Markers + reference

Petunia

2 species · Solanaceae · Solanales

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Species 2
Genome length 157–157 kb
Candidate markers 271
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 409 0.0098 1.00 51.4 yes View details
trnK-UUU-rps16 LSC 698 0.0057 1.00 62.3 yes View details
trnG-GCC-trnfM-CAU LSC 233 0.0129 1.00 59.9 yes View details
petD LSC 1232 0.0024 1.00 52.4 yes View details
rpoA LSC 1014 0.0030 1.00 51.7 yes View details
rpl36-rps8 LSC 427 0.0094 1.00 60.5 yes View details
ycf15-trnL-CAA IRb 348 0.0115 1.00 60.1 yes View details
ycf1 IRb 1005 0.0000 1.00 40.0 no View details
ndhF-rpl32 SSC 776 0.0064 1.00 62.5 yes View details
ycf1 SSC 5724 0.0035 1.00 42.4 yes View details
ndhB-trnL-CAA IRa 539 0.0000 1.00 34.5 yes View details
trnL-CAA-Ycf15 IRa 348 0.0115 1.00 60.1 yes View details
matK LSC 1524 0.0039 1.00 61.0 yes View details
trnS-GCU-trnG-UCC LSC 707 0.0000 0.98 60.8 yes View details
trnT-UGU-trnL-UAA LSC 711 0.0028 1.00 60.5 yes View details
ndhC-trnV-UAC LSC 1102 0.0027 1.00 60.3 yes View details
accD-psaI LSC 754 0.0027 1.00 60.3 yes View details
rpoB-trnC-GCA LSC 1284 0.0023 1.00 60.1 yes View details
ycf3-trnS-GGA LSC 840 0.0024 1.00 60.1 yes View details
petN-psbM LSC 1117 0.0018 1.00 59.8 yes View details
petA-psbJ LSC 1097 0.0018 1.00 59.8 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 100 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 479–481 1.000 79.0
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TTCCCTCTAGACCTAGCTGC 493–495 1.000 79.0
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TTCCCTCTAGACCTAGCTGC 492–494 1.000 79.0
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TTCCCTCTAGACCTAGCTGC 494–496 1.000 79.0
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCGTGCTAACCTTGGTATGG 528–530 1.000 76.9
matK_p1 matK ACTCAGTTGATTTACCCCTT CCCTCAAAATCTTCCATCTTTGG 1659 1.000 40.3
matK_p2 matK ACTCAGTTGATTTACCCCTT TCCATCTTTGGTTCAAATCGA 1647 1.000 40.3
matK_p3 matK ACTCAGTTGATTTACCCCTT CTTCCATCTTTGGTTCAAATCGA 1649 1.000 40.3
matK_p4 matK ACTCAGTTGATTTACCCCTT TCTTCCATCTTTGGTTCAAATCG 1650 1.000 40.3
matK_p5 matK ACTCAGTTGATTTACCCCTT TCCATCTTTGGTTCAAATCGAA 1647 1.000 40.3
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TTGAAAAAGGGGCTCAACCT 829–830 1.000 75.5
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TTGAAAAAGGGGCTCAACCT 828–829 1.000 75.5
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCAGTCGTGGTCTTCCAAAC TTGAAAAAGGGGCTCAACCT 914–915 1.000 74.9
trnK-UUU-rps16_p4 trnK-UUU-rps16 CAGTCGTGGTCTTCCAAACT TTGAAAAAGGGGCTCAACCT 913–914 1.000 74.8
trnK-UUU-rps16_p5 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA TTGAAAAAGGGGCTCAACCT 838–839 1.000 74.5
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA ACGAATCACACTTTTACCACT 766–781 1.000 53.0
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA ACGAATCACACTTTTACCACT 815–830 1.000 52.0
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA AGAACGAATCACACTTTTACCAC 769–784 1.000 51.9
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA GAACGAATCACACTTTTACCACT 768–783 1.000 51.9
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA AACGAATCACACTTTTACCACT 767–782 1.000 51.0
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CTCATTTCCATCCCCGAGC CCGGATTTGAACTGGGGAAA 1368 1.000 71.4
rpoB-trnC-GCA_p2 rpoB-trnC-GCA ATTCCCTCATTTCCATCCCC CCGGATTTGAACTGGGGAAA 1373 1.000 70.9
rpoB-trnC-GCA_p3 rpoB-trnC-GCA TCATTTCCATCCCCGAGCAT CCGGATTTGAACTGGGGAAA 1367 1.000 70.3
rpoB-trnC-GCA_p4 rpoB-trnC-GCA CTCATTTCCATCCCCGAGC AGTCCTCTGCCTTACCACTC 1337 1.000 68.6
rpoB-trnC-GCA_p5 rpoB-trnC-GCA CATTTCCATCCCCGAGCAT CCGGATTTGAACTGGGGAAA 1366 1.000 68.1
petN-psbM_p1 petN-psbM ACTCGTAGTGTGGGGAAGAA AGTTCCTACCGCTTTTCTACT 1206 1.000 59.2
petN-psbM_p2 petN-psbM TCGTAGTGTGGGGAAGAAGT AGTTCCTACCGCTTTTCTACT 1204 1.000 59.2
petN-psbM_p3 petN-psbM TCTTGCTTGGGCTGCTTTAA AGTTCCTACCGCTTTTCTACT 1251 1.000 59.2
petN-psbM_p4 petN-psbM CGTAGTGTGGGGAAGAAGTG AGTTCCTACCGCTTTTCTACT 1203 1.000 58.6
petN-psbM_p5 petN-psbM AGTAAGTCTTGCTTGGGCTG AGTTCCTACCGCTTTTCTACT 1257 1.000 57.7

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (2)

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

Species Accession Length (bp) Link
Petunia exserta NC_050782.1 156597 View on NCBI ↗
Petunia x hybrida NC_040178.1 156575 View on NCBI ↗