) insertions in cis-regulatory regions and the C3-C4 intermediacy. Specifically, our
study revealed 113 gene models in which presence of a TE within a gene correlates with C3-C4 intermediate
photosynthesis. In this set, genes involved in the photorespiratory glycine shuttle are enriched, including the
glycine decarboxylase P-protein whose expression domain undergoes a spatial shift during the transition to
C3-C4 photosynthesis. When further interrogating this gene, we discovered independent TE insertions in its
upstream region which we conclude to be responsible for causing the spatial shift in _GLDP1_ gene expression.
Our findings hint at a pivotal role of TEs in the evolution of C3-C4 intermediacy, especially in mediating
differential spatial gene expression.
## Breakdown of the computation analysis
## Creating structural gene annotation with Helixer
This was performed at the commits Helixer bb840b4, GeenuFF 1f6cffb, and
HelixerPost 08c6215
Updates to the code since mean that this is not the _recommended_ way anymore,
but uncommented code in the scripts are provided exactly as used for accuracy.
Comments have been added to indicate where scripts or commands would need to be
changed to run with more current (e.g. v0.3) versions of the code.
And for clarity / explanation.
#### Structure
The scripts assume the input is provided in the following format
```
raw/<researcher>/
├── b_gravinae
│ └── b_gravinae.fasta
├── b_juncea
│ └── b_juncea.fasta
├── b_napus
│ └── b_napus.fasta
├── b_nigra
│ └── b_nigra.fasta
...
```
The final gff3 output + log files will then end up here
```
helixer_post/<researcher>/
├── b_gravinae
│ ├── b_gravinae.gff3
│ ├── hp.err
│ └── hp.out
├── b_juncea
│ ├── b_juncea.gff3
│ ├── hp.err
│ └── hp.out
├── b_napus
│ ├── b_napus.gff3
│ ├── hp.err
│ └── hp.out
├── b_nigra
│ ├── b_nigra.gff3
│ ├── hp.err
│ └── hp.out
...
```
(example excerpt only)
#### Annotating
##### generate numeric encoding of genome sequence
This step takes the CATGs from the fasta file, and encodes
them as 1-hot (except ambiguity characters) numeric
vectors for inputting into our network.
example to run one sequence
```
bash toh5.sh raw/<researcher>/b_gravinae/b_gravinae.fasta
```
#### raw base-wise predictions of genic class & phase
This part has to run on the GPU, and it was easiest
to do so for the number of species used with nni,
which uses the files 'config.yml' and 'search_space.json'.
###### prep
###### Acquire the trained model.
E.g.
```
wget https://uni-duesseldorf.sciebo.de/s/C68s4YLv5ZqqXus/download
mv download land_plant_v0.3_m_0100.h5
```
(for clarity note that `land_plant_v0.3_m_0100.h5` and `fullmoon_211117_17.h5`
are two names for the same model)
###### prep search\_space.json
This file requires full paths to the model and the h5 files created
above to be set exactly for the machine in question. The provided
file is an example only.
##### Start all predictions
```
export hppath=<path/to/repository>/Helixer
nnictl create -c config.yml
```
which then generates a folder `$HOME/nni-experiments/<NNI-ID>`
with the results. Each species in search_space.json,
will be in a different trial folder: `$HOME/nni-experiments/<NNI-ID>/trials/<TRIAL-ID>`
##### post processing into final predictions
run once for each trial ID / species
```
bash helixer_post.sh $HOME/nni-experiments/<NNI-ID>/trials/<TRIAL-ID>
```
And you're done, this should create the gff3 files, e.g.
`helixer_post/<researcher>/b_gravinae/b_gravinae.gff3`
#### Recommendation.
This three step process made sense when running the previous version
of the code and still does for running many genomes with unbalanced
GPU vs CPU availability.
However, to run on a single genome and also just to take advantage of usability
improvements, the above could now be accomplished for any single genome
as shown below using b\_granvinae as an example (structure simplified).
```
Helixer.py --fasta-path b_gravinae.fasta \
--gff-output-path b_gravinae.gff3 --species b_gravinae
--overlap-core-length=53460 --overlap-offset=13365
--lineage land_plant
```
This method additionally provides exact instructions on how to download the
best available model for the lineage, if not already present.
## performing TE annotation using EDTA
run EDTA using something like: <br />
```bash
perl EDTA.pl --genome <genome> --anno 1 --sensitive 1 --overwrite 0
```
EDTA will produce multiple outputs:
- for FRAGMENTED TEs use: .fasta.mod.EDTA.TEanno.gff3 file
- for INTACT TEs use: .fasta.mod.EDTA.intact.gff3 file
make sure to delete headers starting with ### in the respecrtive files, they can't be read by numpy!
### Fig. 2: EDTA results analysis:
The [code for the results presented in Fig.2](https://git.nfdi4plants.org/hhu-plant-biochemistry/triesch2023_brassicaceae_transposons/-/blob/main/workflows/Fig2_genome_size.ipynb) contains a basic analysis of the `EDTA` results. The genome size were hard-coded from the amount of bases in the respective genome .fasta files. It was distinguished between the "FRAGMENTED" and "INTACT" outputs of `EDTA`.
### Fig.3: TE classes
The [code for Fig.3](https://git.nfdi4plants.org/hhu-plant-biochemistry/triesch2023_brassicaceae_transposons/-/blob/main/workflows/Fig3_TE_types.ipynb) contains a breakdown of the TE classes as analyzed in `EDTA`. The lengths of the TEs (as numbers of base pairs) were counted and compared.
### Fig.4: LTR age calculation
For the [LTR age calculation as presented in Fig.4](https://git.nfdi4plants.org/hhu-plant-biochemistry/triesch2023_brassicaceae_transposons/-/blob/main/workflows/Fig4_LTR_age.ipynb) LTR-TEs were extracted from the `EDTA` results, sorted by photosynthesis phenotype and visualized. Furthermore, statistical parameters were calculated.
### Fig.5 f: TE-gene association:
The [TE-gene association analysis](https://git.nfdi4plants.org/hhu-plant-biochemistry/triesch2023_brassicaceae_transposons/-/blob/main/workflows/Fig5_TE_gene_association.py) was conducted using the .gff3 annotation files from `Helixer` and `EDTA`. Only the INTACT TEs predicted by `EDTA` were used, the FRAGMENTED were ignored to reduce the amount of false-positive hits. For each contigs, it was check if a TE was starting/ending in a gene, residing inside a gene, spanning a gene or residing up- or downstream of a gene. Strand specificity was considered. Results were written to a `.tsv` file and visualized using [this code](https://git.nfdi4plants.org/hhu-plant-biochemistry/triesch2023_brassicaceae_transposons/-/blob/main/workflows/Fig5_stackedbar.ipynb). <br>
Single genes were visualized using [this code snippet](https://git.nfdi4plants.org/hhu-plant-biochemistry/triesch2023_brassicaceae_transposons/-/blob/main/workflows/Fig6_single_gene_visualization.ipynb). <br>
Statistics were performed using [this code](https://git.nfdi4plants.org/hhu-plant-biochemistry/triesch2023_brassicaceae_transposons/-/blob/main/workflows/Tab1_statistics.ipynb).
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This diff is collapsed.
species type location number_of_associated_tes
a_alpina c3 start_end 1665
a_alpina c3 upstream 1801
a_alpina c3 downstream 639
a_alpina c3 inside 234
a_thaliana c3 start_end 654
a_thaliana c3 upstream 292
a_thaliana c3 downstream 82
a_thaliana c3 inside 66
b_gravinae_unkown c34 start_end 1866
b_gravinae_unkown c34 upstream 2030
b_gravinae_unkown c34 downstream 833
b_gravinae_unkown c34 inside 397
b_oleracea c3 start_end 834
b_oleracea c3 upstream 1128
b_oleracea c3 downstream 488
b_oleracea c3 inside 294
b_tournefortii c3 start_end 154
b_tournefortii c3 upstream 125
b_tournefortii c3 downstream 79
b_tournefortii c3 inside 41
c_annua c3 start_end 1130
c_annua c3 upstream 1249
c_annua c3 downstream 631
c_annua c3 inside 239
c_gynandra c4 start_end 1866
c_gynandra c4 upstream 2030
c_gynandra c4 downstream 833
c_gynandra c4 inside 397
d_erucoides c34 start_end 1875
d_erucoides c34 upstream 1812
d_erucoides c34 downstream 747
d_erucoides c34 inside 286
d_tenuifolia c34 start_end 1534
d_tenuifolia c34 upstream 1862
d_tenuifolia c34 downstream 816
d_tenuifolia c34 inside 310
d_viminea c3 start_end 1147
d_viminea c3 upstream 1087
d_viminea c3 downstream 460
d_viminea c3 inside 218
h_incana1 c3 start_end 1564
h_incana1 c3 upstream 1528
h_incana1 c3 downstream 584
h_incana1 c3 inside 296
h_incana3 c34 start_end 1144
h_incana3 c34 upstream 1144
h_incana3 c34 downstream 422
h_incana3 c34 inside 196
m_arvensis c34 start_end 1449
m_arvensis c34 upstream 2285
m_arvensis c34 downstream 1017
m_arvensis c34 inside 446
m_moricandioides c3 start_end 899
m_moricandioides c3 upstream 1273
m_moricandioides c3 downstream 535
m_moricandioides c3 inside 227
m_nitens c34 start_end 693
m_nitens c34 upstream 1231
m_nitens c34 downstream 531
m_nitens c34 inside 251
m_suffruticosa c34 start_end 842
m_suffruticosa c34 upstream 1450
m_suffruticosa c34 downstream 653
m_suffruticosa c34 inside 257
This diff is collapsed.
a_alpina c3 NaN
a_thaliana c3 60.03
b_gravinae_unkown c34 32.34
b_oleracea c3 50.52
b_tournefortii c3 48.22
c_annua c3 55.33
c_gynandra c4 4.28
d_erucoides c34 33.04
d_tenuifolia c34 12.68
d_viminea c3 51.08
h_incana1 c3 50.5
h_incana3 c34 38.37
m_arvensis c34 24.42
m_moricandioides c3 51.59
m_nitens c34 21.04
m_suffruticosa c34 24.87
734765 contig_4352 HelixerPost gene 8689 9981 . - . ID=m_arvensis_contig_4352_000002
441753 contig_2043 HelixerPost gene 41863 43211 . - . ID=m_arvensis_contig_2043_000016
720147 contig_5732 HelixerPost gene 9495 10636 . - . ID=m_arvensis_contig_5732_000006
566703 scaffold_23574 HelixerPost gene 37966 39559 . - . ID=m_arvensis_scaffold_23574_000001
509658 contig_4598 HelixerPost gene 9886 10713 . - . ID=m_arvensis_contig_4598_000008
729308 contig_17565 HelixerPost gene 5258 6669 . + . ID=m_arvensis_contig_17565_000003
729322 contig_17565 HelixerPost gene 6671 7029 . + . ID=m_arvensis_contig_17565_000004
641102 contig_2215 HelixerPost gene 12820 14656 . + . ID=m_arvensis_contig_2215_000002
641110 contig_2215 HelixerPost gene 15899 17232 . + . ID=m_arvensis_contig_2215_000003
641102 contig_2215 HelixerPost gene 12820 14656 . + . ID=m_arvensis_contig_2215_000002
641110 contig_2215 HelixerPost gene 15899 17232 . + . ID=m_arvensis_contig_2215_000003
641102 contig_2215 HelixerPost gene 12820 14656 . + . ID=m_arvensis_contig_2215_000002
641110 contig_2215 HelixerPost gene 15899 17232 . + . ID=m_arvensis_contig_2215_000003
641188 contig_2215 HelixerPost gene 24453 24911 . - . ID=m_arvensis_contig_2215_000010
641196 contig_2215 HelixerPost gene 22928 24451 . - . ID=m_arvensis_contig_2215_000011
646741 contig_15434 HelixerPost gene 13245 15620 . - . ID=m_arvensis_contig_15434_000009
339364 contig_2021 HelixerPost gene 49625 50675 . - . ID=m_arvensis_contig_2021_000017
316638 contig_2995 HelixerPost gene 63359 64771 . - . ID=m_arvensis_contig_2995_000002
481041 contig_3077 HelixerPost gene 72727 73338 . - . ID=m_arvensis_contig_3077_000011
644261 contig_1336 HelixerPost gene 41572 42263 . - . ID=m_arvensis_contig_1336_000014
425919 contig_1399 HelixerPost gene 8604 9534 . - . ID=m_arvensis_contig_1399_000003
425931 contig_1399 HelixerPost gene 8097 8598 . - . ID=m_arvensis_contig_1399_000004
562919 contig_1812 HelixerPost gene 6556 8609 . - . ID=m_arvensis_contig_1812_000006
108885 contig_1101 HelixerPost gene 127651 128994 . - . ID=m_arvensis_contig_1101_000012
112861 contig_1453 HelixerPost gene 29426 30279 . - . ID=m_arvensis_contig_1453_000008
404261 contig_5363 HelixerPost gene 19298 19629 . - . ID=m_arvensis_contig_5363_000017
404159 contig_5363 HelixerPost gene 93475 94329 . - . ID=m_arvensis_contig_5363_000008
132097 contig_525 HelixerPost gene 40400 41839 . - . ID=m_arvensis_contig_525_000020
67826 contig_1608 HelixerPost gene 152060 153204 . - . ID=m_arvensis_contig_1608_000003
265347 contig_2267 HelixerPost gene 85110 86865 . - . ID=m_arvensis_contig_2267_000005
715368 contig_9236 HelixerPost gene 18226 19489 . + . ID=m_arvensis_contig_9236_000001
302572 contig_4293 HelixerPost gene 82325 83559 . + . ID=m_arvensis_contig_4293_000003
103656 contig_3619 HelixerPost gene 5065 6601 . - . ID=m_arvensis_contig_3619_000060
103526 contig_3619 HelixerPost gene 59615 60790 . - . ID=m_arvensis_contig_3619_000049
103212 contig_3619 HelixerPost gene 181472 181743 . - . ID=m_arvensis_contig_3619_000025
103218 contig_3619 HelixerPost gene 180451 180866 . - . ID=m_arvensis_contig_3619_000026
754846 contig_11113 HelixerPost gene 7119 7721 . - . ID=m_arvensis_contig_11113_000002
187001 contig_3941 HelixerPost gene 11390 12859 . - . ID=m_arvensis_contig_3941_000005
213774 contig_3039 HelixerPost gene 127767 130410 . - . ID=m_arvensis_contig_3039_000007
733454 contig_6594 HelixerPost gene 11679 13463 . - . ID=m_arvensis_contig_6594_000002
753505 contig_25679 HelixerPost gene 4784 6726 . + . ID=m_arvensis_contig_25679_000001
305787 contig_2309 HelixerPost gene 78853 80184 . + . ID=m_arvensis_contig_2309_000006
367786 contig_4080 HelixerPost gene 23278 23709 . - . ID=m_arvensis_contig_4080_000008
367735 contig_4080 HelixerPost gene 84255 88821 . + . ID=m_arvensis_contig_4080_000006
161719 contig_3533 HelixerPost gene 170045 175784 . + . ID=m_arvensis_contig_3533_000003
416012 contig_1902 HelixerPost gene 56344 56766 . - . ID=m_arvensis_contig_1902_000011
626323 contig_5170 HelixerPost gene 40803 41621 . - . ID=m_arvensis_contig_5170_000005
230619 contig_5783 HelixerPost gene 18532 20592 . - . ID=m_arvensis_contig_5783_000006
230643 contig_5783 HelixerPost gene 17920 18479 . - . ID=m_arvensis_contig_5783_000007
401302 contig_13352 HelixerPost gene 52361 54263 . - . ID=m_arvensis_contig_13352_000016
401314 contig_13352 HelixerPost gene 52188 52359 . - . ID=m_arvensis_contig_13352_000017
417970 contig_3917 HelixerPost gene 15308 19982 . + . ID=m_arvensis_contig_3917_000002
418004 contig_3917 HelixerPost gene 20665 21528 . + . ID=m_arvensis_contig_3917_000003
4745 contig_2460 HelixerPost gene 676825 679042 . + . ID=m_arvensis_contig_2460_000089
377483 contig_7636 HelixerPost gene 99462 100981 . - . ID=m_arvensis_contig_7636_000009
624016 contig_13142 HelixerPost gene 21603 23807 . - . ID=m_arvensis_contig_13142_000002
135899 contig_1843 HelixerPost gene 73699 74577 . - . ID=m_arvensis_contig_1843_000016
656718 contig_22439 HelixerPost gene 20030 20823 . - . ID=m_arvensis_contig_22439_000004
236495 contig_2307 HelixerPost gene 112431 114449 . + . ID=m_arvensis_contig_2307_000002
479891 contig_3548 HelixerPost gene 75963 77693 . - . ID=m_arvensis_contig_3548_000007
690877 contig_5896 HelixerPost gene 19830 26544 . + . ID=m_arvensis_contig_5896_000001
598045 contig_246 HelixerPost gene 6693 8673 . - . ID=m_arvensis_contig_246_000004
606951 contig_173 HelixerPost gene 28636 29804 . - . ID=m_arvensis_contig_173_000006
396728 contig_4102 HelixerPost gene 20019 21846 . - . ID=m_arvensis_contig_4102_000006
417926 contig_1669 HelixerPost gene 42720 43528 . - . ID=m_arvensis_contig_1669_000002
541090 contig_12797 HelixerPost gene 33727 35258 . + . ID=m_arvensis_contig_12797_000006
683845 contig_23038 HelixerPost gene 9081 12954 . + . ID=m_arvensis_contig_23038_000003
598876 contig_756 HelixerPost gene 22851 23709 . - . ID=m_arvensis_contig_756_000013
323590 contig_2026 HelixerPost gene 62673 63952 . - . ID=m_arvensis_contig_2026_000011
651825 contig_24676 HelixerPost gene 17246 19220 . - . ID=m_arvensis_contig_24676_000002
651835 contig_24676 HelixerPost gene 16987 17242 . - . ID=m_arvensis_contig_24676_000003
566709 contig_12564 HelixerPost gene 2273 4991 . + . ID=m_arvensis_contig_12564_000001
554996 contig_3259 HelixerPost gene 21029 22713 . + . ID=m_arvensis_contig_3259_000001
499157 contig_16909 HelixerPost gene 9199 10511 . - . ID=m_arvensis_contig_16909_000010
278802 contig_5911 HelixerPost gene 94757 96070 . - . ID=m_arvensis_contig_5911_000020
341984 contig_4600 HelixerPost gene 8835 10429 . - . ID=m_arvensis_contig_4600_000014
580058 contig_10905 HelixerPost gene 51496 54012 . - . ID=m_arvensis_contig_10905_000005
60868 contig_2117 HelixerPost gene 116032 116935 . - . ID=m_arvensis_contig_2117_000037
60868 contig_2117 HelixerPost gene 116032 116935 . - . ID=m_arvensis_contig_2117_000037
611019 contig_5376 HelixerPost gene 37577 40731 . + . ID=m_arvensis_contig_5376_000001
372700 contig_5423 HelixerPost gene 96981 99807 . + . ID=m_arvensis_contig_5423_000009
312936 contig_2643 HelixerPost gene 22507 23030 . + . ID=m_arvensis_contig_2643_000001
312936 contig_2643 HelixerPost gene 22507 23030 . + . ID=m_arvensis_contig_2643_000001
716071 contig_28239 HelixerPost gene 18628 20616 . - . ID=m_arvensis_contig_28239_000004
487027 contig_8040 HelixerPost gene 26360 27637 . - . ID=m_arvensis_contig_8040_000015
634415 contig_243 HelixerPost gene 24379 25490 . + . ID=m_arvensis_contig_243_000001
309842 contig_5473 HelixerPost gene 56677 58189 . + . ID=m_arvensis_contig_5473_000003
479621 contig_10913 HelixerPost gene 42029 43193 . - . ID=m_arvensis_contig_10913_000014
735604 contig_28643 HelixerPost gene 6059 7616 . - . ID=m_arvensis_contig_28643_000001
692248 contig_6832 HelixerPost gene 27744 28549 . - . ID=m_arvensis_contig_6832_000002
27299 contig_686 HelixerPost gene 136087 139189 . + . ID=m_arvensis_contig_686_000006
632204 contig_33963 HelixerPost gene 10258 11621 . + . ID=m_arvensis_contig_33963_000001
72620 contig_4180 HelixerPost gene 152537 153230 . - . ID=m_arvensis_contig_4180_000004
72594 contig_4180 HelixerPost gene 172574 174839 . - . ID=m_arvensis_contig_4180_000003
423677 contig_2253 HelixerPost gene 14809 15456 . - . ID=m_arvensis_contig_2253_000003
423687 contig_2253 HelixerPost gene 12875 14807 . - . ID=m_arvensis_contig_2253_000004
696732 contig_7080 HelixerPost gene 30545 33074 . - . ID=m_arvensis_contig_7080_000001
89060 contig_1808 HelixerPost gene 23938 28044 . + . ID=m_arvensis_contig_1808_000001
454421 contig_7222 HelixerPost gene 52952 53320 . - . ID=m_arvensis_contig_7222_000006
270987 contig_5004 HelixerPost gene 103363 104684 . + . ID=m_arvensis_contig_5004_000002
86461 contig_3058 HelixerPost gene 140374 140576 . - . ID=m_arvensis_contig_3058_000004
86469 contig_3058 HelixerPost gene 139664 140330 . - . ID=m_arvensis_contig_3058_000005
660109 contig_26251 HelixerPost gene 21321 23210 . - . ID=m_arvensis_contig_26251_000007
735105 contig_15951 HelixerPost gene 6326 7721 . - . ID=m_arvensis_contig_15951_000003
11407 contig_726 HelixerPost gene 523052 527032 . + . ID=m_arvensis_contig_726_000010
695373 contig_6162 HelixerPost gene 15361 17726 . - . ID=m_arvensis_contig_6162_000001
137055 contig_1650 HelixerPost gene 86095 86874 . + . ID=m_arvensis_contig_1650_000015
137055 contig_1650 HelixerPost gene 86095 86874 . + . ID=m_arvensis_contig_1650_000015
36081 contig_494 HelixerPost gene 209003 209852 . - . ID=m_arvensis_contig_494_000042
666136 contig_4451 HelixerPost gene 10421 12037 . - . ID=m_arvensis_contig_4451_000003
739285 contig_24079 HelixerPost gene 14557 15394 . + . ID=m_arvensis_contig_24079_000002
345804 contig_2122 HelixerPost gene 70951 71814 . + . ID=m_arvensis_contig_2122_000002
558451 contig_26118 HelixerPost gene 53299 54585 . - . ID=m_arvensis_contig_26118_000007
40367 contig_625 HelixerPost gene 7565 8442 . + . ID=m_arvensis_contig_625_000003
40649 contig_625 HelixerPost gene 156335 157171 . + . ID=m_arvensis_contig_625_000022
107865 contig_3964 HelixerPost gene 120819 122362 . + . ID=m_arvensis_contig_3964_000001
44587 contig_1596 HelixerPost gene 282570 285097 . + . ID=m_arvensis_contig_1596_000035
725094 contig_27530 HelixerPost gene 16744 17454 . + . ID=m_arvensis_contig_27530_000001
725104 contig_27530 HelixerPost gene 17461 17712 . + . ID=m_arvensis_contig_27530_000002
425197 contig_4596 HelixerPost gene 63461 64177 . - . ID=m_arvensis_contig_4596_000008
354124 contig_1764 HelixerPost gene 14988 16139 . + . ID=m_arvensis_contig_1764_000001
461574 contig_3793 HelixerPost gene 60043 62698 . + . ID=m_arvensis_contig_3793_000008
25308 contig_858 HelixerPost gene 4548 6286 . + . ID=m_arvensis_contig_858_000001
25308 contig_858 HelixerPost gene 4548 6286 . + . ID=m_arvensis_contig_858_000001
712024 contig_31185 HelixerPost gene 9268 11291 . - . ID=m_arvensis_contig_31185_000001
109344 contig_3767 HelixerPost gene 13370 14294 . - . ID=m_arvensis_contig_3767_000028
109130 contig_3767 HelixerPost gene 195437 197043 . - . ID=m_arvensis_contig_3767_000012
600783 contig_3119 HelixerPost gene 25511 26213 . + . ID=m_arvensis_contig_3119_000002
684184 contig_7216 HelixerPost gene 28279 29052 . - . ID=m_arvensis_contig_7216_000001
738711 contig_33023 HelixerPost gene 11496 13628 . - . ID=m_arvensis_contig_33023_000002
667441 contig_4050 HelixerPost gene 37706 39998 . + . ID=m_arvensis_contig_4050_000003
451929 contig_6917 HelixerPost gene 72414 73349 . - . ID=m_arvensis_contig_6917_000008
231935 contig_4657 HelixerPost gene 139320 139471 . - . ID=m_arvensis_contig_4657_000017
20805 contig_1017 HelixerPost gene 340086 341410 . + . ID=m_arvensis_contig_1017_000044
20817 contig_1017 HelixerPost gene 341434 342303 . + . ID=m_arvensis_contig_1017_000045
351024 contig_9329 HelixerPost gene 12516 14009 . + . ID=m_arvensis_contig_9329_000002
332099 contig_5394 HelixerPost gene 102355 103737 . - . ID=m_arvensis_contig_5394_000003
616316 contig_10487 HelixerPost gene 52689 53469 . - . ID=m_arvensis_contig_10487_000008
170113 contig_5724 HelixerPost gene 101341 102208 . - . ID=m_arvensis_contig_5724_000022
188809 contig_1498 HelixerPost gene 114031 115160 . - . ID=m_arvensis_contig_1498_000022
117398 contig_361 HelixerPost gene 87458 88365 . - . ID=m_arvensis_contig_361_000018
585257 contig_32476 HelixerPost gene 9065 11548 . - . ID=m_arvensis_contig_32476_000012
486703 contig_1055 HelixerPost gene 47185 48083 . - . ID=m_arvensis_contig_1055_000018
651477 contig_10909 HelixerPost gene 16384 16983 . - . ID=m_arvensis_contig_10909_000004
651483 contig_10909 HelixerPost gene 16133 16294 . - . ID=m_arvensis_contig_10909_000005
165297 contig_4244 HelixerPost gene 41128 41964 . - . ID=m_arvensis_contig_4244_000016
165297 contig_4244 HelixerPost gene 41128 41964 . - . ID=m_arvensis_contig_4244_000016
577607 contig_5398 HelixerPost gene 20528 22471 . - . ID=m_arvensis_contig_5398_000008
324759 contig_11145 HelixerPost gene 55490 57695 . + . ID=m_arvensis_contig_11145_000014
691763 contig_14989 HelixerPost gene 20029 22449 . - . ID=m_arvensis_contig_14989_000003
160117 contig_1317 HelixerPost gene 31400 33389 . - . ID=m_arvensis_contig_1317_000019
171294 contig_3435 HelixerPost gene 125494 127012 . + . ID=m_arvensis_contig_3435_000010
521496 contig_3396 HelixerPost gene 27947 29139 . - . ID=m_arvensis_contig_3396_000005
521445 contig_3396 HelixerPost gene 69557 72350 . - . ID=m_arvensis_contig_3396_000002
169309 contig_358 HelixerPost gene 49946 51197 . - . ID=m_arvensis_contig_358_000019
169125 contig_358 HelixerPost gene 84370 89816 . + . ID=m_arvensis_contig_358_000008
438682 contig_3062 HelixerPost gene 10903 13232 . - . ID=m_arvensis_contig_3062_000016
394140 contig_376 HelixerPost gene 8328 10320 . - . ID=m_arvensis_contig_376_000005
480075 contig_8068 HelixerPost gene 70861 72445 . - . ID=m_arvensis_contig_8068_000006
668727 contig_23898 HelixerPost gene 21973 23763 . - . ID=m_arvensis_contig_23898_000002
658731 contig_8273 HelixerPost gene 35427 37580 . + . ID=m_arvensis_contig_8273_000002
17648 contig_1666 HelixerPost gene 305683 306291 . - . ID=m_arvensis_contig_1666_000031
17570 contig_1666 HelixerPost gene 409465 410337 . - . ID=m_arvensis_contig_1666_000023
487907 contig_761 HelixerPost gene 60498 63390 . + . ID=m_arvensis_contig_761_000002
90096 contig_3507 HelixerPost gene 169880 171382 . + . ID=m_arvensis_contig_3507_000025
90096 contig_3507 HelixerPost gene 169880 171382 . + . ID=m_arvensis_contig_3507_000025
754320 contig_32488 HelixerPost gene 1393 2611 . + . ID=m_arvensis_contig_32488_000001
734829 contig_22555 HelixerPost gene 4298 6258 . + . ID=m_arvensis_contig_22555_000001
182586 contig_3552 HelixerPost gene 128743 130709 . + . ID=m_arvensis_contig_3552_000012
671275 contig_7681 HelixerPost gene 3135 7042 . + . ID=m_arvensis_contig_7681_000001
575432 contig_204 HelixerPost gene 51325 52261 . - . ID=m_arvensis_contig_204_000006
129953 contig_123 HelixerPost gene 123726 125477 . - . ID=m_arvensis_contig_123_000014
129859 contig_123 HelixerPost gene 143059 146516 . + . ID=m_arvensis_contig_123_000007
760292 contig_8739 HelixerPost gene 5062 6672 . - . ID=m_arvensis_contig_8739_000002
760306 contig_8739 HelixerPost gene 4572 4952 . - . ID=m_arvensis_contig_8739_000003
617715 contig_5427 HelixerPost gene 35842 38261 . - . ID=m_arvensis_contig_5427_000002
177102 contig_1959 HelixerPost gene 88539 90644 . + . ID=m_arvensis_contig_1959_000001
649350 contig_4725 HelixerPost gene 24499 25541 . - . ID=m_arvensis_contig_4725_000004
649366 contig_4725 HelixerPost gene 24039 24462 . - . ID=m_arvensis_contig_4725_000005
536044 contig_6302 HelixerPost gene 662 2432 . + . ID=m_arvensis_contig_6302_000001
332563 contig_20631 HelixerPost gene 70900 71418 . - . ID=m_arvensis_contig_20631_000010
549081 contig_5526 HelixerPost gene 21639 23060 . - . ID=m_arvensis_contig_5526_000013
490087 contig_5354 HelixerPost gene 22936 25323 . + . ID=m_arvensis_contig_5354_000005
67731 contig_693 HelixerPost gene 180449 180930 . - . ID=m_arvensis_contig_693_000006
589732 contig_3641 HelixerPost gene 5880 6666 . + . ID=m_arvensis_contig_3641_000001
557466 contig_5561 HelixerPost gene 12434 13304 . + . ID=m_arvensis_contig_5561_000001
174474 contig_6435 HelixerPost gene 106117 107165 . - . ID=m_arvensis_contig_6435_000014
517462 contig_3232 HelixerPost gene 55289 57952 . - . ID=m_arvensis_contig_3232_000001
337749 contig_4188 HelixerPost gene 44778 46536 . - . ID=m_arvensis_contig_4188_000004
501114 contig_4656 HelixerPost gene 49110 52438 . + . ID=m_arvensis_contig_4656_000002
335019 contig_1248 HelixerPost gene 60352 61674 . + . ID=m_arvensis_contig_1248_000004
335019 contig_1248 HelixerPost gene 60352 61674 . + . ID=m_arvensis_contig_1248_000004
357909 contig_7885 HelixerPost gene 13708 14652 . - . ID=m_arvensis_contig_7885_000009
115707 contig_543 HelixerPost gene 106303 106781 . - . ID=m_arvensis_contig_543_000004
111610 contig_121 HelixerPost gene 192912 195209 . - . ID=m_arvensis_contig_121_000012
152020 contig_1948 HelixerPost gene 64675 64795 . - . ID=m_arvensis_contig_1948_000020
112498 contig_2155 HelixerPost gene 131786 132485 . + . ID=m_arvensis_contig_2155_000006
695215 contig_6650 HelixerPost gene 31750 33625 . - . ID=m_arvensis_contig_6650_000001
168276 contig_5299 HelixerPost gene 160672 161816 . - . ID=m_arvensis_contig_5299_000004
335727 contig_5125 HelixerPost gene 66323 67919 . + . ID=m_arvensis_contig_5125_000007
588815 contig_5876 HelixerPost gene 31548 33371 . - . ID=m_arvensis_contig_5876_000002
437748 contig_1136 HelixerPost gene 75650 77406 . - . ID=m_arvensis_contig_1136_000006
607003 contig_11412 HelixerPost gene 8692 10751 . + . ID=m_arvensis_contig_11412_000002
388553 contig_2478 HelixerPost gene 55734 56583 . - . ID=m_arvensis_contig_2478_000017
419036 contig_2921 HelixerPost gene 3204 14242 . + . ID=m_arvensis_contig_2921_000001
531909 contig_14287 HelixerPost gene 34469 36464 . + . ID=m_arvensis_contig_14287_000001
412998 contig_10664 HelixerPost gene 17434 18704 . - . ID=m_arvensis_contig_10664_000018
313576 contig_1785 HelixerPost gene 40432 42649 . + . ID=m_arvensis_contig_1785_000005
313584 contig_1785 HelixerPost gene 42651 43262 . + . ID=m_arvensis_contig_1785_000006
313596 contig_1785 HelixerPost gene 43264 43399 . + . ID=m_arvensis_contig_1785_000007
114928 contig_534 HelixerPost gene 13712 14657 . - . ID=m_arvensis_contig_534_000056
142225 contig_378 HelixerPost gene 99090 99697 . - . ID=m_arvensis_contig_378_000026
231137 contig_5943 HelixerPost gene 22660 27579 . + . ID=m_arvensis_contig_5943_000004
91432 contig_3766 HelixerPost gene 155967 156330 . - . ID=m_arvensis_contig_3766_000013
91442 contig_3766 HelixerPost gene 155819 155965 . - . ID=m_arvensis_contig_3766_000014
91450 contig_3766 HelixerPost gene 154882 155817 . - . ID=m_arvensis_contig_3766_000015
91394 contig_3766 HelixerPost gene 205673 206955 . - . ID=m_arvensis_contig_3766_000011
52488 contig_2693 HelixerPost gene 135131 136714 . + . ID=m_arvensis_contig_2693_000015
52488 contig_2693 HelixerPost gene 135131 136714 . + . ID=m_arvensis_contig_2693_000015
290722 contig_1456 HelixerPost gene 64751 65646 . - . ID=m_arvensis_contig_1456_000014
317367 contig_3100 HelixerPost gene 93489 95223 . - . ID=m_arvensis_contig_3100_000009
72056 contig_5632 HelixerPost gene 38995 40022 . - . ID=m_arvensis_contig_5632_000045
94341 contig_3882 HelixerPost gene 42349 42780 . - . ID=m_arvensis_contig_3882_000015
619575 contig_4326 HelixerPost gene 45322 46195 . - . ID=m_arvensis_contig_4326_000004
190767 CP002686 HelixerPost gene 8533967 8536470 . + . ID=a_thaliana_shortenedheade_CP002686_001251;associated_TE_type=LTR/Gypsy
192775 CP002686 HelixerPost gene 9776948 9780558 . + . ID=a_thaliana_shortenedheade_CP002686_001399;associated_TE_type=DNA/DTH
193993 CP002686 HelixerPost gene 10505779 10509269 . + . ID=a_thaliana_shortenedheade_CP002686_001482;associated_TE_type=DNA/Helitron
194733 CP002686 HelixerPost gene 11648285 11650935 . + . ID=a_thaliana_shortenedheade_CP002686_001543;associated_TE_type=LTR/Copia
194745 CP002686 HelixerPost gene 11671701 11672200 . + . ID=a_thaliana_shortenedheade_CP002686_001544;associated_TE_type=DNA/DTM
195088 CP002686 HelixerPost gene 13237323 13238800 . + . ID=a_thaliana_shortenedheade_CP002686_001575;associated_TE_type=LTR/Gypsy
195100 CP002686 HelixerPost gene 13304710 13304946 . + . ID=a_thaliana_shortenedheade_CP002686_001576;associated_TE_type=DNA/Helitron
195106 CP002686 HelixerPost gene 13304948 13306041 . + . ID=a_thaliana_shortenedheade_CP002686_001577;associated_TE_type=DNA/Helitron
227319 CP002686 HelixerPost gene 13374343 13374824 . - . ID=a_thaliana_shortenedheade_CP002686_003751;associated_TE_type=LTR/Copia
227319 CP002686 HelixerPost gene 13374343 13374824 . - . ID=a_thaliana_shortenedheade_CP002686_003751;associated_TE_type=DNA/DTM
195189 CP002686 HelixerPost gene 14072300 14072886 . + . ID=a_thaliana_shortenedheade_CP002686_001582;associated_TE_type=LTR/Gypsy
195195 CP002686 HelixerPost gene 14072909 14073051 . + . ID=a_thaliana_shortenedheade_CP002686_001583;associated_TE_type=LTR/Gypsy
227171 CP002686 HelixerPost gene 14109670 14111046 . - . ID=a_thaliana_shortenedheade_CP002686_003738;associated_TE_type=DNA/DTA
195273 CP002686 HelixerPost gene 14724033 14728257 . + . ID=a_thaliana_shortenedheade_CP002686_001589;associated_TE_type=LTR/Gypsy
195687 CP002686 HelixerPost gene 15367593 15370050 . + . ID=a_thaliana_shortenedheade_CP002686_001618;associated_TE_type=DNA/DTM
195797 CP002686 HelixerPost gene 15538758 15539615 . + . ID=a_thaliana_shortenedheade_CP002686_001625;associated_TE_type=LTR/Copia
195947 CP002686 HelixerPost gene 15707084 15709686 . + . ID=a_thaliana_shortenedheade_CP002686_001638;associated_TE_type=LTR/Gypsy
226260 CP002686 HelixerPost gene 15774027 15775763 . - . ID=a_thaliana_shortenedheade_CP002686_003683;associated_TE_type=LTR/Copia
197127 CP002686 HelixerPost gene 16673140 16676450 . + . ID=a_thaliana_shortenedheade_CP002686_001721;associated_TE_type=DNA/Helitron
201520 CP002686 HelixerPost gene 18973167 18974928 . + . ID=a_thaliana_shortenedheade_CP002686_002007;associated_TE_type=DNA/Helitron
110230 CP002685 HelixerPost gene 905728 909211 . + . ID=a_thaliana_shortenedheade_CP002685_000101;associated_TE_type=LTR/unknown
110979 CP002685 HelixerPost gene 1385432 1385984 . + . ID=a_thaliana_shortenedheade_CP002685_000154;associated_TE_type=LTR/Copia
110987 CP002685 HelixerPost gene 1387689 1388565 . + . ID=a_thaliana_shortenedheade_CP002685_000155;associated_TE_type=LTR/Copia
110997 CP002685 HelixerPost gene 1388602 1388754 . + . ID=a_thaliana_shortenedheade_CP002685_000156;associated_TE_type=LTR/Copia
111909 CP002685 HelixerPost gene 2072548 2073555 . + . ID=a_thaliana_shortenedheade_CP002685_000228;associated_TE_type=LTR/Gypsy
111919 CP002685 HelixerPost gene 2074076 2074986 . + . ID=a_thaliana_shortenedheade_CP002685_000229;associated_TE_type=LTR/Gypsy
112287 CP002685 HelixerPost gene 2894944 2901236 . + . ID=a_thaliana_shortenedheade_CP002685_000247;associated_TE_type=LTR/Copia
114414 CP002685 HelixerPost gene 5818578 5821679 . + . ID=a_thaliana_shortenedheade_CP002685_000426;associated_TE_type=DNA/DTM
115074 CP002685 HelixerPost gene 6418121 6419371 . + . ID=a_thaliana_shortenedheade_CP002685_000471;associated_TE_type=LTR/Copia
115280 CP002685 HelixerPost gene 6677294 6677781 . + . ID=a_thaliana_shortenedheade_CP002685_000491;associated_TE_type=DNA/Helitron
117246 CP002685 HelixerPost gene 8026981 8028211 . + . ID=a_thaliana_shortenedheade_CP002685_000631;associated_TE_type=DNA/Helitron
117318 CP002685 HelixerPost gene 8097594 8098762 . + . ID=a_thaliana_shortenedheade_CP002685_000640;associated_TE_type=DNA/DTM
117526 CP002685 HelixerPost gene 8170021 8172563 . + . ID=a_thaliana_shortenedheade_CP002685_000653;associated_TE_type=DNA/Helitron
118300 CP002685 HelixerPost gene 8550198 8551922 . + . ID=a_thaliana_shortenedheade_CP002685_000702;associated_TE_type=DNA/DTA
162699 CP002685 HelixerPost gene 8887452 8888417 . - . ID=a_thaliana_shortenedheade_CP002685_003627;associated_TE_type=MITE/DTM
162711 CP002685 HelixerPost gene 8887114 8887450 . - . ID=a_thaliana_shortenedheade_CP002685_003628;associated_TE_type=MITE/DTM
162720 CP002685 HelixerPost gene 8886025 8886450 . - . ID=a_thaliana_shortenedheade_CP002685_003629;associated_TE_type=MITE/DTM
119412 CP002685 HelixerPost gene 9089268 9089869 . + . ID=a_thaliana_shortenedheade_CP002685_000771;associated_TE_type=DNA/Helitron
136323 CP002685 HelixerPost gene 17902449 17904305 . + . ID=a_thaliana_shortenedheade_CP002685_001886;associated_TE_type=DNA/Helitron
333189 CP002688 HelixerPost gene 9208657 9210594 . + . ID=a_thaliana_shortenedheade_CP002688_001234;associated_TE_type=LTR/Gypsy
333490 CP002688 HelixerPost gene 9377369 9379507 . + . ID=a_thaliana_shortenedheade_CP002688_001255;associated_TE_type=LTR/unknown
333886 CP002688 HelixerPost gene 9553416 9557543 . + . ID=a_thaliana_shortenedheade_CP002688_001277;associated_TE_type=DNA/Helitron
334118 CP002688 HelixerPost gene 9657006 9662664 . + . ID=a_thaliana_shortenedheade_CP002688_001291;associated_TE_type=MITE/DTC
337057 CP002688 HelixerPost gene 14690273 14692964 . + . ID=a_thaliana_shortenedheade_CP002688_001482;associated_TE_type=DNA/Helitron
338290 CP002688 HelixerPost gene 15578756 15579752 . + . ID=a_thaliana_shortenedheade_CP002688_001584;associated_TE_type=DNA/Helitron
340481 CP002688 HelixerPost gene 16711332 16711960 . + . ID=a_thaliana_shortenedheade_CP002688_001744;associated_TE_type=DNA/Helitron
341093 CP002688 HelixerPost gene 16968661 16970475 . + . ID=a_thaliana_shortenedheade_CP002688_001782;associated_TE_type=MITE/DTM
341093 CP002688 HelixerPost gene 16968661 16970475 . + . ID=a_thaliana_shortenedheade_CP002688_001782;associated_TE_type=MITE/DTM
341322 CP002688 HelixerPost gene 17088673 17089605 . + . ID=a_thaliana_shortenedheade_CP002688_001794;associated_TE_type=LTR/Copia
343779 CP002688 HelixerPost gene 18487915 18489884 . + . ID=a_thaliana_shortenedheade_CP002688_001964;associated_TE_type=LTR/Copia
344647 CP002688 HelixerPost gene 18977425 18978063 . + . ID=a_thaliana_shortenedheade_CP002688_002026;associated_TE_type=DNA/DTM
344653 CP002688 HelixerPost gene 18979005 18980115 . + . ID=a_thaliana_shortenedheade_CP002688_002027;associated_TE_type=DNA/DTM
352467 CP002688 HelixerPost gene 22609438 22612451 . + . ID=a_thaliana_shortenedheade_CP002688_002516;associated_TE_type=LTR/Copia
255154 CP002687 HelixerPost gene 1939161 1943021 . + . ID=a_thaliana_shortenedheade_CP002687_000211;associated_TE_type=LTR/Gypsy
255558 CP002687 HelixerPost gene 2181510 2188576 . + . ID=a_thaliana_shortenedheade_CP002687_000234;associated_TE_type=LTR/Copia
256142 CP002687 HelixerPost gene 2602999 2604287 . + . ID=a_thaliana_shortenedheade_CP002687_000272;associated_TE_type=DNA/DTM
256292 CP002687 HelixerPost gene 2693618 2694610 . + . ID=a_thaliana_shortenedheade_CP002687_000282;associated_TE_type=MITE/DTH
256298 CP002687 HelixerPost gene 2694934 2695329 . + . ID=a_thaliana_shortenedheade_CP002687_000283;associated_TE_type=MITE/DTH
257657 CP002687 HelixerPost gene 5902816 5905395 . + . ID=a_thaliana_shortenedheade_CP002687_000381;associated_TE_type=LTR/Copia
306557 CP002687 HelixerPost gene 7385775 7386816 . - . ID=a_thaliana_shortenedheade_CP002687_003580;associated_TE_type=DNA/Helitron
260242 CP002687 HelixerPost gene 7568108 7569636 . + . ID=a_thaliana_shortenedheade_CP002687_000569;associated_TE_type=MITE/DTA
305556 CP002687 HelixerPost gene 7910935 7912899 . - . ID=a_thaliana_shortenedheade_CP002687_003502;associated_TE_type=DNA/Helitron
263126 CP002687 HelixerPost gene 9184177 9187090 . + . ID=a_thaliana_shortenedheade_CP002687_000766;associated_TE_type=DNA/Helitron
263146 CP002687 HelixerPost gene 9187094 9188705 . + . ID=a_thaliana_shortenedheade_CP002687_000767;associated_TE_type=DNA/Helitron
266099 CP002687 HelixerPost gene 10896667 10899128 . + . ID=a_thaliana_shortenedheade_CP002687_000964;associated_TE_type=LTR/unknown
8860 CP002684 HelixerPost gene 3777262 3780317 . + . ID=a_thaliana_shortenedheade_CP002684_000529;associated_TE_type=DNA/DTM
86856 CP002684 HelixerPost gene 9812906 9815565 . - . ID=a_thaliana_shortenedheade_CP002684_005706;associated_TE_type=DNA/DTH
24941 CP002684 HelixerPost gene 11681774 11684432 . + . ID=a_thaliana_shortenedheade_CP002684_001634;associated_TE_type=DNA/DTC
25766 CP002684 HelixerPost gene 12180671 12182356 . + . ID=a_thaliana_shortenedheade_CP002684_001697;associated_TE_type=DNA/Helitron
27114 CP002684 HelixerPost gene 13208683 13210540 . + . ID=a_thaliana_shortenedheade_CP002684_001787;associated_TE_type=DNA/Helitron
27164 CP002684 HelixerPost gene 13330758 13331577 . + . ID=a_thaliana_shortenedheade_CP002684_001792;associated_TE_type=LTR/Gypsy
27964 CP002684 HelixerPost gene 16548404 16550901 . + . ID=a_thaliana_shortenedheade_CP002684_001832;associated_TE_type=LTR/Copia
80091 CP002684 HelixerPost gene 17232010 17233043 . - . ID=a_thaliana_shortenedheade_CP002684_005252;associated_TE_type=DNA/DTH
29299 CP002684 HelixerPost gene 17525333 17526289 . + . ID=a_thaliana_shortenedheade_CP002684_001923;associated_TE_type=LTR/unknown
29389 CP002684 HelixerPost gene 17601061 17602859 . + . ID=a_thaliana_shortenedheade_CP002684_001930;associated_TE_type=DNA/Helitron
29397 CP002684 HelixerPost gene 17603422 17604827 . + . ID=a_thaliana_shortenedheade_CP002684_001931;associated_TE_type=DNA/Helitron
78766 CP002684 HelixerPost gene 18008969 18009897 . - . ID=a_thaliana_shortenedheade_CP002684_005163;associated_TE_type=DNA/Helitron
32074 CP002684 HelixerPost gene 19023454 19026838 . + . ID=a_thaliana_shortenedheade_CP002684_002112;associated_TE_type=DNA/DTA
34389 CP002684 HelixerPost gene 20167663 20169770 . + . ID=a_thaliana_shortenedheade_CP002684_002259;associated_TE_type=MITE/DTA
34761 CP002684 HelixerPost gene 20323030 20328170 . + . ID=a_thaliana_shortenedheade_CP002684_002283;associated_TE_type=DNA/DTM
36686 CP002684 HelixerPost gene 21520402 21522503 . + . ID=a_thaliana_shortenedheade_CP002684_002409;associated_TE_type=LTR/Copia
38959 CP002684 HelixerPost gene 22943616 22944219 . + . ID=a_thaliana_shortenedheade_CP002684_002566;associated_TE_type=MITE/DTA
49809 CP002684 HelixerPost gene 28906464 28911568 . + . ID=a_thaliana_shortenedheade_CP002684_003351;associated_TE_type=DNA/DTA
283351 61481 HelixerPost gene 3473998 3474822 . + . ID=b_tournefortii_61481_000421;associated_TE_type=DNA/Helitron
283357 61481 HelixerPost gene 3476266 3477081 . + . ID=b_tournefortii_61481_000422;associated_TE_type=DNA/Helitron
283351 61481 HelixerPost gene 3473998 3474822 . + . ID=b_tournefortii_61481_000421;associated_TE_type=DNA/Helitron
283357 61481 HelixerPost gene 3476266 3477081 . + . ID=b_tournefortii_61481_000422;associated_TE_type=DNA/Helitron
284653 61481 HelixerPost gene 4352407 4354935 . + . ID=b_tournefortii_61481_000523;associated_TE_type=DNA/DTA
284671 61481 HelixerPost gene 4355494 4357796 . + . ID=b_tournefortii_61481_000524;associated_TE_type=DNA/DTA
285174 61481 HelixerPost gene 4764443 4768573 . + . ID=b_tournefortii_61481_000563;associated_TE_type=MITE/DTA
286629 61481 HelixerPost gene 6089155 6089948 . + . ID=b_tournefortii_61481_000674;associated_TE_type=MITE/DTA
287656 61481 HelixerPost gene 6903395 6905471 . + . ID=b_tournefortii_61481_000752;associated_TE_type=DNA/DTA
288770 61481 HelixerPost gene 7589552 7595518 . + . ID=b_tournefortii_61481_000823;associated_TE_type=LTR/Copia
290200 61481 HelixerPost gene 8766092 8770254 . + . ID=b_tournefortii_61481_000913;associated_TE_type=DNA/DTM
290460 61481 HelixerPost gene 8950692 8952320 . + . ID=b_tournefortii_61481_000928;associated_TE_type=DNA/DTC
290460 61481 HelixerPost gene 8950692 8952320 . + . ID=b_tournefortii_61481_000928;associated_TE_type=DNA/DTM
291274 61481 HelixerPost gene 9784963 9785286 . + . ID=b_tournefortii_61481_000982;associated_TE_type=LTR/Copia
295904 61481 HelixerPost gene 11023136 11024636 . - . ID=b_tournefortii_61481_001340;associated_TE_type=LTR/Copia
292535 61481 HelixerPost gene 11321655 11323914 . + . ID=b_tournefortii_61481_001081;associated_TE_type=LTR/unknown
292715 61481 HelixerPost gene 11511569 11512611 . + . ID=b_tournefortii_61481_001093;associated_TE_type=DNA/DTA
292725 61481 HelixerPost gene 11512738 11513007 . + . ID=b_tournefortii_61481_001094;associated_TE_type=DNA/DTA
295112 61481 HelixerPost gene 12186780 12187931 . - . ID=b_tournefortii_61481_001281;associated_TE_type=DNA/Helitron
294094 61481 HelixerPost gene 14428981 14430820 . + . ID=b_tournefortii_61481_001214;associated_TE_type=LTR/Gypsy
199342 61479 HelixerPost gene 863413 867288 . + . ID=b_tournefortii_61479_000005;associated_TE_type=DNA/DTH
235173 61479 HelixerPost gene 2238269 2239636 . - . ID=b_tournefortii_61479_002484;associated_TE_type=MITE/DTA
234215 61479 HelixerPost gene 3781813 3783236 . - . ID=b_tournefortii_61479_002424;associated_TE_type=MITE/DTH
201058 61479 HelixerPost gene 3921476 3925328 . + . ID=b_tournefortii_61479_000125;associated_TE_type=LTR/unknown
201071 61479 HelixerPost gene 3925333 3925688 . + . ID=b_tournefortii_61479_000126;associated_TE_type=LTR/unknown
201085 61479 HelixerPost gene 3946775 3947577 . + . ID=b_tournefortii_61479_000128;associated_TE_type=LTR/Gypsy
201481 61479 HelixerPost gene 4380381 4382145 . + . ID=b_tournefortii_61479_000156;associated_TE_type=DNA/DTM
201491 61479 HelixerPost gene 4382221 4382496 . + . ID=b_tournefortii_61479_000157;associated_TE_type=DNA/DTM
203032 61479 HelixerPost gene 5792397 5794611 . + . ID=b_tournefortii_61479_000258;associated_TE_type=MITE/DTA
203040 61479 HelixerPost gene 5795540 5796195 . + . ID=b_tournefortii_61479_000259;associated_TE_type=MITE/DTA
231775 61479 HelixerPost gene 6492984 6494782 . - . ID=b_tournefortii_61479_002253;associated_TE_type=MITE/DTM
231459 61479 HelixerPost gene 6764554 6764696 . - . ID=b_tournefortii_61479_002229;associated_TE_type=LTR/unknown
231465 61479 HelixerPost gene 6764365 6764518 . - . ID=b_tournefortii_61479_002230;associated_TE_type=LTR/unknown
204728 61479 HelixerPost gene 7466419 7470685 . + . ID=b_tournefortii_61479_000372;associated_TE_type=DNA/Helitron
205626 61479 HelixerPost gene 8355964 8358932 . + . ID=b_tournefortii_61479_000433;associated_TE_type=DNA/Helitron
206737 61479 HelixerPost gene 9180754 9185994 . + . ID=b_tournefortii_61479_000508;associated_TE_type=DNA/DTA
207645 61479 HelixerPost gene 10001685 10002920 . + . ID=b_tournefortii_61479_000577;associated_TE_type=MITE/DTA
207659 61479 HelixerPost gene 10002926 10003190 . + . ID=b_tournefortii_61479_000578;associated_TE_type=MITE/DTA
208175 61479 HelixerPost gene 10376532 10377623 . + . ID=b_tournefortii_61479_000610;associated_TE_type=LTR/Copia
208547 61479 HelixerPost gene 10927831 10929380 . + . ID=b_tournefortii_61479_000640;associated_TE_type=MITE/DTA
226647 61479 HelixerPost gene 11056357 11057260 . - . ID=b_tournefortii_61479_001915;associated_TE_type=DNA/Helitron
208759 61479 HelixerPost gene 11113177 11114644 . + . ID=b_tournefortii_61479_000656;associated_TE_type=MITE/DTM
212759 61479 HelixerPost gene 13976035 13977374 . + . ID=b_tournefortii_61479_000916;associated_TE_type=DNA/DTC
213457 61479 HelixerPost gene 14340253 14343089 . + . ID=b_tournefortii_61479_000971;associated_TE_type=MITE/DTC
214218 61479 HelixerPost gene 14909676 14914794 . + . ID=b_tournefortii_61479_001030;associated_TE_type=MITE/DTM
215242 61479 HelixerPost gene 15434104 15436924 . + . ID=b_tournefortii_61479_001101;associated_TE_type=MITE/DTA
215922 61479 HelixerPost gene 15719749 15721772 . + . ID=b_tournefortii_61479_001142;associated_TE_type=MITE/DTA
215934 61479 HelixerPost gene 15722096 15722506 . + . ID=b_tournefortii_61479_001143;associated_TE_type=MITE/DTA
215942 61479 HelixerPost gene 15722690 15722947 . + . ID=b_tournefortii_61479_001144;associated_TE_type=MITE/DTA
216271 61479 HelixerPost gene 15977072 15979371 . + . ID=b_tournefortii_61479_001169;associated_TE_type=LTR/Copia
236912 0a HelixerPost gene 561298 562704 . + . ID=b_tournefortii_0a_000080;associated_TE_type=MITE/DTA
241607 0a HelixerPost gene 3291366 3291777 . + . ID=b_tournefortii_0a_000386;associated_TE_type=DNA/DTM
271384 0a HelixerPost gene 3502060 3503400 . - . ID=b_tournefortii_0a_002426;associated_TE_type=DNA/DTM
249332 0a HelixerPost gene 8404315 8405248 . + . ID=b_tournefortii_0a_000905;associated_TE_type=MITE/DTA
249456 0a HelixerPost gene 8543291 8545729 . + . ID=b_tournefortii_0a_000914;associated_TE_type=MITE/DTH
249804 0a HelixerPost gene 8698345 8700727 . + . ID=b_tournefortii_0a_000933;associated_TE_type=LTR/Gypsy
251840 0a HelixerPost gene 10660659 10665180 . + . ID=b_tournefortii_0a_001085;associated_TE_type=DNA/DTA
252730 0a HelixerPost gene 11561913 11563704 . + . ID=b_tournefortii_0a_001150;associated_TE_type=MITE/DTM
259907 0a HelixerPost gene 11588351 11589230 . - . ID=b_tournefortii_0a_001651;associated_TE_type=DNA/DTC
252746 0a HelixerPost gene 11648041 11650208 . + . ID=b_tournefortii_0a_001152;associated_TE_type=LTR/unknown
258913 0a HelixerPost gene 12588992 12591187 . - . ID=b_tournefortii_0a_001589;associated_TE_type=LTR/Copia
254652 0a HelixerPost gene 13686335 13688525 . + . ID=b_tournefortii_0a_001294;associated_TE_type=DNA/Helitron
255294 0a HelixerPost gene 14238460 14243396 . + . ID=b_tournefortii_0a_001337;associated_TE_type=LTR/Gypsy
256091 0a HelixerPost gene 15646223 15649067 . + . ID=b_tournefortii_0a_001397;associated_TE_type=DNA/DTC
256885 0a HelixerPost gene 15907691 15908709 . - . ID=b_tournefortii_0a_001450;associated_TE_type=LTR/unknown
256287 0a HelixerPost gene 16146507 16149416 . + . ID=b_tournefortii_0a_001410;associated_TE_type=LTR/Gypsy
312380 61475 HelixerPost gene 79783 81816 . + . ID=b_tournefortii_61475_000001;associated_TE_type=DNA/DTM
312646 61475 HelixerPost gene 1003235 1005881 . + . ID=b_tournefortii_61475_000017;associated_TE_type=DNA/DTA
313278 61475 HelixerPost gene 2356698 2358921 . + . ID=b_tournefortii_61475_000065;associated_TE_type=DNA/Helitron
313510 61475 HelixerPost gene 2650894 2652882 . + . ID=b_tournefortii_61475_000081;associated_TE_type=DNA/DTC
313670 61475 HelixerPost gene 2919514 2922739 . + . ID=b_tournefortii_61475_000093;associated_TE_type=MITE/DTH
313966 61475 HelixerPost gene 3255738 3257519 . + . ID=b_tournefortii_61475_000117;associated_TE_type=LTR/Copia
314328 61475 HelixerPost gene 3644540 3647477 . + . ID=b_tournefortii_61475_000144;associated_TE_type=MITE/DTA
314478 61475 HelixerPost gene 3780229 3780932 . + . ID=b_tournefortii_61475_000153;associated_TE_type=LTR/Copia
316322 61475 HelixerPost gene 5342639 5344745 . + . ID=b_tournefortii_61475_000282;associated_TE_type=MITE/DTA
316628 61475 HelixerPost gene 5722886 5725302 . + . ID=b_tournefortii_61475_000306;associated_TE_type=MITE/DTH
316978 61475 HelixerPost gene 6361613 6367839 . + . ID=b_tournefortii_61475_000331;associated_TE_type=MITE/DTH
317132 61475 HelixerPost gene 6542807 6544139 . + . ID=b_tournefortii_61475_000339;associated_TE_type=DNA/Helitron
321810 61475 HelixerPost gene 10810004 10811214 . + . ID=b_tournefortii_61475_000698;associated_TE_type=LTR/Gypsy
324013 61475 HelixerPost gene 12700523 12701588 . + . ID=b_tournefortii_61475_000853;associated_TE_type=DNA/Helitron
324603 61475 HelixerPost gene 13233261 13235721 . + . ID=b_tournefortii_61475_000905;associated_TE_type=LTR/Copia