Markers + reference

Cnidium

2 species · Apiaceae · Apiales

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Species 2
Genome length 147–151 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

12 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
psbA LSC 1062 0.0038 1.00 48.1 yes View details
trnK-UUU-rps16 LSC 702 0.0228 1.00 59.3 yes View details
trnS-GCU-trnG-UCC LSC 573 0.0196 0.98 60.0 yes View details
trnE-UUC-trnT-GGU LSC 750 0.0242 0.99 59.4 yes View details
psbE-petL LSC 999 0.0142 0.99 53.5 yes View details
ycf2 IRb 6321 0.0097 0.99 49.8 yes View details
ycf1 IRb 2013 0.0115 0.99 54.2 no View details
ndhF SSC 2229 0.0104 1.00 49.1 yes View details
ndhF-rpl32 SSC 1052 0.0201 0.95 61.9 yes View details
ycf1 SSC 5480 0.0106 1.00 47.9 yes View details
trnL-CAA-ycf2 IRa 1148 0.1033 0.83 80.8 yes View details
ycf2 IRa 3381 NA 0.00 42.0 no View details
trnH-GUG-psbA LSC 206 0.0777 1.00 72.6 yes View details
atpH-atpI LSC 1155 0.0150 0.98 69.1 yes View details
trnC-GCA-petN LSC 700 0.0158 0.99 67.2 yes View details
trnT-GGU-psbD LSC 1437 0.0126 0.99 66.6 yes View details
pafI-trnS-GGA LSC 832 0.0122 0.98 66.6 yes View details
rps16 LSC 1098 0.0110 0.99 65.8 yes View details
psbM-trnD-GUC LSC 637 0.0065 0.97 65.2 yes View details
rbcL LSC 1428 0.0112 1.00 65.2 yes View details
trnG-UCC-trnR-UCU LSC 161 0.0362 0.86 64.1 yes View details
accD-psaI LSC 404 0.0149 1.00 63.5 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 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 AGCTCCATCTACAAATGGGT 250–262 1.000 69.5
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA AGCTCCATCTACAAATGGGT 264–276 1.000 69.2
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC AGCTCCATCTACAAATGGGT 263–275 1.000 69.2
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC AGCTCCATCTACAAATGGGT 265–277 1.000 69.2
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG AAGCTCCATCTACAAATGGGT 251–263 1.000 67.7
psbA_p1 psbA ACTCGTATATACTAAAACCCGGTC AAATTCGTGTGCTTGGGAGT 1137 1.000 45.6
psbA_p2 psbA ACTCGTATATACTAAAACCCGGTC TGCTTGGGAGTCCCTGATAA 1128 1.000 45.5
psbA_p3 psbA ACTCGTATATACTAAAACCCGGT AAATTCGTGTGCTTGGGAGT 1137 1.000 45.2
psbA_p4 psbA ACTCGTATATACTAAAACCCGGT TGCTTGGGAGTCCCTGATAA 1128 1.000 45.0
psbA_p5 psbA AACTCGTATATACTAAAACCCGGT AAATTCGTGTGCTTGGGAGT 1138 1.000 42.4
trnK-UUU-rps16_p1 trnK-UUU-rps16 TCCCTCGCTTCATCCAAATG AAAGGCAGAGGTTTTTAAGT 802–811 1.000 41.6
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCGATGGTATGGACGAATCC AAAGGCAGAGGTTTTTAAGT 819–828 1.000 41.6
trnK-UUU-rps16_p3 trnK-UUU-rps16 CGATGGTATGGACGAATCCC AAAGGCAGAGGTTTTTAAGT 818–827 1.000 41.6
trnK-UUU-rps16_p4 trnK-UUU-rps16 TCCCTCGCTTCATCCAAATG AAAAGGCAGAGGTTTTTAAGT 803–812 1.000 41.6
trnK-UUU-rps16_p5 trnK-UUU-rps16 CGATGGTATGGACGAATCCC AAAAGGCAGAGGTTTTTAAGT 819–828 1.000 41.6
rps16_p1 rps16 TCAATTTTGTTTGATTAGGACCA TGTATCGACGGAACCAATGAC 1199–1206 1.000 41.3
rps16_p2 rps16 TCAATTTTGTTTGATTAGGACCA GTATCGACGGAACCAATGACT 1198–1205 1.000 41.3
rps16_p3 rps16 TCAATTTTGTTTGATTAGGACCAAG TGTATCGACGGAACCAATGAC 1199–1206 1.000 41.3
rps16_p4 rps16 TCAATTTTGTTTGATTAGGACCA TGTATCGACGGAACCAATGA 1199–1206 1.000 41.3
rps16_p5 rps16 TCAATTTTGTTTGATTAGGACCAAG GTATCGACGGAACCAATGACT 1198–1205 1.000 41.3
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA GGGGGTTACTCGAACGAATC 649–660 1.000 81.8
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA TAAGGGGGTTACTCGAACGA 652–663 1.000 80.7
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA AGGGGGTTACTCGAACGAAT 650–661 1.000 78.9
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC GCTTTAGTCCACTCAGCCAT GGGGGTTACTCGAACGAATC 635–646 1.000 78.9
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AGTCCACTCAGCCATCTCTC GGGGGTTACTCGAACGAATC 630–641 1.000 78.1
trnG-UCC-trnR-UCU_p1 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 218–241 1.000 69.1
trnG-UCC-trnR-UCU_p2 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 221–244 1.000 68.8
trnG-UCC-trnR-UCU_p3 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 224–247 1.000 68.4
trnG-UCC-trnR-UCU_p4 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 227–250 1.000 68.1
trnG-UCC-trnR-UCU_p5 trnG-UCC-trnR-UCU CCCTAGCCTTCCAAGCTAAC AGAAGACCTCTGTCCTATCCA 222–245 1.000 66.6

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
Cnidium dauricum NC_071791.1 151320 View on NCBI ↗
Cnidium monnieri PV613214.1 147359 View on NCBI ↗