Markers + reference

Eryngium

3 species · Apiaceae · Apiales

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Species 3
Genome length 155–156 kb
Candidate markers 268
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

12 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
trnH-GUG-psbA LSC 412 0.0527 0.98 76.7 yes View details
trnK-UUU-rps16 LSC 867 0.0493 1.00 83.7 yes View details
trnS-GCU-trnG-UCC LSC 753 0.0423 0.98 76.9 yes View details
rpoB-trnC-GCA LSC 1282 0.0367 1.00 84.5 yes View details
trnC-GCA-petN LSC 840 0.0708 1.00 87.7 yes View details
trnT-GGU-psbD LSC 987 0.0312 0.92 64.4 yes View details
trnT-UGU-trnL-UAA LSC 728 0.0441 0.99 82.0 yes View details
ndhC-trnV-UAC LSC 1232 0.0423 0.98 80.0 yes View details
accD-psaI LSC 333 0.0710 0.93 78.3 yes View details
ycf1 IRb 1851 0.0097 1.00 50.3 no View details
rpl32-trnL-UAG SSC 959 0.0461 1.00 79.3 yes View details
ycf1 SSC 5370 0.0240 1.00 53.8 yes View details
trnG-UCC-trnR-UCU LSC 199 0.0556 0.99 85.6 yes View details
psbC-trnS-UGA LSC 259 0.0618 1.00 80.7 yes View details
rps16-trnQ-UUG LSC 1368 0.0364 1.00 77.2 yes View details
pafI-trnS-GGA LSC 871 0.0326 0.99 76.6 yes View details
trnE-UUC-trnT-GGU LSC 673 0.0387 1.00 76.4 yes View details
psbM-trnD-GUC LSC 702 0.0328 1.00 75.3 yes View details
psbI-trnS-GCU LSC 133 0.0451 1.00 73.9 yes View details
rpoC1-rpoB LSC 26 0.0513 1.00 73.9 yes View details
atpH-atpI LSC 1163 0.0264 1.00 73.4 yes View details
atpF-atpH LSC 388 0.0438 1.00 71.5 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 105 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 GAGCTTAGTTTCCGTCTGGG 1064–1103 1.000 85.7
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG GAGTGGGAGCTTAGTTTCCG 1070–1109 1.000 85.7
trnH-GUG-psbA_p3 trnH-GUG-psbA GATCCACTTGGCTACATCCG GGAGCTTAGTTTCCGTCTGG 1065–1104 1.000 85.7
trnH-GUG-psbA_p4 trnH-GUG-psbA GATCCACTTGGCTACATCCG GGGAGCTTAGTTTCCGTCTG 1066–1105 1.000 85.7
trnH-GUG-psbA_p5 trnH-GUG-psbA CAATCCACTGCCTTGATCCA GAGCTTAGTTTCCGTCTGGG 1078–1117 1.000 85.6
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT AGAAAGGCGGAGGTTTTTAAGT 915–942 1.000 70.1
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AGAAAGGCGGAGGTTTTTAAGT 914–941 1.000 70.1
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT GAAAGGCGGAGGTTTTTAAGT 914–941 1.000 69.2
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GAAAGGCGGAGGTTTTTAAGT 913–940 1.000 69.2
trnK-UUU-rps16_p5 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA AGAAAGGCGGAGGTTTTTAAGT 924–951 1.000 69.1
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GGGTTTTGGTCCCGGTATTC 1425–1469 1.000 82.7
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TCGGAGGTTCGAATCCTTTC 1407–1451 1.000 81.7
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TAAGGCAACGGGTTTTGGTC 1434–1478 1.000 81.5
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CGGATCGTGTCCTTCAAGTC GGGTTTTGGTCCCGGTATTC 1440–1484 1.000 80.8
rps16-trnQ-UUG_p5 rps16-trnQ-UUG GGATCGTGTCCTTCAAGTCG GGGTTTTGGTCCCGGTATTC 1439–1483 1.000 80.8
psbI-trnS-GCU_p1 psbI-trnS-GCU GTCGTAATCCTGGACGTGAA TAAAGCGGCGGATTGCTAAT 227–228 1.000 78.1
psbI-trnS-GCU_p2 psbI-trnS-GCU CGTAATCCTGGACGTGAAGA TAAAGCGGCGGATTGCTAAT 225–226 1.000 75.8
psbI-trnS-GCU_p3 psbI-trnS-GCU TCGTAATCCTGGACGTGAAG TAAAGCGGCGGATTGCTAAT 226–227 1.000 75.8
psbI-trnS-GCU_p4 psbI-trnS-GCU GTCGTAATCCTGGACGTGAA CGAGTTATTCGTACCGAGGG 199–200 1.000 75.7
psbI-trnS-GCU_p5 psbI-trnS-GCU GTCGTAATCCTGGACGTGAA ATGGCTGAGTGGACTAAAGC 241–242 1.000 74.9
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA ACGAATCACACTTTTACCACT 821–830 1.000 58.2
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA AGAACGAATCACACTTTTACCAC 824–833 1.000 57.1
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA GAACGAATCACACTTTTACCACT 823–832 1.000 57.1
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA ACGAATCACACTTTTACCACT 870–879 1.000 56.9
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA AACGAATCACACTTTTACCACT 822–831 1.000 56.3
trnG-UCC-trnR-UCU_p1 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 274–279 1.000 72.0
trnG-UCC-trnR-UCU_p2 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 277–282 1.000 71.7
trnG-UCC-trnR-UCU_p3 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 280–285 1.000 71.2
trnG-UCC-trnR-UCU_p4 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 283–288 1.000 70.9
trnG-UCC-trnR-UCU_p5 trnG-UCC-trnR-UCU CCCTAGCCTTCCAAGCTAAC AGAAGACCTCTGTCCTATCCA 278–283 1.000 69.5

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
Eryngium alpinum NC_084330.1 156209 View on NCBI ↗
Eryngium campestre OK585059.1 155529 View on NCBI ↗
Eryngium foetidum NC_068234.1 155268 View on NCBI ↗