Markers + reference

Pastinaca

2 species · Apiaceae · Apiales

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Species 2
Genome length 149–150 kb
Candidate markers 264
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 264 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps2 LSC 711 0.0028 1.00 46.3 yes View details
trnE-UUC-trnT-GGU LSC 791 0.0166 0.99 63.4 yes View details
ndhC-trnV-UAC LSC 1104 0.0138 0.98 68.5 yes View details
petB LSC 1399 0.0086 1.00 63.7 yes View details
ycf2 LSC 6306 0.0117 1.00 59.3 yes View details
trnH-GUG-trnL-CAA IRb 1499 0.0173 0.97 63.3 yes View details
ycf1 IRb 1886 0.0016 1.00 44.9 no View details
ycf1 SSC 5487 0.0078 1.00 44.7 yes View details
trnL-CAA-trnH-GUG IRa 1501 0.0172 0.97 63.2 yes View details
atpH-atpI LSC 1155 0.0142 0.98 66.8 yes View details
trnT-UGU-trnL-UAA LSC 767 0.0117 1.00 65.5 yes View details
psbI-trnS-GCU LSC 140 0.0214 1.00 64.8 yes View details
rps16 LSC 1091 0.0101 1.00 64.7 yes View details
rps2-rpoC2 LSC 213 0.0425 1.00 64.1 yes View details
petN-psbM LSC 1149 0.0079 1.00 63.7 yes View details
rps8-rpl14 LSC 197 0.0255 0.99 63.4 yes View details
rpoB-trnC-GCA LSC 1214 0.0066 0.99 63.1 yes View details
ycf3-trnS-GGA LSC 821 0.0110 1.00 62.7 yes View details
rps12-trnV-GAC IRb 1906 0.0027 0.97 62.7 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps16_p1 rps16 TCAATTTTGTTTGATTAGGACCA TGTATCGACGGAACCAATGAC 1198–1199 1.000 40.9
rps16_p2 rps16 TCAATTTTGTTTGATTAGGACCA GTATCGACGGAACCAATGACT 1197–1198 1.000 40.9
rps16_p3 rps16 TCAATTTTGTTTGATTAGGACCAAG TGTATCGACGGAACCAATGAC 1198–1199 1.000 40.9
rps16_p4 rps16 TCAATTTTGTTTGATTAGGACCA TGTATCGACGGAACCAATGA 1198–1199 1.000 40.9
rps16_p5 rps16 TCAATTTTGTTTGATTAGGACCAAG GTATCGACGGAACCAATGACT 1197–1198 1.000 40.9
psbI-trnS-GCU_p1 psbI-trnS-GCU ATCTAATGATCCGGGGCGTA TAAAGCGGCGGATTGCTAAT 248 1.000 80.1
psbI-trnS-GCU_p2 psbI-trnS-GCU TATCTAATGATCCGGGGCGT TAAAGCGGCGGATTGCTAAT 249 1.000 80.1
psbI-trnS-GCU_p3 psbI-trnS-GCU ATCTAATGATCCGGGGCGTA ATTGGGAGAGATGGCTGAGT 272 1.000 79.5
psbI-trnS-GCU_p4 psbI-trnS-GCU TATCTAATGATCCGGGGCGT ATTGGGAGAGATGGCTGAGT 273 1.000 79.5
psbI-trnS-GCU_p5 psbI-trnS-GCU TCTAATGATCCGGGGCGTAA TAAAGCGGCGGATTGCTAAT 247 1.000 78.3
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT ATAGGGGAATCCATGGAGGG 1192–1217 1.000 81.9
atpH-atpI_p2 atpH-atpI TACCTTGACCAACTCCAGGT ATAGGGGAATCCATGGAGGG 1248–1273 1.000 81.2
atpH-atpI_p3 atpH-atpI AGCCAATCCAGCAGCAATAA ATAGGGGAATCCATGGAGGG 1208–1233 1.000 81.0
atpH-atpI_p4 atpH-atpI AATAACGGAAGCGGCAGAAA ATAGGGGAATCCATGGAGGG 1193–1218 1.000 80.7
atpH-atpI_p5 atpH-atpI GCAGTACCTTGACCAACTCC ATAGGGGAATCCATGGAGGG 1252–1277 1.000 80.5
rps2_p1 rps2 GCGCTCCTGACCAATTAGAA AGGCCTGAAAGAGAACGTTG 1782–1786 1.000 79.6
rps2_p2 rps2 AAGCGCTCCTGACCAATTAG AGGCCTGAAAGAGAACGTTG 1784–1788 1.000 79.6
rps2_p3 rps2 ACGTGAGTAAAGCCAAAGCA AGGCCTGAAAGAGAACGTTG 1875–1879 1.000 79.5
rps2_p4 rps2 GCGCTCCTGACCAATTAGAA GTACCGGATTCGAGGGATTG 1738–1742 1.000 79.4
rps2_p5 rps2 AAGCGCTCCTGACCAATTAG GTACCGGATTCGAGGGATTG 1740–1744 1.000 79.3
rps2-rpoC2_p1 rps2-rpoC2 GATGTTCCAATATCTTTTTGTCA TCCACGATACGTCAGAACAA 290–294 1.000 42.7
rps2-rpoC2_p2 rps2-rpoC2 GATGTTCCAATATCTTTTTGTCA TTCCACGATACGTCAGAACA 291–295 1.000 42.7
rps2-rpoC2_p3 rps2-rpoC2 GATGTTCCAATATCTTTTTGTCA TTCCACGATACGTCAGAACAA 291–295 1.000 42.7
rps2-rpoC2_p4 rps2-rpoC2 GATGTTCCAATATCTTTTTGTCA TTTCCACGATACGTCAGAACA 292–296 1.000 42.7
rps2-rpoC2_p5 rps2-rpoC2 GATGTTCCAATATCTTTTTGTCAT TCCACGATACGTCAGAACAA 290–294 1.000 42.7
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CCACGAACCTACAAAAGCCT CCGGATTTGAACTGGGGAAA 1351–1358 1.000 79.4
rpoB-trnC-GCA_p2 rpoB-trnC-GCA TCCACGAACCTACAAAAGCC CCGGATTTGAACTGGGGAAA 1352–1359 1.000 79.3
rpoB-trnC-GCA_p3 rpoB-trnC-GCA CCACGAACCTACAAAAGCCT TTATTGATCAGGCGACACCC 1369–1376 1.000 77.4
rpoB-trnC-GCA_p4 rpoB-trnC-GCA TCCACGAACCTACAAAAGCC TTATTGATCAGGCGACACCC 1370–1377 1.000 77.4
rpoB-trnC-GCA_p5 rpoB-trnC-GCA CCACGAACCTACAAAAGCCT AAAAGGATTTGCAGTCCCCC 1333–1340 1.000 77.2

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
Pastinaca pimpinellifolia NC_027450.1 149758 View on NCBI ↗
Pastinaca sativa MT561034.1 149479 View on NCBI ↗