Markers + reference

Peperomia

2 species · Piperaceae · Piperales

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Species 2
Genome length 151–156 kb
Candidate markers 277
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

13 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 277 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-GCU-trnG-UCC LSC 908 0.0472 0.77 69.5 yes View details
rpoB-trnC-GCA LSC 1132 0.0390 1.00 74.1 yes View details
petN-psbM LSC 915 0.0462 0.80 78.0 yes View details
trnT-GGU-psbD LSC 1665 0.0382 0.98 73.6 yes View details
trnP-UGG-psaJ LSC 468 0.0556 0.96 79.8 yes View details
psaJ-rpl33 LSC 428 0.0598 0.98 72.2 yes View details
rpl23 IRb 282 0.0035 1.00 43.5 no View details
ycf1 IRb 1481 0.0663 0.68 69.3 yes View details
ndhD SSC 1497 0.0160 1.00 53.3 yes View details
rps15-ycf1 SSC 499 0.1737 0.81 78.2 yes View details
ycf1 SSC 531 0.0769 0.02 53.6 no View details
ycf1 IRa 1481 0.0065 0.52 56.1 no View details
rpl23 IRa 282 NA 0.00 31.4 yes View details
ndhC-trnV-UAC LSC 1456 0.0341 0.95 82.9 yes View details
rps19-rpl2 IRb 134 0.0687 0.98 80.9 yes View details
petG-trnW-CCA LSC 142 0.0942 0.97 80.2 yes View details
rpl23-trnI-CAU IRb 162 0.0688 0.99 78.3 yes View details
trnE-UUC-trnT-GGU LSC 545 0.0462 0.87 78.2 yes View details
rps3-rpl22 LSC 89 0.1351 0.83 77.4 yes View details
ndhD-psaC SSC 140 0.0677 0.95 75.7 yes View details
rps8-rpl14 LSC 234 0.0526 0.97 74.4 yes View details
rpl14-rpl16 LSC 137 0.1176 0.99 74.3 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC TCCTGGACGTGAGGACTAAA CGCGAGGTTCCTTAGGAAAA 1484–1648 1.000 83.5
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC CGGAGAGAGAGGGATTCGAA CGCGAGGTTCCTTAGGAAAA 1285–1445 1.000 83.3
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC TCCTGGACGTGAGGACTAAA GTTTTCATTCGGCTCCTCCA 1745–1907 1.000 82.9
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC TCCTGGACGTGAGGACTAAA TGTTTTCATTCGGCTCCTCC 1746–1908 1.000 82.9
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC CGGAGAGAGAGGGATTCGAA GTTTTCATTCGGCTCCTCCA 1546–1704 1.000 82.8
rpoB-trnC-GCA_p1 rpoB-trnC-GCA ATGAAGTTCTTCGGCCAACC CCGGATTTGAACTGGGGAAA 1303–1379 1.000 78.5
rpoB-trnC-GCA_p2 rpoB-trnC-GCA ATGAAGTTCTTCGGCCAACC TGGGGAAAAAGGGATTTGCA 1291–1367 1.000 78.3
rpoB-trnC-GCA_p3 rpoB-trnC-GCA ATGAAGTTCTTCGGCCAACC TTGTTGATTAGGCGACACCC 1321–1397 1.000 77.6
rpoB-trnC-GCA_p4 rpoB-trnC-GCA GCCAACCCCCAATCAATGAA CCGGATTTGAACTGGGGAAA 1290–1366 1.000 76.4
rpoB-trnC-GCA_p5 rpoB-trnC-GCA GCCAACCCCCAATCAATGAA TGGGGAAAAAGGGATTTGCA 1278–1354 1.000 76.2
petN-psbM_p1 petN-psbM TCTTGCTTGGGCTGCTTTAA GCTGTTTATTCTAGTTCCTACTGC 924–1076 1.000 49.9
petN-psbM_p2 petN-psbM ACCTTTTCCCTTTCGCTTGT GCTGTTTATTCTAGTTCCTACTGC 893–1045 1.000 49.5
petN-psbM_p3 petN-psbM AGTAAGTCTTGCTTGGGCTG GCTGTTTATTCTAGTTCCTACTGC 930–1082 1.000 48.4
petN-psbM_p4 petN-psbM ATGGGGAAGAAGTGGACTCT GCTGTTTATTCTAGTTCCTACTGC 870–1022 1.000 47.3
petN-psbM_p5 petN-psbM GGGGACATAATTGGCATGGA GCTGTTTATTCTAGTTCCTACTGC 953–1105 1.000 46.9
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU TCGTAGAACCTTACCCCCAG ACGTCTTACCATGGCGTTAC 601–670 1.000 85.6
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU TCGTAGAACCTTACCCCCAG CCATGGCGTTACTCTACCAC 593–662 1.000 85.1
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU TCGTAGAACCTTACCCCCAG TGGCGTTACTCTACCACTGA 590–659 1.000 85.0
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG ACGTCTTACCATGGCGTTAC 565–634 1.000 84.8
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU TTCGTAGAACCTTACCCCCA ACGTCTTACCATGGCGTTAC 602–671 1.000 84.2
trnT-GGU-psbD_p1 trnT-GGU-psbD GTAACGCCATGGTAAGACGT ACAAAAACGAAACGGTCCCT 1810–1853 1.000 82.5
trnT-GGU-psbD_p2 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG ACAAAAACGAAACGGTCCCT 1818–1861 1.000 82.0
trnT-GGU-psbD_p3 trnT-GGU-psbD GTAACGCCATGGTAAGACGT CCCTTCGTAACCAGTCATCC 1794–1837 1.000 82.0
trnT-GGU-psbD_p4 trnT-GGU-psbD TCAGTGGTAGAGTAACGCCA ACAAAAACGAAACGGTCCCT 1821–1864 1.000 81.8
trnT-GGU-psbD_p5 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG CCCTTCGTAACCAGTCATCC 1802–1845 1.000 81.5
ndhC-trnV-UAC_p1 ndhC-trnV-UAC CCCCGGAAATTTGAAATGCC AGAAGGTCTACGGTTCGAGT 1535–1577 1.000 84.7
ndhC-trnV-UAC_p2 ndhC-trnV-UAC CCCCGGAAATTTGAAATGCC GAAGGTCTACGGTTCGAGTC 1534–1576 1.000 81.9
ndhC-trnV-UAC_p3 ndhC-trnV-UAC GGGCTAAAACCCCGGAAATT AGAAGGTCTACGGTTCGAGT 1544–1586 1.000 81.3
ndhC-trnV-UAC_p4 ndhC-trnV-UAC GGGGATTCATTAATCGGGGC AGAAGGTCTACGGTTCGAGT 1560–1602 1.000 81.1
ndhC-trnV-UAC_p5 ndhC-trnV-UAC CCCCGGAAATTTGAAATGCC GTTCGAGTCCGTATAGCCCT 1523–1565 1.000 80.8

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
Peperomia griseoargentea NC_087888.1 155934 View on NCBI ↗
Peperomia latifolia NC_080992.1 151016 View on NCBI ↗