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Table 1 ASAP PCR primers. Primer sequences, annealing site and the relative position in tobacco (Nt), Arabidopsis (At) and maize (Zm) are presented, along with the anticipated amplicon size. * represent the primers with low sequence similarity in maize.

From: ASAP: Amplification, sequencing & annotation of plastomes

Primer

Gene (Nicotiana)

Sequence 5' to 3'

Position in Nt

Size

Position in At

Size

Position in Zm

Size

IRB1F

Upstream of JLB

ggatttttttttagtgaacgtgtcac

86657–86682

804

84258–84283

812

82644–82669*

1001

IRB1R

Intron rpl2

aagtatcgacgtaatttcatagagtc

87436–87461

 

85045–85070

 

83622–83647

 

IRB2F

Intron rpl2

catctggcttatgttcttcatgtagc

87397–87422

1048

85006–85031

1049

83583–83608

1043

IRB2R

rpl23 3'end

caactaggacagaaataaagcattgg

88420–88445

 

86030–86055

 

84601–84626

 

IRB3F

rpl23 3'end

atacgtctgtaatgcattgtatgtcc

88310–88335

1001

85920–85945

980

84491–84516

 

IRB3R

YCF2/ORF2280 5'

gaagatacaggagcgaaacaatcaac

89285–89311

 

86875–86900

 

Deleted

 

IRB4F

YCF2/ORF2280

aagaaaaaatctctatttgatagggc

89181–89206

1031

86770–86795

1037

Deleted

 

IRB4R

YCF2/ORF2280

tttcgttccgtttgaagaaaggaagg

90212–90187

 

87782–87807

 

Deleted

 

IRB5F

YCF2/ORF2280

ggattccattagtaatgaggattcgg

90096–90121

1162

87685–87710

1171

Deleted

 

IRB5R

YCF2/ORF2280

gaggctcgaaccatttcttctgactc

91233–91258

 

88831–88856

 

Deleted

 

IRB6F

YCF2/ORF2280

cttcgaatatggaattcaaagggatc

91131–91156

1042

88729–88754

1081

Deleted

 

IRB6R

YCF2/ORF2280

tgaatatgttagatacctgtgactcg

92148–92173

 

89785–89810

 

Deleted

 

IRB7F

YCF2/ORF2280

acaattcctcaatatcttgttcattc

92049–92074

1091

89680–89705

1088

Deleted

 

IRB7R

YCF2/ORF2280

tcttctagagaatctcctaattgttc

93115–93140

 

90743–90768

 

Deleted

 

IRB8F

YCF2/ORF2280

gaaaaggtcaaatctttgatgattcc

92995–93020

1041

90623–90648

1035

Deleted

 

IRB8R

YCF2/ORF2280

tttccggcatcatatccatagttagc

94011–94036

 

91633–91658

 

Deleted

 

IRB9F

YCF2/ORF2280

ctgaacaagttcctggataacaagcc

93853–93878

1169

91493–91518

1151

Deleted

 

IRB9R

YCF2/ORF2280

aaatctctgatcaaggatagaacaag

94997–95022

 

92619–92644

 

Deleted

 

IRB10F

YCF2/ORF2280

gatctagttcatggcctattagaagt

94849–94874

1025

92471–92496

1021

86077–86102

1138

IRB10R

ORF 87/YCF 15

taacatattcttccatggagctaagg

93849–95874

 

93475–93492

 

87190–87215*

 

IRB11F

YCF2/ORF2280 3'

cggatgaaatgaaaattggattcatg

95669–95724

1094

93330–93355

1319

No similarity

 

IRB11R

ORF 79

aatcggacctgctttttacatatctc

96739–96763

 

94624–94649

 

No similarity

 

IRB12F

ORF 79

ccaattgcttcgatttgaattatccg

96626–96644

1061

94483–94508

1101

88794–88819

1079

IRB12R

ndhB 3' exon

tggaaatcctagctattcttagcatg

97662–97687

 

95559–95584

 

89848–89873

 

IRB13F

ndhB 3' exon

attccaataattacatatccgatttg

97567–97592

1043

95464–95489

1049

89753–89778

1068

IRB13R

ndhB 5' exon

cttatcaatacacaaatgtataactc

98585–98610

 

96488–96513

 

90796–90821

 

IRB14F

ndhB 5' exon

tacgtcaggagtccattgatgagaag

98494–98519

1171

96397–96422

1206

90705–90730

1192

IRB14R

rps 7 5'end

aatatggctttcaaattaagttccga

99640–99665

 

97578–97603

 

91872–91897

 

IRB15F

rps 7 5'end

gtgcaaaagctctatttgcctctgcc

99551–99576

1230

97489–97514

1231

91783–91808

1245

IRB15R

rps12 exon 2

tcactgcttatatacccggtattggc

100754–100781

 

98695–98720

 

93003–93028

 

IRB16F

rps12 exon 2

tcctcgaacaatgtgatatctcacac

100699–100694

968

98608–98633

1079

92916–92941

859

IRB16R

Spacer

caacataggtcatcgaaaggatctcg

101642–101667

 

99662–99687

 

93750–93775

 

IRB17F

Spacer

gtgtgagcttatccatgcggttatgc

101554–101581

1116

99576–99601

1345

93669–93694

1339

IRB17R

rrn16 start

gcttcatattcgcccggagttcgctc

102645–102670

 

100896–100921

 

95043–95068*

 

IRB18F

trnV 3' end

aagtcatcagttcgagcctgattatc

102504–102529

1117

100751–100776

1122

94901–94926

1121

IRB18R

rrn16 start

tgagtttcattcttgcgaacgtactc

103596–103621

 

101848–101873

 

95997–96022

 

IRB19F

rrn16

cgacactgacactgagagacgaaagc

103452–103477

1343

101704–101729

1341

95853–95878

1347

IRB19R

trnI Intron/OriA

atcgaaagttggatctacattggatc

104770–104795

 

103020–103045

 

97175–97200

 

IRB20F

trnI start

gggctattagctcagtggtagagcgc

104551–104576

877

102801–102826

898

96953–96978

1119

IRB20R

trnA start

caagagcggagctctaccaactgagc

105403–105428

 

103674–103699

 

98047–98072

 

IRB21F

trnI end

gaggtctctggttcaagtccaggatg

105229–105324

941

103571–103596

962

97943–97968

968

IRB21R

trnA end

ataagcggactcgaaccgctgacatc

106145–106170

 

104508–104533

 

98886–98911

 

IRB22F

trnA intron

agattttgagaagagttgctctttgg

106003–106028

1190

104367–104392

1188

98743–98768

1193

IRB22R

23S

tagatgtccagtcaactgctgcgcct

107168–107193

 

105530–105555

 

99911–99936

 

IRB23F

23S

gaaactaagtggaggtccgaaccgac

107053–107079

1225

105416–105441

1224

99797–99822

1291

IRB23R

23S

cgctaccttaggaccgttatagttac

108253–108278

 

106615–106640

 

101063–101088

 

IRB24F

23S

ggtctccgcaaagtcgtaagaccatg

108131–108156

1172

106493–106518

1169

100941–100966

1156

IRB24R

4.5S

acatcactgcacttccacttgacacc

109278–109303

 

107637–107662

 

102072–102097

 

IRB25F

23S end

ctgctgaaagcatctaagtagtaagc

109089–109115

963

107451–107476

929

101897–101922

920

IRB25R

trnR end

ggttgtgggcgaggagggattcgaac

110027–110052

 

108355–108380

 

102792–102817

 

IRB26F

Spacer

aaatggctggggagaggaaaggttcc

109905–109930

1182

108231–108256

1232

No similarity

 

IRB26R

ORF350

attatcttcatgcataaggatactag

111062–111087

 

109438–109463

 

No similarity

 

IRB27F

Spacer

tggctctatttcattatattccatcc

110844–110869

1036

109225–109250

986

No similarity

 

IRB27R

ORF 350

agtggatccctcttgttcctgtttag

111855–111880

 

110186–110211

 

No similarity

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