Table 4 Most significant plant cis-regulatory motifs detected by RSAT dna-pattern in TE sequences adjacent to stress-responsive genes for A. thaliana (Atha) and S. lycopersicum (Slyc)

Atha_proteasome_mutant_B_ intron_down_SINE

GTTAGGTTC

ACIII element (MYB)

17

49.4

0.0174

Atha_proteasome_mutant_B_ intron_up_Gypsy

tACACGbmACyk

NAC019

20

177.8

0

vyaCACGgmAcyr

NAC055

20

177.8

0

aYACGCAA

NAC080

50

22.2

5.83E-06

mrCACGTGyk

MYC4 (BHLH)

20

118.5

3.45E-05

rrCACGTGyy

ILR3 (BHLH)

20

59.3

0.00049

Atha_proteasome_mutant_B_ downstream_up_Gypsy

GTGGaCCCrs

TCP16

10

889

0

TACCGACGA

DRE-like

10

889

0

GGCCGACGT

DRE-like

10

592.7

0

mrCACGTGyk

MYC4 (BHLH)

10

592.7

0

dwwkvhsACGTGKCa

GBF3 (bZIP)

10

444.5

0

vGAAssTTCy

HSFB2A

10

63.5

0

Atha_photorespiratory_mutant_B_upstream_down_Mariner

CAATGATTG

AtHB5

29

36.8

0.0005

CAATSATTG

AtHB2

29

36.8

0.0005

yCAATCAWtg

AtHB7

29

29.6

0.0009

wAATATATTw

AHL20 (AT-hook)

57

4.5

0.0136

Atha_paraquat_A_ intron_down_Pogo

wawawAAATATCtwa

AT3G10113 (SANT/MYB)

14

84.7

0.0265

aAAATATCTt

CCA1 (SANT/MYB)

29

16.9

0.0322

awycTTATCtthwy

AT3G11280 (SANT/MYB)

14

50.8

0.0322

AGAAATTTCT

HSEs binding site motif

14

28.2

0.0449

TACGTACAA

SBP-box (zinc finger)

14

31.8

0.0449

Atha_heat_B_ upstream_up_Copia

ACAGAG

REF6

32

2.3

0.0088

TGGGCY

SITEIIATCYTC (TCP)

25

2.1

0.0326

ayACGywAy

AtNAC6

13

2.8

0.0394

Atha_heat_B_ intron_up_Gypsy

AGCCGACGA

DRE-like

11

65.9

0.0180

Atha_salt_heat_A_ upstream_up_Copia

ACAGAG

REF6

28

2.1

0.0212

ayACGywAy

AtNAC6

14

2.9

0.0224

GGGCC

SORLIP2

22

2.3

0.0228

TGGGCY

SITEIIATCYTC (TCP)

25

2.1

0.0237

Atha_salt_heat_A_ intron_up_Gypsy

AGCCGACGA

DRE-like

9

53.9

0.0295

Slyc_infection_necrotrophic_C_ upstream_down_EPRV

GATAAGR

I-box core

71

3.7

0.0664

Slyc_infection_necrotrophic_C_ intron_down_hAT

wAAwwwwTTw

AHL12 (AT-hook)

94

3.9

1.03E-09

rTTTAAAh

TCX6 (CXC)

72

3.6

1.60E-05

rTTTrAAw

SOL1 (CXC)

83

2.7

2.98E-05

dAwTTAAwTw

AGF1 (AT-hook)

56

5.0

3.38E-05

rwWAAmGT

COG1 (DOF)

78

2.7

0.0001

Slyc_infection_necrotrophic_A_ downstream_up_Retrotransposon

CCAATAAAGG

CArG-box (MADS)

13

69.7

0.0343

CCTTTATTGG

CArG-box (MADS)

13

69.7

0.0343

Slyc_infection_viral_A_ intron_up_EPRV

yaahawhwwCAmCAACawyahh

AT1G18960 (SANT/MYB)

10

135.5

0.0037

wwwwwTdACCGTTrr

MYB3R1 (SANT/MYB)

10

125.4

0.0037

wthwwwACCGTTA

LOF2 (SANT/MYB)

10

80.6

0.0068

GGCCGACAA

DRE-like

10

69.1

0.0068

tmayTAATyAhgwww

ZFHD2

10

51.3

0.0101

Slyc_infection_viral_A_ intron_up_hAT

ATATTTAWW

SEF1MOTIF

67

5.4

4.57E-06

wAAwwwwTTw

AHL12 (AT-hook)

83

3.4

5.42E-06

tAWWTAWWta

AHL13 (AT-hook)

56

4.6

0.0001

AAATTAAA

Bellringer/replumless/pennywise (AG/HD)

56

4.5

0.0001

ATtwawaATTwAATt

AT1G76110 (HMG/ARID)

11

78.4

0.0002

dACCGGTw

MYB94

11

7.1

0.0379

Slyc_stress_tolerance_A_ intron_down_MuDR

wwwCGhATwWT

AtHB32 (HD)

12

3.6

0.0338

kATGTTGC

TEM2 (AP2/ERF/B3)

17

2.7

0.0414

AAATTAAA

Bellringer/replumless/pennywise (AG/HD)

29

2.3

0.0220

TTWTWTTWTT

MARTBOX

39

2.3

0.0042

TTNCGTA

NAC binding site

24

2.2

0.0402

Slyc_light_A_ downstream_up_Retrotransposon

CATTAATTAG

Soybean homeodomein leucine zippers (GmHdl56, GmHdl57)

18

56.1

8.62E-06

TTTTACTAGT

SORLREP1

14

29.9

0.0008

yGCCGCC

ERF2 (tobacco)

23

8.7

0.0033

rCACGTGy

BHLH3

18

10.8

0.0039

ywTTTACyGc

BRADI1G77610 (MYB)

14

13.3

0.0066

Slyc_light_A_ intron_up_Retrotransposon

CATTAATTAG

Soybean homeodomein leucine zippers (GmHdl56, GmHdl57)

13

50

7.02E-15

dwwGAAATGAwr

AT2G31460 (auxin response factor 70)

16

5.6

1.68E-05

KWGTGRWAAWRW

GT-1 motif rbcS (pea)

11

2.7

0.0440

wgawAAmGt

DOF4.7

17

2.1

0.0491

wtcaGTTr

AtMYB87

21

2.0

0.0225

Slyc_lightB_ intron_up_Retrotransposon

CATTAATTAG

Soybean homeodomein leucine zippers (GmHdl56, GmHdl57)

12

44.7

1.23E-11

dwwGAAATGAwr

AT2G31460 (auxin response factor 70)

12

4.3

0.0048

Slyc_light_C_ intron_up_Retrotransposon

CATTAATTAG

Soybean homeodomein leucine zippers (GmHdl56, GmHdl57)

15

55.3

1.84E-15

dwwGAAATGAwr

AT2G31460 (auxin response factor 70)

15

5.3

0.0002

waATgAtTAh

YAB5 (YABBY)

11

4.0

0.0087

Slyc_light_D_ intron_up_Retrotransposon

CATTAATTAG

Soybean homeodomein leucine zippers (GmHdl56, GmHdl57)

15

54.6

2.18E-15

dwwGAAATGAwr

AT2G31460 (auxin response factor 70)

15

5.2

0.0002

waATgAtTAh

YAB5 (YABBY)

11

4.0

0.0101

Slyc_light_C_ intron_up_Harbinger

AACCAAAC

MYB binding site

15

3.2

0.0002

ACCAAAC

MYB4

27

2.6

7.97E-06

rymAGTTA

AtMYB4

32

2.1

4.21E-05

TATTAG

CPBCSPOR

51

2.0

4.27E-08

Slyc_light_D_ intron_up_Harbinger

TATTAG

CPBCSPOR

53

2.1

2.02E-10

rymAGTTA

AtMYB4

31

2.1

2.85E-05

ACCAAAC

MYB4

27

2.6

3.29E-06

CATGCAT

RY repeat motif (soybean)

18

2.0

0.0134

AACCAAAC

MYB binding site

15

3.3

4.67E-05

CTAACCA

AtMYB2

14

2.1

0.0283

rwakATtCyc

GAMMAMYB2

11

3.4

0.0007