Markers + reference

Platostoma

2 species · Lamiaceae · Lamiales

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Species 2
Genome length 153–153 kb
Candidate markers 268
Primer pairs 100

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 10 remaining regions by MarkerSeek score (out of 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 569 0.0035 1.00 55.0 yes View details
rps16-trnQ-UUG LSC 920 0.0022 1.00 60.0 yes View details
atpA LSC 1524 0.0007 1.00 56.8 yes View details
atpH-atpI LSC 1014 0.0020 1.00 49.3 yes View details
rpoC2 LSC 4152 0.0010 1.00 54.4 yes View details
petA-psbJ LSC 1023 0.0020 0.99 61.0 yes View details
clpP LSC 1921 0.0016 1.00 55.4 yes View details
rpoA LSC 1008 0.0030 1.00 60.5 yes View details
rps15-ycf1 SSC 446 0.0045 1.00 58.6 yes View details
rpl2-rpl23 IRb 18 0.0556 1.00 81.9 yes View details
rpl23-rpl2 IRa 18 0.0556 1.00 81.9 yes View details
psbE-petL LSC 893 0.0034 1.00 60.7 yes View details
rpl20-rps12 LSC 725 0.0028 1.00 60.3 yes View details
psaA-ycf3 LSC 750 0.0000 0.99 60.0 yes View details
rps4-trnT-UGU LSC 400 0.0026 0.96 59.9 yes View details
trnS-GCU-trnG-UCC LSC 782 0.0000 0.99 59.6 yes View details
rps2 LSC 711 0.0014 1.00 59.6 yes View details
trnF-GAA-ndhJ LSC 660 0.0015 1.00 59.6 yes View details
rbcL-accD LSC 643 0.0016 1.00 59.6 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
trnK-UUU-rps16_p1 trnK-UUU-rps16 TCTAGCCGCACTTAAAAGCC AAAAGGAGCTCAACCCACAG 677–678 1.000 78.1
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA AAAAGGAGCTCAACCCACAG 672–673 1.000 78.0
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCGCGGTCTTCCAAAGTTTA AAAAGGAGCTCAACCCACAG 744–745 1.000 76.0
trnK-UUU-rps16_p4 trnK-UUU-rps16 CGCGGTCTTCCAAAGTTTAC AAAAGGAGCTCAACCCACAG 743–744 1.000 75.5
trnK-UUU-rps16_p5 trnK-UUU-rps16 TCTAGCCGCACTTAAAAGCC AAAAAGGAGCTCAACCCACA 678–679 1.000 74.6
rps16-trnQ-UUG_p1 rps16-trnQ-UUG TCCACAACGGGTCATATCCT GAGGTTCGAATCCTTCCGTC 1015–1016 1.000 78.5
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 993–994 1.000 78.4
rps16-trnQ-UUG_p3 rps16-trnQ-UUG TCCACAACGGGTCATATCCT TAGCAATTGAAATGGGGCGT 1075–1076 1.000 77.9
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TAGCAATTGAAATGGGGCGT 1053–1054 1.000 77.8
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CCACAACGGGTCATATCCTT GAGGTTCGAATCCTTCCGTC 1014–1015 1.000 73.9
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA ACGAATCGCACTTTTACCACT 844–851 1.000 70.7
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC ACGAATCGCACTTTTACCACT 843–850 1.000 70.7
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA ACGAATCGCACTTTTACCAC 844–851 1.000 70.7
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC ACGAATCGCACTTTTACCAC 843–850 1.000 70.7
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA ACGAATCGCACTTTTACCACT 898–905 1.000 69.5
atpA_p1 atpA GGTTCAAATCCTATTGGACGC CGATGAAAGAAATAACTGATTAGTCT 1763–1764 1.000 40.0
atpA_p2 atpA GGTTCAAATCCTATTGGACGC CGATGAAAGAAATAACTGATTAGTC 1763–1764 1.000 40.0
atpA_p3 atpA GGTTCAAATCCTATTGGACGC CGATGAAAGAAATAACTGATTAGTCTT 1763–1764 1.000 40.0
atpA_p4 atpA GGTTCAAATCCTATTGGACGC CGATGAAAGAAATAACTGATTAGT 1763–1764 1.000 40.0
atpA_p5 atpA GTTCAAATCCTATTGGACGCA CGATGAAAGAAATAACTGATTAGTCT 1762–1763 1.000 40.0
atpH-atpI_p1 atpH-atpI AACGGAAGCAGCAGAAATCA TCCCTGTCATGTTCCTTGGA 1146–1148 1.000 77.4
atpH-atpI_p2 atpH-atpI AGCCAATCCAGCAGCAATAA TCCCTGTCATGTTCCTTGGA 1164–1166 1.000 77.0
atpH-atpI_p3 atpH-atpI GCCAATCCAGCAGCAATAAC TCCCTGTCATGTTCCTTGGA 1163–1165 1.000 76.5
atpH-atpI_p4 atpH-atpI TCCAGCAGCAATAACGGAAG TCCCTGTCATGTTCCTTGGA 1158–1160 1.000 76.1
atpH-atpI_p5 atpH-atpI AACGGAAGCAGCAGAAATCA TTTTTGCAACTTTAGCCGCG 1098–1100 1.000 75.3
rps2_p1 rps2 ACCGATTCCATAAATCTATCCGA ACGGTAGAAGAGAAGGTTCCA 865–868 1.000 40.1
rps2_p2 rps2 ACCGATTCCATAAATCTATCCGA AGAAGAGAAGGTTCCATCGGA 860–863 1.000 40.1
rps2_p3 rps2 ACCGATTCCATAAATCTATCCGA TGGCCAATCTACGGTAGAAGA 875–878 1.000 40.1
rps2_p4 rps2 ACCGATTCCATAAATCTATCCGA TGGCCAATCTACGGTAGAAG 875–878 1.000 40.1
rps2_p5 rps2 ACCGATTCCATAAATCTATCCGA GAAGAGAAGGTTCCATCGGA 859–862 1.000 40.1

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
Platostoma chinense MT328397.1 152547 View on NCBI ↗
Platostoma palustre PV476670.1 152535 View on NCBI ↗