Markers + reference

Phytolacca

11 species · Phytolaccaceae · Caryophyllales

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Species 11
Genome length 155–157 kb
Candidate markers 263
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 263 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 777 0.0427 1.00 80.1 yes View details
trnS-GCU-trnG-UCC LSC 810 0.0307 0.95 65.9 yes View details
psaA-ycf3 LSC 511 0.0281 1.00 57.4 yes View details
trnT-UGU-trnL-UAA LSC 744 0.0273 0.92 63.9 yes View details
ndhC-trnV-UAC LSC 1197 0.0291 1.00 67.5 yes View details
trnM-CAU-atpE LSC 307 0.0485 0.99 65.8 yes View details
accD-psaI LSC 669 0.0251 0.99 59.3 yes View details
rpl2 IRb 825 0.0016 1.00 31.2 no View details
ndhF-rpl32 SSC 1192 0.0308 0.98 72.7 yes View details
rpl32-trnL-UAG SSC 1179 0.0267 1.00 65.7 yes View details
rpl2 IRa 825 0.0016 1.00 36.3 yes View details
rps4-trnT-UGU LSC 510 0.0294 0.98 72.2 yes View details
trnK-UUU-rps16 LSC 616 0.0156 0.98 66.0 yes View details
rpl33-rps18 LSC 207 0.0389 1.00 65.2 yes View details
psbM-trnD-GUC LSC 993 0.0114 1.00 62.5 yes View details
ccsA-ndhD SSC 199 0.0433 1.00 62.2 yes View details
atpH-atpI LSC 716 0.0146 1.00 61.1 yes View details
trnD-GUC-trnY-GUA LSC 483 0.0198 0.99 61.0 yes View details
petA-psbJ LSC 969 0.0209 0.99 59.6 yes View details
psbE-petL LSC 973 0.0187 0.98 59.1 yes View details
psbI-trnS-GCU LSC 204 0.0260 1.00 56.8 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
trnK-UUU-rps16_p1 trnK-UUU-rps16 ACGAATCCCTTGCTTCATCC GGAGGGCAGGAGTTTTGAAA 704–752 1.000 86.7
trnK-UUU-rps16_p2 trnK-UUU-rps16 ACGAATCCCTTGCTTCATCC GCTCAACCTACAGAAACCGT 738–786 1.000 85.3
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCCTAGCCGCACTTAAAAGC GGAGGGCAGGAGTTTTGAAA 670–718 1.000 85.0
trnK-UUU-rps16_p4 trnK-UUU-rps16 GAATCCCTTGCTTCATCCGA GGAGGGCAGGAGTTTTGAAA 702–750 1.000 84.4
trnK-UUU-rps16_p5 trnK-UUU-rps16 TCCTAGCCGCACTTAAAAGC GCTCAACCTACAGAAACCGT 704–752 1.000 83.6
rps16-trnQ-UUG_p1 rps16-trnQ-UUG TATGTCCTTCAAGTCGCACG GAGGTTCGAATCCTTCCGTC 536–920 1.000 90.8
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TATGTCCTTCAAGTCGCACG TAAGGCATCGGGTTTTGGTC 566–950 1.000 89.8
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GCACGTTGCTTTTTACCACA GAGGTTCGAATCCTTCCGTC 521–905 1.000 89.5
rps16-trnQ-UUG_p4 rps16-trnQ-UUG GCACGTTGCTTTTTACCACA TAAGGCATCGGGTTTTGGTC 551–935 1.000 88.4
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AGTCGCACGTTGCTTTTTAC GAGGTTCGAATCCTTCCGTC 525–909 1.000 88.0
psbI-trnS-GCU_p1 psbI-trnS-GCU GTTTGGCAAGCTGCTGTAAG GCTTTGGGGCGAAGAAGTAT 1335–1405 1.000 86.1
psbI-trnS-GCU_p2 psbI-trnS-GCU CACAATCCGGATCACCTTGT GCTTTGGGGCGAAGAAGTAT 1181–1251 1.000 85.7
psbI-trnS-GCU_p3 psbI-trnS-GCU GTTTGGCAAGCTGCTGTAAG AGGCCGCGGGAATAATAAAA 1364–1434 1.000 85.2
psbI-trnS-GCU_p4 psbI-trnS-GCU GTTTGGCAAGCTGCTGTAAG ATCCGTTGTACGACTCGTTC 821–865 0.636 68.6
psbI-trnS-GCU_p5 psbI-trnS-GCU CACAATCCGGATCACCTTGT ATCCGTTGTACGACTCGTTC 667–711 0.636 68.0
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CTTTCGTCCACTCAGCCATC CGGAATAGTAATCAAACCGGGA 878–920 1.000 67.6
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC CTTTCGTCCACTCAGCCATC TCGGAATAGTAATCAAACCGGG 879–921 1.000 67.6
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC TTTCGTCCACTCAGCCATCT CGGAATAGTAATCAAACCGGGA 877–919 1.000 64.5
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC TTTCGTCCACTCAGCCATCT TCGGAATAGTAATCAAACCGGG 878–920 1.000 64.5
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC CTTTCGTCCACTCAGCCATC CGGAATAGTAATCAAACCGGG 878–920 1.000 64.1
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT CGAATCCATGGAGGGTCATC 766–792 1.000 82.9
atpH-atpI_p2 atpH-atpI TACCTTGACCAACTCCAGGT CGAATCCATGGAGGGTCATC 822–848 1.000 82.0
atpH-atpI_p3 atpH-atpI AGCCAATCCAGCAGCAATAA CGAATCCATGGAGGGTCATC 782–808 1.000 82.0
atpH-atpI_p4 atpH-atpI AATAACGGAAGCGGCAGAAA CGAATCCATGGAGGGTCATC 767–793 1.000 81.8
atpH-atpI_p5 atpH-atpI GCAGTACCTTGACCAACTCC CGAATCCATGGAGGGTCATC 826–852 1.000 81.4
psbM-trnD-GUC_p1 psbM-trnD-GUC TCATTTTGGCTGACCGTTTT GTTCCCGGGGATTGTAGTTC 1148–1177 1.000 71.8
psbM-trnD-GUC_p2 psbM-trnD-GUC AATCATTTTGGCTGACCGTT GTTCCCGGGGATTGTAGTTC 1150–1179 1.000 69.9
psbM-trnD-GUC_p3 psbM-trnD-GUC ATCATTTTGGCTGACCGTTT GTTCCCGGGGATTGTAGTTC 1149–1178 1.000 69.9
psbM-trnD-GUC_p4 psbM-trnD-GUC TCATTTTGGCTGACCGTTTTT GTTCCCGGGGATTGTAGTTC 1148–1177 1.000 69.8
psbM-trnD-GUC_p5 psbM-trnD-GUC TCATTTTGGCTGACCGTTTT AGTTCCCGGGGATTGTAGTT 1149–1178 1.000 69.4

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (11)

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

Species Accession Length (bp) Link
Phytolacca acinosa NC_040941.1 155121 View on NCBI ↗
Phytolacca americana NC_067846.1 155092 View on NCBI ↗
Phytolacca americana var. americana MH286315.1 155094 View on NCBI ↗
Phytolacca dioica NC_068261.1 155365 View on NCBI ↗
Phytolacca icosandra NC_068266.1 155605 View on NCBI ↗
Phytolacca insularis NC_041113.1 156419 View on NCBI ↗
Phytolacca japonica NC_068264.1 156591 View on NCBI ↗
Phytolacca latbenia NC_068262.1 156633 View on NCBI ↗
Phytolacca polyandra NC_068263.1 156628 View on NCBI ↗
Phytolacca rivinoides NC_068267.1 155576 View on NCBI ↗
Phytolacca thyrsiflora NC_068265.1 155789 View on NCBI ↗