Markers + reference

Rehmannia

7 species · Orobanchaceae · Lamiales

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Species 7
Genome length 154–154 kb
Candidate markers 273
Primer pairs 85

Genome-wide nucleotide diversity

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

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 273 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rpoB-trnC(GCA) LSC 1127 0.0098 1.00 56.4 yes View details
psbZ-trnG(GCC) LSC 291 0.0349 1.00 57.3 yes View details
psaA-ycf3 LSC 952 0.0377 0.99 81.9 yes View details
psbE-petL LSC 710 0.0310 1.00 77.2 yes View details
rps12-trnV(GAC) IRb 1615 0.0111 1.00 56.5 yes View details
ndhG-ndhI SSC 361 0.0327 0.95 76.4 yes View details
ndhA SSC 2064 0.0058 0.99 51.6 yes View details
rpl2-trnH(GUG) LSC 466 0.0841 0.45 70.8 no View details
trnT(UGU)-trnL(UAA) LSC 581 0.0100 0.99 66.2 yes View details
ndhD-psaC SSC 99 0.0337 0.96 62.2 yes View details
cemA-petA LSC 241 0.0277 0.95 60.4 yes View details
rrn23-trnA(UGC) IRa 167 0.0180 1.00 59.8 yes View details
trnV(GAC)-rps12 IRa 1615 0.0012 1.00 54.8 yes View details
atpF-atpH LSC 371 0.0039 1.00 54.3 yes View details
trnS(GCU)-trnG(UCC) LSC 747 0.0066 0.99 52.3 yes View details
rpl32-trnL(UAG) SSC 717 0.0093 1.00 51.3 yes View details
atpB-rbcL LSC 766 0.0036 1.00 50.8 yes View details
rpl20-rps12 LSC 805 0.0033 1.00 50.7 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 85 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnS(GCU)-trnG(UCC)_p1 trnS(GCU)-trnG(UCC) CAATCCGACGCTTTAGTCCA ACGAATCACACTTTTACCACT 793–850 1.000 56.6
trnS(GCU)-trnG(UCC)_p2 trnS(GCU)-trnG(UCC) AATCCGACGCTTTAGTCCAC ACGAATCACACTTTTACCACT 792–849 1.000 56.5
trnS(GCU)-trnG(UCC)_p3 trnS(GCU)-trnG(UCC) CAATCCGACGCTTTAGTCCA AGAACGAATCACACTTTTACCAC 796–853 1.000 55.5
trnS(GCU)-trnG(UCC)_p4 trnS(GCU)-trnG(UCC) CAATCCGACGCTTTAGTCCA GAACGAATCACACTTTTACCACT 795–852 1.000 55.5
trnS(GCU)-trnG(UCC)_p5 trnS(GCU)-trnG(UCC) AATCCGACGCTTTAGTCCAC GAACGAATCACACTTTTACCACT 794–851 1.000 55.5
atpF-atpH_p1 atpF-atpH TGGCCCAAAGAAACGAAAGA CCGAGGCAGAGGGAAAAATA 526–532 1.000 76.4
atpF-atpH_p2 atpF-atpH GTGGCCCAAAGAAACGAAAG CCGAGGCAGAGGGAAAAATA 527–533 1.000 75.8
atpF-atpH_p3 atpF-atpH AGTGGCCCAAAGAAACGAAA CCGAGGCAGAGGGAAAAATA 528–534 1.000 75.0
atpF-atpH_p4 atpF-atpH TTAAATCCGAAACTCCCGGC CCGAGGCAGAGGGAAAAATA 556–562 1.000 74.7
atpF-atpH_p5 atpF-atpH TGGCCCAAAGAAACGAAAGA GCAGAGGGAAAAATACGAGGA 521–527 1.000 72.0
rpoB-trnC(GCA)_p1 rpoB-trnC(GCA) ATCATTTGCATCCCCGAGC ATGTTGATTAGGCGACACCC 1217–1277 1.000 74.5
rpoB-trnC(GCA)_p2 rpoB-trnC(GCA) ATCATTTGCATCCCCGAGC CCGGATTTGAACTGGGGAAA 1199–1259 1.000 74.2
rpoB-trnC(GCA)_p3 rpoB-trnC(GCA) CATTTGCATCCCCGAGCAT ATGTTGATTAGGCGACACCC 1215–1275 1.000 72.1
rpoB-trnC(GCA)_p4 rpoB-trnC(GCA) ATCATTTGCATCCCCGAGC AAAAGGATTTGCAGTCCCCC 1181–1241 1.000 72.1
rpoB-trnC(GCA)_p5 rpoB-trnC(GCA) CATTTGCATCCCCGAGCAT CCGGATTTGAACTGGGGAAA 1197–1257 1.000 71.8
psbZ-trnG(GCC)_p1 psbZ-trnG(GCC) ACCCGTCGTATTTGCTTCTC AATCCTGTCTCCGCAACATC 634–704 1.000 87.0
psbZ-trnG(GCC)_p2 psbZ-trnG(GCC) ACCCGTCGTATTTGCTTCTC GGGTAGAGCAGTTTGGTAGC 688–758 1.000 86.8
psbZ-trnG(GCC)_p3 psbZ-trnG(GCC) ACCCGTCGTATTTGCTTCTC CGTTGTTTTTCGACCGGAAG 961–1031 1.000 86.2
psbZ-trnG(GCC)_p4 psbZ-trnG(GCC) TCCATTTCCCCTGACTCCAT CGTTGTTTTTCGACCGGAAG 1200–1270 1.000 85.0
psbZ-trnG(GCC)_p5 psbZ-trnG(GCC) CAACCACTCAGCCATCTCTC CGTTGTTTTTCGACCGGAAG 1384–1454 1.000 84.4
psaA-ycf3_p1 psaA-ycf3 TGAGAAATGACCCGGTTTGG ATCAAGCCGCTGAGTATTGG 948–1160 1.000 89.2
psaA-ycf3_p2 psaA-ycf3 GCCCATTCCTCGAAAGAAGT ATCAAGCCGCTGAGTATTGG 929–1141 1.000 89.1
psaA-ycf3_p3 psaA-ycf3 TGAGAAATGACCCGGTTTGG TTGAAGATCACGAGGCGTTT 877–1089 1.000 88.6
psaA-ycf3_p4 psaA-ycf3 GCCCATTCCTCGAAAGAAGT TTGAAGATCACGAGGCGTTT 858–1070 1.000 88.6
psaA-ycf3_p5 psaA-ycf3 TGAGAAATGACCCGGTTTGG TTGGTTGAAGATCACGAGGC 881–1093 1.000 88.4
trnT(UGU)-trnL(UAA)_p1 trnT(UGU)-trnL(UAA) GCGATGCTCTAACCTCTGAG CCGTAGCGTCTACCGATTTC 625–824 1.000 82.7
trnT(UGU)-trnL(UAA)_p2 trnT(UGU)-trnL(UAA) TAGGAAAAAGCCGGCTATCG CCGTAGCGTCTACCGATTTC 676–875 1.000 81.8
trnT(UGU)-trnL(UAA)_p3 trnT(UGU)-trnL(UAA) GGAATCGAACCGATGACCAT CCGTAGCGTCTACCGATTTC 657–856 1.000 81.7
trnT(UGU)-trnL(UAA)_p4 trnT(UGU)-trnL(UAA) GCGATGCTCTAACCTCTGAG CGTCTACCGATTTCGCCATA 619–818 1.000 81.4
trnT(UGU)-trnL(UAA)_p5 trnT(UGU)-trnL(UAA) GCGATGCTCTAACCTCTGAG GGTTTCCATACCAAGGCTCA 657–856 1.000 80.5

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (7)

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

Species Accession Length (bp) Link
Rehmannia chingii NC_033534.1 154055 View on NCBI ↗
Rehmannia chrysantha PX170676.1 153789 View on NCBI ↗
Rehmannia elata NC_034312.1 153772 View on NCBI ↗
Rehmannia glutinosa NC_034308.1 153622 View on NCBI ↗
Rehmannia henryi NC_034309.1 153890 View on NCBI ↗
Rehmannia piasezkii NC_034311.1 153925 View on NCBI ↗
Rehmannia solanifolia NC_034310.1 153989 View on NCBI ↗