Markers + reference

Pedicularis

13 species · Orobanchaceae · Lamiales

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Species 13
Genome length 147–162 kb
Candidate markers 236
Primer pairs 65

Genome-wide nucleotide diversity

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

Candidate markers

3 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 236 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnN-GUU-trnL-UAG SSC 3244 0.1289 0.83 75.5 yes View details
trnL-UAG-psaC SSC 2790 0.0756 0.99 82.0 yes View details
psaC-rps15 SSC 4489 0.0863 0.99 77.6 yes View details
trnC-GCA-petN LSC 831 0.0479 0.99 88.7 yes View details
petN-psbM LSC 911 0.0544 0.96 87.6 yes View details
trnE-UUC-trnT-GGU LSC 638 0.0540 0.93 85.3 yes View details
trnT-UGU-trnL-UAA LSC 699 0.0451 1.00 84.6 yes View details
psbE-petL LSC 828 0.0517 1.00 83.9 yes View details
ycf3-trnS-GGA LSC 851 0.0546 0.94 83.6 yes View details
trnS-GCU-trnS-CGA LSC 722 0.0522 0.90 81.4 yes View details
ycf4-cemA LSC 552 0.0518 0.98 81.3 yes View details
rps16 LSC 1115 0.0522 0.98 81.2 yes View details
psbC-trnS-UGA LSC 245 0.0895 1.00 80.8 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 65 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps16_p1 rps16 TTTGTCGTTCTAGGCCATCG GAGGTTCGAATCCTTCCGTC 1894–1989 0.692 79.0
rps16_p2 rps16 TGTCGTTCTAGGCCATCGTA GAGGTTCGAATCCTTCCGTC 1892–1987 0.615 74.0
rps16_p3 rps16 TTTGTCGTTCTAGGCCATCG ATGTAACGATTGAGGCAGGG 1619–1658 0.538 70.8
rps16_p4 rps16 AAACACAAACCCGGTTCACT GAGGTTCGAATCCTTCCGTC 2362–2391 0.154 50.8
rps16_p5 rps16 AACACAAACCCGGTTCACTT GAGGTTCGAATCCTTCCGTC 2361–2390 0.154 50.8
trnS-GCU-trnS-CGA_p1 trnS-GCU-trnS-CGA CAATCCGACGCTTTAGTCCA CATCGTTAGCTTGGAAGGCT 1412–1486 0.923 88.6
trnS-GCU-trnS-CGA_p2 trnS-GCU-trnS-CGA AATCCGACGCTTTAGTCCAC CATCGTTAGCTTGGAAGGCT 1411–1485 0.923 88.6
trnS-GCU-trnS-CGA_p3 trnS-GCU-trnS-CGA CAATCCGACGCTTTAGTCCA CGTTAGCTTGGAAGGCTAGG 1409–1483 0.923 88.4
trnS-GCU-trnS-CGA_p4 trnS-GCU-trnS-CGA AATCCGACGCTTTAGTCCAC CGTTAGCTTGGAAGGCTAGG 1408–1482 0.923 88.4
trnS-GCU-trnS-CGA_p5 trnS-GCU-trnS-CGA ATCTAATGATCCGGGGCGTA CATCGTTAGCTTGGAAGGCT 1616–1697 0.923 88.1
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG TTCTAGAGCCCACTTCTCCC 935–1091 0.923 87.2
trnC-GCA-petN_p2 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGCCCAAGCGAGACTTACTA 870–1026 0.923 87.1
trnC-GCA-petN_p3 trnC-GCA-petN GGGGGACTGCAAATCCTTTT TTCTAGAGCCCACTTCTCCC 953–1109 0.846 81.9
trnC-GCA-petN_p4 trnC-GCA-petN GGGGGACTGCAAATCCTTTT AGCCCAAGCGAGACTTACTA 888–1044 0.846 81.8
trnC-GCA-petN_p5 trnC-GCA-petN CCAGTTCAAATCCGGGTGTC TTCTAGAGCCCACTTCTCCC 930–1086 0.923 81.2
petN-psbM_p1 petN-psbM TAGTAAGTCTCGCTTGGGCT AGTTCCTACGGCTTTTCTACT 1000–1052 1.000 69.9
petN-psbM_p2 petN-psbM TAGTAAGTCTCGCTTGGGCT TCATTCTAGTTCCTACGGCT 1007–1059 1.000 69.8
petN-psbM_p3 petN-psbM TAGTAAGTCTCGCTTGGGCT TCATTCTAGTTCCTACGGCTT 1007–1059 1.000 68.2
petN-psbM_p4 petN-psbM TAGTAAGTCTCGCTTGGGCT TTCATTCTAGTTCCTACGGCT 1008–1060 1.000 68.2
petN-psbM_p5 petN-psbM TAGTAAGTCTCGCTTGGGCT AGTTCCTACGGCTTTTCTACTT 1010–1052 0.923 64.6
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU AAACCACTAGACGATGGGGG TACCGCTGAGTTAAAAGGGC 620–710 1.000 82.4
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU AACCACTAGACGATGGGGG TACCGCTGAGTTAAAAGGGC 619–709 1.000 80.0
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU CCTAAACCACTAGACGATGGG TACCGCTGAGTTAAAAGGGC 623–713 1.000 79.5
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU CTAAACCACTAGACGATGGGG TACCGCTGAGTTAAAAGGGC 622–712 1.000 79.5
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU GCCTCCTTGAAAGAGAGATGT TACCGCTGAGTTAAAAGGGC 644–734 1.000 78.2
psbC-trnS-UGA_p1 psbC-trnS-UGA CCTGTTCTTTCCATGACCCC GAGAGATGGCTGAGTGGTTG 340–383 1.000 90.5
psbC-trnS-UGA_p2 psbC-trnS-UGA CCTGTTCTTTCCATGACCCC ATAGCCCCGGTCTTGAAAAC 320–363 1.000 89.7
psbC-trnS-UGA_p3 psbC-trnS-UGA GCAGCCGGATTTGAAAAAGG GAGAGATGGCTGAGTGGTTG 379–422 1.000 89.5
psbC-trnS-UGA_p4 psbC-trnS-UGA CCTGTTCTTTCCATGACCCC GGGTTCGAATCCCTCTCTCT 271–314 1.000 89.0
psbC-trnS-UGA_p5 psbC-trnS-UGA GCAGCCGGATTTGAAAAAGG ATAGCCCCGGTCTTGAAAAC 359–402 1.000 88.7

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (13)

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

Species Accession Length (bp) Link
Pedicularis armata PX776210.1 149113 View on NCBI ↗
Pedicularis bicolor NC_087843.1 152785 View on NCBI ↗
Pedicularis chinensis NC_080928.1 149828 View on NCBI ↗
Pedicularis corydaloides NC_080927.1 149240 View on NCBI ↗
Pedicularis crenata NC_080926.1 147082 View on NCBI ↗
Pedicularis dissecta NC_056312.1 152120 View on NCBI ↗
Pedicularis ishidoyana NC_029700.1 152571 View on NCBI ↗
Pedicularis lyrata NC_080921.1 149508 View on NCBI ↗
Pedicularis megalantha NC_080920.1 148399 View on NCBI ↗
Pedicularis oliveriana NC_080918.1 162362 View on NCBI ↗
Pedicularis plicata NC_080917.1 147800 View on NCBI ↗
Pedicularis rupicola NC_080915.1 147805 View on NCBI ↗
Pedicularis siphonantha NC_080914.1 148407 View on NCBI ↗