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Table 1 Novel or candidate miRNAs found in apple (excerpteda)

From: Apple miRNAs and tasiRNAs with novel regulatory networks

     

Match

 

Normalized reads

Name

miRNA sequence

Contigb

Len

Str

position

miRNA* sequencec

Leaf

Root

Flower

Fruit

Total

miRC1

ACAGGGAAGAGGTAGAGCATG

MDC006505.260

21

-

3,797

ATGCACTGCCTCTTCCCTGGC

1,091

23,246

0

12

24,349

miRC2

ACCTAGCTCTGATACCATGAA

MDC018599.370

21

+

9,369

TGTGGTATCAGGACTATGTTA

893

261

5,364

1,823

8,341

miRC3

CTACCGATGCCACTAAGTCCCA

MDC017130.228

22

+

6,809

GGACTTAGTAGCTCGGTGA

266

247

1,567

671

2,751

miRC4

TGTTATATTGTCAGATTGTCA

MDC019554.272

21

-

10,154

ACAGTCTGACAATATAACGTG

1,035

502

6

0

1,543

miRC5

AATGGAAGGGTAGGAAAGAAG

MDC006350.123

21

-

2,997

TCTTTCCTATCCCTCCCATTCC

1,021

324

144

0

1,490

miRC6a

TCCTCTTGGTGATCGCCCTGT

MDC009272.709

21

-

4,184

AGGGTGATTAACAAAGGGATG

359

279

336

319

1,294

miRC6b

TCCTCTTGGTGATCGCCCTGC

MDC006081.961

21

-

466

AGGGTGGTTACCAATGGGATG

122

218

0

46

385

miRC7

TTATACAGAGAAATCACGGTCG

MDC009778.59

22

-

4,735

ACCGTGTTTTTCTGTATAAAG

511

624

108

27

1,270

miRC8

AAGAGCGGGATGTGTAAAAGG

MDC001018.301

21

+

2,490

CTTTTACCTATCCCATTCTGT

248

0

0

0

248

miRC9

TCTGTCGTGGGTGAGATGGTGC

MDC011178.406

22

-

16,699

TTCATCTCTCCTCGACAGAAG

137

90

0

4

231

miRC10

GAATTCCTTCTCCTCTCCTTT

MDC026449.10

21

-

340

AGGAGGGAGAGAGGGTTTTAC

0

0

166

7

173

miRC11

CACCAATATCAACTTTATTTG

MDC005581.168

21

+

2,657

AATAAAGTTGATATTGGTGTG

6

12

44

38

100

miRC12

TCTGTCGAAGGTGAGATGGTGC

MDC003092.251

22

+

8,878

TTCATCCCTCCTCGACTGAAG

10

64

0

0

73

miRC13

ATCCAACGAAGCAGGAGCTGA

MDC009318.175

21

+

3,804

AGCTGCTGACTCGTTGGTTCA

0

0

18

42

60

miRC14

CGAACTTATTGCAACTAGCTT

MDC008558.180

21

+

6,507

CAAGCTAGTTGTAATAAGTTC

24

0

13

0

38

miRC15

AAAGTATCAAGGAGCGCAAAG

MDC014075.204

21

-

26,060

TTGCGTTCCACTGATTCTTTCG

8

8

9

2

27

miRC16

CATCTGGGTCGTTCAAATTTA

MDC009589.307

21

-

1,975

AATTTGAACGGCCCAGATGGG

10

12

0

0

22

miRC17

ATCATGCGATCCCTTCGGACG

MDC005391.194

21

+

11,429

TCCAAAGGGATCGCATTGATCT

11

0

0

0

11

miRC18

ATACTCATCGAATTTGTCATA

MDC012422.128

21

+

849

TGACAAATTGGATGAGTATTC

3

0

4

0

8

miRC19

TGGGATGTTGGTATGGTTCAA

MDC016463.170

21

-

5,187

GAGCCGTGCCAATATCACAGT

0

7

0

0

7

miRC20

TGAAGAGAAGAGCGTTGTTTGG

MDC001494.456

22

-

33,010

TGACAGCCTCTTCTTCTCATG

6

0

0

0

6

miRC21

ATCATTAACACTTAATAACGA

MDC006081.432

21

+

219

TTATTAAGTGTTAATGATTGG

0

0

0

2

2

miRC22

CCATATGTCCCTCCATATACT

MDC016302.308

21

+

5,368

No star found

0

0

72

8

80

miRC23

AATGATGATCAAACAACCCTT

MDC020884.221

21

+

4,086

No star found

0

0

46

2

48

miRC24

TGAACTTGGCTGAATGTGGACT

MDC001394.253

22

-

378

No star found

22

19

0

0

40

miRC25

TTTCGGAACCACTTACACCCA

MDC017130.228

21

+

9,764

No star found

0

0

24

0

24

miRC26

TCCCCAAAACCCCTCATTCCAA

MDC017130.228

22

+

9,967

No star found

0

0

15

0

15

miRC27

TTGCCAAAGGAGATCTGCTCAG

MDC019485.283

22

-

7,997

No star found

6

0

0

6

12

miRC28

TGCATTTGCACCTGCACTTGT

MDC007946.169

21

-

672

No star found

0

0

9

3

11

miRC29

CAAAGCTTTTAATATCAGTCGA

MDC018873.313

22

-

10,447

No star found

0

0

5

6

10

miRC30

TCCCTCAAGGGCTTCCAATATT

MDC004268.215

22

+

9,006

No star found

0

0

0

10

10

miRC31

TCCATAATTTTTCCAGATCAA

MDC005072.383

21

+

9,885

No star found

0

0

8

0

8

miRC32

TGGTTTGGTTGGAAAACGGCT

MDC006935.286

21

-

27,531

No star found

0

7

0

0

7

miRC33

AATTAGGCTGGCATTAGACAA

MDC009589.310

21

+

3,312

No star found

6

0

0

0

6

miRC34

TGGTGATAGGATAGTTGGAAG

MDC010150.221

21

-

29,453

No star found

6

0

0

0

6

miRC35

TACTGTTATAATGGCATTCCC

MDC001086.52

21

+

12,332

No star found

5

0

0

0

5

miRC36

CTCAATTTGAACGCGTGGCTA

MDC015454.116

21

+

3,773

No star found

0

5

0

0

5

miRC37

TGGCCTTGGTGGAAGAGATCC

MDC000614.265

21

-

5,670

No star found

0

4

0

0

4

miRC38

TGGGCCTGGTCAGGAGGATCC

MDC018501.179

21

-

2,535

No star found

0

4

0

0

4

miRC39

TTAAATACAAGCAGGAGCTCT

MDC011810.169

21

+

42,284

No star found

0

3

0

0

3

miRC40

CACCTGGGACTTGCAGCCATG

MDC009540.166

21

+

1,015

No star found

3

0

0

0

3

miRC41

CATCCGAATTACCAATAACTG

MDC009746.72

21

+

18,725

No star found

0

0

3

0

3

miRC42

ATAGATGGAAGCTACCAACCC

MDC013676.252

21

+

6,707

No star found

0

0

0

3

3

  1. aDetailed information is listed in Table S5 in Additional file 1. bOnly one matched locus is shown in this table. Others are included in Table S5 in Additional file 1. cThe star sequence may have multiple variants. Only the best star sequence is shown in this table. Len, length; Str, strand.
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Genome Biology

ISSN: 1474-760X

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