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Table 1 Primers used in the in silico PCR extraction of the HVRs

From: DAIRYdb: a manually curated reference database for improved taxonomy annotation of 16S rRNA gene sequences from dairy products

Label

Name - ARB primers

HVR

Location*

bp

Primer sequence

GC%

Reference

Original reference primer

8F_v1f

S-D-Bact-0008-d-S-20

v1F

8-27

20

AGAGTTTGATCMTGGCTCAG

50

[67]

 

120R_v1r

S-D-Bact-0120-e-A-20

v1R

101-120

20

TTACTCACCCGTNCGCCRCT

55

mod. rev-compl. after [68]

 

101F_v2f

S-D-Bact-0101-a-S-20

v2F

101-120

20

AGYGGCGNACGGGTGAGTAA

55

mod. after [68]

 

355R_v2r

S-D-Bact-0355-a-A-18

v2R

338-355

18

GCWGCCTCCCGTAGGAGT

66

mod. after [69]

 

338F_v3f

S-D-Bact-0338-a-S-20

v3F

337-354

20

ACWCCTACGGGWGGCAGCAG

65

mod. after [70]

 

534R_v3r

S-D-Bact-0518-b-A-17

v3R

518-534

17

ATTACCGCGGCTGCTGG

65

[71]

 

515F_v4f

S-*-Univ-0515-b-S-19

v4F

515-533

19

GTGNCAGCMGCCGCGGTAA

63

mod. after [72]

 

806R_v4r

S-D-Bact-0756-a-A-20

v4R

787-806

20

GGACTACHVGGGTWTCTAAT

40

mod. after [72]

 

784F_v5f

S-*-Univ-0779-a-S-15

v5F

784-798

15

RGGATTAGATACCCY

40

mod. after [73]

 

926R_v5r

S-D-Bact-0907-b-A-20

v5R

907-926

20

CCGTCAATTYYTTTRAGTTT

25

mod. after [74]

 

907F_v6f

S-D-Bact-0907-a-S-20

v6F

907-926

20

AAACTYAAARRAATTGACGG

25

[75]

 

1114R_v6r

S-D-Bact-1114-b-A-16

v6R

1099-1114

16

GGGTYKCGCTCGTTRY

50

mod. after [73]

S-D-Bact-1114-a-A-16

1099F_v7f

S-*-Univ-1099-a-S-16

v7F

1099-1114

16

RYAACGAGCGMRACCC

50

new primer

S-*-Univ-1100-a-S-15

1200R_v7r

S-D-Bact-1200-a-A-16

v7R

1185-1200

16

GAYTTGACRTCVTCCM

38

new primer

 

1185F_v8f

S-D-Bact-1185-a-S-16

v8F

1185-1200

16

KGGABCACCGCYCGYC

63

new primer

 

1407R_v8r

S-D-Bact-1407-a-A-16

v8R

1391-1407

16

GRCGRGCGGTGWGTRC

63

mod. after [76]

S-D-Bact-1391-a-A-17

1391F_v9f

S-D-Bact-1391-a-S-16

v9F

1391-1407

16

GYACWCACCGCYCGYC

63

new primer

 

1510R_v9r

S-*-Univ-1510-b-A-19

v9R

1492-1510

19

GGNTACCTTGTTACGACTT

42

mod. after [77]

S-*-Univ-1492-a-A-21

  1. *E. coli position as a reference