Markers + reference

Prangos

2 species · Apiaceae · Apiales

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Species 2
Genome length 154–154 kb
Candidate markers 268
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 11 remaining regions by MarkerSeek score (out of 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 729 0.0138 0.99 53.3 yes View details
rps16-trnQ-UUG LSC 1185 0.0152 0.83 57.7 yes View details
psbK-psbI LSC 324 0.0252 0.98 61.2 yes View details
rpoB-trnC-GCA LSC 1236 0.0149 0.98 64.7 yes View details
trnE-UUC-trnT-GGU LSC 691 0.0147 0.99 63.2 yes View details
trnT-GGU-psbD LSC 1434 0.0128 0.98 59.3 yes View details
clpP LSC 2078 0.0107 0.99 58.2 yes View details
petB LSC 1398 0.0143 1.00 53.0 yes View details
rps8 LSC 405 0.0025 1.00 42.3 yes View details
ycf1 IRb 1674 0.0024 1.00 59.8 no View details
ycf1 SSC 5484 0.0093 1.00 44.6 yes View details
rpl2-trnH-GUG LSC 242 0.0455 1.00 74.1 no View details
accD-psaI LSC 499 0.0164 0.98 68.4 yes View details
atpH-atpI LSC 773 0.0092 0.99 65.1 yes View details
rps8-rpl14 LSC 201 0.0398 1.00 65.0 yes View details
ndhI-ndhA SSC 93 0.0215 1.00 64.9 yes View details
atpF-atpH LSC 281 0.0214 1.00 64.8 yes View details
ndhC-trnV-UAC LSC 1115 0.0099 1.00 64.4 yes View details
petN-psbM LSC 1116 0.0081 0.99 63.9 yes View details
trnT-UGU-trnL-UAA LSC 804 0.0137 1.00 63.3 yes View details
petA-psbJ LSC 635 0.0079 1.00 63.3 yes View details
rpl2 LSC 1475 0.0075 1.00 63.0 yes View details
rpl2 IRa 567 0.0096 0.18 38.3 no 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
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCCTTTCAGGATCAGTCGTG CGATTCAAAGTGTATCGCGC 1590–1591 1.000 80.9
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCCTTTCAGGATCAGTCGTG GATTCAAAGTGTATCGCGCG 1589–1590 1.000 80.9
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG CGATTCAAAGTGTATCGCGC 1589–1590 1.000 80.9
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG GATTCAAAGTGTATCGCGCG 1588–1589 1.000 80.9
trnK-UUU-rps16_p5 trnK-UUU-rps16 CGAATCCTCGCTTCATCCAA GATTCAAAGTGTATCGCGCG 1541–1542 1.000 80.6
rps16-trnQ-UUG_p1 rps16-trnQ-UUG TGCTTTCTACCACAGCGTTT AAATATAGATGGGGCGTGGC 1114–1304 1.000 83.1
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TTGCTTTCTACCACAGCGTT AAATATAGATGGGGCGTGGC 1115–1305 1.000 83.1
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA AAATATAGATGGGGCGTGGC 1125–1315 1.000 82.3
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TGCTTTCTACCACAGCGTTT GGGTTTTGGTCCCGGTATTC 1078–1268 1.000 80.5
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TTGCTTTCTACCACAGCGTT GGGTTTTGGTCCCGGTATTC 1079–1269 1.000 80.5
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG ACGCCCCGGATCATTAGATA 439–444 1.000 81.6
psbK-psbI_p2 psbK-psbI GTTTGGCAAGCTGCTGTAAG TACGCCCCGGATCATTAGAT 440–445 1.000 81.5
psbK-psbI_p3 psbK-psbI GTTTGGCAAGCTGCTGTAAG TTACGCCCCGGATCATTAGA 441–446 1.000 79.7
psbK-psbI_p4 psbK-psbI TGGCAAGCTGCTGTAAGTTT ACGCCCCGGATCATTAGATA 436–441 1.000 79.5
psbK-psbI_p5 psbK-psbI TGGCAAGCTGCTGTAAGTTT TACGCCCCGGATCATTAGAT 437–442 1.000 79.5
atpF-atpH_p1 atpF-atpH ATTAAACCCGAAACTCCCGG GCCTGGTTGTAGCATTAGCA 397–402 1.000 78.3
atpF-atpH_p2 atpF-atpH CCAGTGGCCTAAAGAAACGA GCCTGGTTGTAGCATTAGCA 370–375 1.000 77.9
atpF-atpH_p3 atpF-atpH ATTAAACCCGAAACTCCCGG TGGCCTGGTTGTAGCATTAG 399–404 1.000 76.9
atpF-atpH_p4 atpF-atpH ATTAAACCCGAAACTCCCGG TGAGGCGGAGGGAAAAATAC 468–473 1.000 76.8
atpF-atpH_p5 atpF-atpH CCAGTGGCCTAAAGAAACGA TGAGGCGGAGGGAAAAATAC 441–446 1.000 76.3
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT ATAGGGGAATCCATGGAGGG 835–846 1.000 80.7
atpH-atpI_p2 atpH-atpI TACCTTGACCAACTCCAGGT ATAGGGGAATCCATGGAGGG 891–902 1.000 80.0
atpH-atpI_p3 atpH-atpI AGCCAATCCAGCAGCAATAA ATAGGGGAATCCATGGAGGG 851–862 1.000 79.8
atpH-atpI_p4 atpH-atpI AATAACGGAAGCGGCAGAAA ATAGGGGAATCCATGGAGGG 836–847 1.000 79.5
atpH-atpI_p5 atpH-atpI GCAGTACCTTGACCAACTCC ATAGGGGAATCCATGGAGGG 895–906 1.000 79.4
rpoB-trnC-GCA_p1 rpoB-trnC-GCA AGCCCTGATCCATGAACCTA CTTACCACTCGGCCATATCG 1335–1349 1.000 80.7
rpoB-trnC-GCA_p2 rpoB-trnC-GCA AGCCCTGATCCATGAACCTA CCGGATTTGAACTGGGGAAA 1375–1389 1.000 80.5
rpoB-trnC-GCA_p3 rpoB-trnC-GCA GCCCTGATCCATGAACCTAC CTTACCACTCGGCCATATCG 1334–1348 1.000 80.2
rpoB-trnC-GCA_p4 rpoB-trnC-GCA GCCCTGATCCATGAACCTAC CCGGATTTGAACTGGGGAAA 1374–1388 1.000 80.0
rpoB-trnC-GCA_p5 rpoB-trnC-GCA AAAGTTCTTCCGTCAAGCCC CTTACCACTCGGCCATATCG 1350–1364 1.000 79.1

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
Prangos fedtschenkoi KY652265.1 153626 View on NCBI ↗
Prangos trifida NC_037852.1 153510 View on NCBI ↗