Markers + reference

Nicotiana

15 species · Solanaceae · Solanales

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Species 15
Genome length 155–156 kb
Candidate markers 264
Primer pairs 80

Genome-wide nucleotide diversity

Sliding-window nucleotide diversity
Sliding-window nucleotide diversity (π) across the plastome.

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 264 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 402 0.0335 1.00 72.4 yes View details
trnK-UUU-rps16 LSC 716 0.0180 0.97 60.9 yes View details
rps16-trnQ-UUG LSC 1207 0.0268 1.00 76.4 yes View details
ndhC-trnV-UAC LSC 1101 0.0154 0.99 62.9 yes View details
ycf1 IRb 1014 0.0021 1.00 36.4 no View details
ndhF-rpl32 SSC 787 0.0141 0.98 62.7 yes View details
rpl32-trnL-UAG SSC 937 0.0180 0.99 64.5 yes View details
rps15-ycf1 SSC 396 0.0224 1.00 53.6 yes View details
ycf1 SSC 5694 0.0116 1.00 48.7 yes View details
rpl2-trnH-GUG IRa 127 0.0511 0.91 73.1 no View details
trnT-GGU-psbD LSC 1219 0.0110 1.00 67.6 yes View details
psbM-trnD-GUC LSC 1074 0.0075 1.00 65.2 yes View details
rps19-rpl2 IRb 62 0.0175 1.00 60.6 yes View details
trnS-GCU-trnG-UCC LSC 790 0.0133 0.99 60.0 yes View details
accD-psaI LSC 757 0.0107 0.99 59.9 yes View details
trnE-UUC-trnT-GGU LSC 860 0.0094 1.00 58.6 yes View details
ycf1-ndhF SSC 30 0.0340 1.00 58.6 yes View details
atpH-atpI LSC 1165 0.0090 0.99 58.1 yes View details
Candidate markers include all hotspot labels marked in the diversity plot, listed in genomic order, plus the top 10 remaining regions by MarkerSeek score. Primer design is attempted for every listed region. Primer available: yes means at least one valid primer pair was found; no means no valid pair passed screening; NA means primer design was skipped.

Primer pairs

Showing the top 30 of 80 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 433–535 1.000 90.4
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TTCCCTCTAGACCTAGCTGC 447–549 1.000 90.3
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TTCCCTCTAGACCTAGCTGC 446–548 1.000 90.3
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TTCCCTCTAGACCTAGCTGC 448–550 1.000 90.3
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCGTGCTAACCTTGGTATGG 482–584 1.000 88.1
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT AGGAACTTCGTCCTAATCAATCC 728–776 1.000 62.9
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT GGAACTTCGTCCTAATCAATCCT 727–775 1.000 62.9
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AGGAACTTCGTCCTAATCAATCC 727–775 1.000 62.9
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GGAACTTCGTCCTAATCAATCCT 726–774 1.000 62.9
trnK-UUU-rps16_p5 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA GGAACTTCGTCCTAATCAATCCT 736–784 1.000 61.9
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1210–1308 1.000 90.3
rps16-trnQ-UUG_p2 rps16-trnQ-UUG CACAACGGATCCTGTCCTTC GAGGTTCGAATCCTTCCGTC 1230–1321 0.933 86.5
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CGGATCCTGTCCTTCAAGTC GAGGTTCGAATCCTTCCGTC 1225–1316 0.933 86.3
rps16-trnQ-UUG_p4 rps16-trnQ-UUG GGATCCTGTCCTTCAAGTCG GAGGTTCGAATCCTTCCGTC 1224–1315 0.933 86.3
rps16-trnQ-UUG_p5 rps16-trnQ-UUG GATCCTGTCCTTCAAGTCGC GAGGTTCGAATCCTTCCGTC 1223–1314 0.933 85.9
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA ACGAATCACACTTTTACCACT 849–879 1.000 57.9
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA AGAACGAATCACACTTTTACCAC 852–882 1.000 56.8
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA GAACGAATCACACTTTTACCACT 851–881 1.000 56.8
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA ACGAATCACACTTTTACCACT 898–928 1.000 56.7
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA AACGAATCACACTTTTACCACT 850–880 1.000 56.0
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT TACCTGTCATGCTCCTTGGA 1292–1311 1.000 83.8
atpH-atpI_p2 atpH-atpI AATAACGGAAGCGGCAGAAA TACCTGTCATGCTCCTTGGA 1293–1312 1.000 82.6
atpH-atpI_p3 atpH-atpI GCCAATCCAGCAGCAATAAC TACCTGTCATGCTCCTTGGA 1307–1326 1.000 82.3
atpH-atpI_p4 atpH-atpI TCCAGCAGCAATAACGGAAG TACCTGTCATGCTCCTTGGA 1302–1321 1.000 82.0
atpH-atpI_p5 atpH-atpI ATCCAGCAGCAATAACGGAA TACCTGTCATGCTCCTTGGA 1303–1322 1.000 80.7
psbM-trnD-GUC_p1 psbM-trnD-GUC AGTAGAAAAGCGGTAGGAACT CCCGTATTTCCCTGGGATTG 1215–1247 1.000 64.2
psbM-trnD-GUC_p2 psbM-trnD-GUC AGTAGAAAAGCGGTAGGAACT TCCCGTATTTCCCTGGGATT 1216–1248 1.000 63.6
psbM-trnD-GUC_p3 psbM-trnD-GUC AAGTAGAAAAGCGGTAGGAACT CCCGTATTTCCCTGGGATTG 1216–1248 1.000 62.0
psbM-trnD-GUC_p4 psbM-trnD-GUC AGAAAAGCGGTAGGAACTAGA CCCGTATTTCCCTGGGATTG 1212–1244 1.000 62.0
psbM-trnD-GUC_p5 psbM-trnD-GUC AAGTAGAAAAGCGGTAGGAACT TCCCGTATTTCCCTGGGATT 1217–1249 1.000 61.4

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (15)

One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.

Species Accession Length (bp) Link
Nicotiana amplexicaulis NC_056976.1 155909 View on NCBI ↗
Nicotiana attenuata NC_035952.1 155886 View on NCBI ↗
Nicotiana debneyi NC_056977.1 156073 View on NCBI ↗
Nicotiana glauca NC_056979.1 156058 View on NCBI ↗
Nicotiana knightiana BK010737.1 155963 View on NCBI ↗
Nicotiana otophora NC_032724.1 156073 View on NCBI ↗
Nicotiana paniculata BK010741.1 155689 View on NCBI ↗
Nicotiana repanda NC_056981.1 155454 View on NCBI ↗
Nicotiana rustica BK010738.1 155850 View on NCBI ↗
Nicotiana stocktonii NC_056980.1 155639 View on NCBI ↗
Nicotiana suaveolens NC_056978.1 155883 View on NCBI ↗
Nicotiana sylvestris NC_007500.1 155941 View on NCBI ↗
Nicotiana tabacum NC_001879.2 155943 View on NCBI ↗
Nicotiana tomentosiformis NC_007602.1 155745 View on NCBI ↗
Nicotiana undulata NC_016068.1 155863 View on NCBI ↗