Markers + reference

Rumex

9 species · Polygonaceae · Caryophyllales

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Species 9
Genome length 159–159 kb
Candidate markers 269
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 9 remaining regions by MarkerSeek score (out of 269 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0022 1.00 33.3 yes View details
rps16-trnQ-UUG LSC 515 0.0745 1.00 76.9 yes View details
trnS-GCU-trnG-UCC LSC 786 0.0421 0.98 79.2 yes View details
rpoB-trnC-GCA LSC 1235 0.0238 1.00 66.3 yes View details
trnC-GCA-petN LSC 586 0.0314 1.00 79.4 yes View details
trnT-GGU-psbD LSC 1216 0.0384 1.00 77.7 yes View details
psaA-ycf3 LSC 789 0.0326 1.00 83.0 yes View details
rps4-trnT-UGU LSC 625 0.0414 1.00 83.2 yes View details
clpP1 LSC 2265 0.0244 1.00 67.2 yes View details
ndhF-rpl32 SSC 1117 0.0293 1.00 71.3 yes View details
rpl32-trnL-UAG SSC 478 0.0446 1.00 81.6 yes View details
psbC-trnS-UGA LSC 290 0.0498 1.00 81.1 yes View details
trnH-GUG-psbA LSC 238 0.0860 0.97 77.9 yes View details
trnT-UGU-trnL-UAA LSC 635 0.0302 1.00 74.8 yes View details
trnE-UUC-trnT-GGU LSC 803 0.0275 1.00 74.1 yes View details
psbI-trnS-GCU LSC 104 0.0364 1.00 72.8 yes View details
atpH-atpI LSC 641 0.0249 1.00 72.2 yes View details
trnK-UUU-rps16 LSC 722 0.0252 1.00 71.2 yes View details
petN-psbM LSC 970 0.0282 0.99 68.3 yes View details
psbE-petL LSC 1244 0.0220 1.00 68.0 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 ATTTCAGGCTGAGCACAACA 760–792 1.000 88.0
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG TTTCAGGCTGAGCACAACAT 759–791 1.000 88.0
trnH-GUG-psbA_p3 trnH-GUG-psbA CAATCCACTGCCTTGATCCA ATTTCAGGCTGAGCACAACA 774–806 1.000 87.8
trnH-GUG-psbA_p4 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TTTCAGGCTGAGCACAACAT 773–805 1.000 87.8
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG CTGTTGCGTATTCAGCTCCT 884–916 1.000 86.8
psbA_p1 psbA GATCCACTTGGCTACATCCG AATGAAAACTGCAAGCACGG 1663–1713 1.000 83.2
psbA_p2 psbA CAATCCACTGCCTTGATCCA AATGAAAACTGCAAGCACGG 1677–1727 1.000 83.1
psbA_p3 psbA AATCCACTGCCTTGATCCAC AATGAAAACTGCAAGCACGG 1676–1726 1.000 83.1
psbA_p4 psbA CCAACCCGCTCAATAGAACA AATGAAAACTGCAAGCACGG 1488–1513 1.000 79.7
psbA_p5 psbA ACCAACCCGCTCAATAGAAC AATGAAAACTGCAAGCACGG 1489–1514 1.000 79.7
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT AGAACTTCGCCCTAATGAAACA 787–814 0.778 54.7
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AGAACTTCGCCCTAATGAAACA 786–813 0.778 54.7
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAAGAACCTAGCCGCACTT AGAACTTCGCCCTAATGAAACA 808–835 0.778 53.9
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA AGAACTTCGCCCTAATGAAACA 796–823 0.778 53.8
trnK-UUU-rps16_p5 trnK-UUU-rps16 TACCGTTGAGTTAGCAACCC AGAACTTCGCCCTAATGAAACA 773–800 0.778 52.4
rps16-trnQ-UUG_p1 rps16-trnQ-UUG GCGTTGCTTTCTACCACATC GTAGAAATCTCAGTGGGGCG 623–679 1.000 87.3
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GCGTTGCTTTCTACCACATC GAGGTTCGAATCCTTCCGTC 562–618 1.000 87.2
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG GTAGAAATCTCAGTGGGGCG 622–678 1.000 85.2
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG GAGGTTCGAATCCTTCCGTC 561–617 1.000 85.1
rps16-trnQ-UUG_p5 rps16-trnQ-UUG GCGTTGCTTTCTACCACATC TAGAAATCTCAGTGGGGCGT 622–678 1.000 84.3
psbI-trnS-GCU_p1 psbI-trnS-GCU CGTAATCCTGGACGTGAAGA GTCATTCGTACCGAGGGTTC 154–170 1.000 82.2
psbI-trnS-GCU_p2 psbI-trnS-GCU CGTAATCCTGGACGTGAAGA TAGGGAGAGATGGCTGAGTG 208–224 1.000 80.7
psbI-trnS-GCU_p3 psbI-trnS-GCU CGTAATCCTGGACGTGAAGAA GTCATTCGTACCGAGGGTTC 154–170 1.000 79.9
psbI-trnS-GCU_p4 psbI-trnS-GCU CGTAATCCTGGACGTGAAGA AGTCATTCGTACCGAGGGTT 155–171 1.000 79.3
psbI-trnS-GCU_p5 psbI-trnS-GCU CGTAATCCTGGACGTGAAGAA TAGGGAGAGATGGCTGAGTG 208–224 1.000 78.3
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA ACGAATCACACTTTTACCACT 909–1368 1.000 61.6
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC CTCGTACAGCGGATTAGCAA ACGAATCACACTTTTACCACT 872–1331 1.000 61.5
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC GACTCGTACAGCGGATTAGC ACGAATCACACTTTTACCACT 874–1333 1.000 61.2
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA AGAACGAATCACACTTTTACCAC 912–1371 1.000 60.6
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA GAACGAATCACACTTTTACCACT 911–1370 1.000 60.6

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (9)

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

Species Accession Length (bp) Link
Rumex alpinus PP541893.1 159031 View on NCBI ↗
Rumex angulatus PP234507.1 159117 View on NCBI ↗
Rumex crispus PP541892.1 159154 View on NCBI ↗
Rumex dentatus MZ964419.1 159103 View on NCBI ↗
Rumex hastatus NC_050928.1 158985 View on NCBI ↗
Rumex japonicus MN720269.1 159292 View on NCBI ↗
Rumex nepalensis NC_057504.1 159110 View on NCBI ↗
Rumex pulcher subsp. pulcher PP541894.1 158876 View on NCBI ↗
Rumex scutatus subsp. scutatus PP541895.1 158899 View on NCBI ↗