Markers + reference

Dysphania

3 species · Amaranthaceae · Caryophyllales

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Species 3
Genome length 152–152 kb
Candidate markers 263
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

10 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
trnK-UUU-rps16 LSC 562 0.0626 0.99 83.5 yes View details
trnS-GCU-trnR-UCU LSC 1625 0.0417 0.99 78.4 yes View details
rpoB-trnC-GCA LSC 960 0.0512 0.99 80.7 yes View details
petN-psbM LSC 1130 0.0572 0.99 78.6 yes View details
ndhC-trnV-UAC LSC 826 0.0541 1.00 85.0 yes View details
psbE-petL LSC 1124 0.0553 1.00 84.9 yes View details
rpl22 LSC 588 0.0684 0.99 79.8 yes View details
ycf1 IRb 1464 0.0066 1.00 50.3 no View details
rpl32-trnL-UAG SSC 1057 0.0824 0.98 84.5 yes View details
ycf1 SSC 5565 0.0391 1.00 64.5 yes View details
rrn23-rrn4.5 IRb 105 0.2159 1.00 85.3 yes View details
rrn4.5-rrn23 IRa 105 0.2159 1.00 85.3 yes View details
trnD-GUC-trnY-GUA LSC 419 0.0636 1.00 82.7 yes View details
psbK-psbI LSC 431 0.0504 0.98 82.5 yes View details
trnT-UGU-trnL-UAA LSC 827 0.0422 0.96 81.8 yes View details
rps16-trnQ-UUG LSC 602 0.0598 1.00 81.4 yes View details
trnT-GGU-psbD LSC 1167 0.0389 0.98 78.5 yes View details
trnP-UGG-psaJ LSC 366 0.0474 1.00 78.5 yes View details
psbA-trnK-UUU LSC 213 0.0485 1.00 78.3 yes View details
trnE-UUC-trnT-GGU LSC 512 0.0412 0.96 77.6 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbA-trnK-UUU_p1 psbA-trnK-UUU ATAGGCTTTCACTTTCGCGT CTCCATCCGATTGGTTCCG 285–294 1.000 77.8
psbA-trnK-UUU_p2 psbA-trnK-UUU ATAGGCTTTCACTTTCGCGT CTACTCCATCCGATTGGTTCC 288–297 1.000 76.9
psbA-trnK-UUU_p3 psbA-trnK-UUU ATAGGCTTTCACTTTCGCGT GATTGGTTCCGGGTTCGAG 277–286 1.000 76.1
psbA-trnK-UUU_p4 psbA-trnK-UUU ATAGGCTTTCACTTTCGCGT TACTCCATCCGATTGGTTCC 287–296 1.000 75.4
psbA-trnK-UUU_p5 psbA-trnK-UUU CATAGGCTTTCACTTTCGCG CTCCATCCGATTGGTTCCG 286–295 1.000 75.0
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TCGACTTAATCAAATGAAGTTCA 603–629 1.000 49.3
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TCGACTTAATCAAATGAAGTTCA 602–628 1.000 49.3
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TCGACTTAATCAAATGAAGTTCAA 602–628 1.000 49.3
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA TCGACTTAATCAAATGAAGTTCA 612–638 1.000 49.2
trnK-UUU-rps16_p5 trnK-UUU-rps16 TCTAGCCGCACTTAAAAGCC TCGACTTAATCAAATGAAGTTCA 617–643 1.000 49.1
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 675–679 1.000 84.7
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TAAGGCATCGGGTTTTGGTC 705–709 1.000 83.6
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GTAAGGCATCGGGTTTTGGT 706–710 1.000 81.3
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GTGGTAAGGCATCGGGTTTT 709–713 1.000 81.3
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TGGTAAGGCATCGGGTTTTG 708–712 1.000 81.3
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG AGGAATCCGAAAATGAAGAGAGA 517–532 1.000 58.4
psbK-psbI_p2 psbK-psbI CTTTTGTTTGGCAAGCTGCT AGGAATCCGAAAATGAAGAGAGA 522–537 1.000 58.3
psbK-psbI_p3 psbK-psbI TGGCAAGCTGCTGTAAGTTT AGGAATCCGAAAATGAAGAGAGA 514–529 1.000 56.4
psbK-psbI_p4 psbK-psbI TTGGCAAGCTGCTGTAAGTT AGGAATCCGAAAATGAAGAGAGA 515–530 1.000 56.4
psbK-psbI_p5 psbK-psbI TTTGGCAAGCTGCTGTAAGT AGGAATCCGAAAATGAAGAGAGA 516–531 1.000 56.3
trnS-GCU-trnR-UCU_p1 trnS-GCU-trnR-UCU ACGGAAAGAGAGGGATTCGA AGAAGACCCATGTCCTATCCA 1747–1750 1.000 73.1
trnS-GCU-trnR-UCU_p2 trnS-GCU-trnR-UCU CGAATGACTCGTACAACGGA AGAAGACCCATGTCCTATCCA 1717–1720 1.000 72.4
trnS-GCU-trnR-UCU_p3 trnS-GCU-trnR-UCU CTTTCGTCCACTCAGCCATC AGAAGACCCATGTCCTATCCA 1683–1686 1.000 69.4
trnS-GCU-trnR-UCU_p4 trnS-GCU-trnR-UCU AACGGAAAGAGAGGGATTCG AGAAGACCCATGTCCTATCCA 1748–1751 1.000 68.9
trnS-GCU-trnR-UCU_p5 trnS-GCU-trnR-UCU ACGGAAAGAGAGGGATTCGA GAAGACCCATGTCCTATCCA 1746–1749 1.000 68.5
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CGAGCCCATATCCTTGCTTT GGGGGTTCGAGTCTTTTGTT 1573–1733 1.000 87.5
rpoB-trnC-GCA_p2 rpoB-trnC-GCA CCCGGGCTTTGCAATATTTG GGGGGTTCGAGTCTTTTGTT 1453–1613 1.000 87.5
rpoB-trnC-GCA_p3 rpoB-trnC-GCA GAAAATACCGGATCCCCACC GGGGGTTCGAGTCTTTTGTT 1780–1940 1.000 87.2
rpoB-trnC-GCA_p4 rpoB-trnC-GCA CGAGCCCATATCCTTGCTTT CGGATTTGAACTGGGGAACA 1533–1693 1.000 87.0
rpoB-trnC-GCA_p5 rpoB-trnC-GCA GAAAATACCGGATCCCCACC CGGATTTGAACTGGGGAACA 1740–1900 1.000 86.6

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

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

Species Accession Length (bp) Link
Dysphania ambrosioides NC_041201.1 151689 View on NCBI ↗
Dysphania botrys NC_042166.1 152055 View on NCBI ↗
Dysphania pumilio NC_041159.1 151962 View on NCBI ↗