Markers + reference

Pterocarpus

9 species · Fabaceae · Fabales

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Species 9
Genome length 158–159 kb
Candidate markers 265
Primer pairs 95

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 265 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnL-UAA-trnT-UGU LSC 1298 0.0230 0.90 67.3 yes View details
atpI-atpH LSC 1344 0.0241 0.96 73.3 yes View details
trnQ-UUG-rps16 LSC 594 0.0261 0.98 71.4 yes View details
clpP-psbB LSC 488 0.0277 0.87 66.9 yes View details
rps11-rpl36 LSC 568 0.0248 0.95 65.7 yes View details
rps8-rpl14 LSC 380 0.0317 0.96 71.1 yes View details
rpl16 LSC 1611 0.0145 0.99 63.7 yes View details
rpl32-trnL-UAG SSC 916 0.0260 0.92 63.1 yes View details
ndhG-ndHI SSC 643 0.0544 0.88 80.4 yes View details
ndhE-ndhG SSC 238 0.0430 1.00 79.6 yes View details
rps3-rps19 LSC 546 0.0219 0.99 71.7 yes View details
trnP-UGG-psaJ LSC 623 0.0188 0.98 68.7 yes View details
trnH-GUG-psbA LSC 260 0.0323 1.00 68.3 yes View details
trnL-UAG-ccsA SSC 99 0.0281 0.97 65.6 yes View details
trnK-UUU-rbcL LSC 743 0.0216 0.99 65.1 yes View details
accD-psaI LSC 547 0.0205 1.00 65.1 yes View details
trnV-UAC-ndhC LSC 538 0.0227 0.93 64.6 yes View details
psbE-petL LSC 1368 0.0095 0.99 64.6 yes View details
psbD-trnT-GGU LSC 1474 0.0130 0.99 64.1 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 95 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 CCTCTAGACCTAGCTGCAGT 262–336 1.000 88.1
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 265–339 1.000 88.0
trnH-GUG-psbA_p3 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCTCTAGACCTAGCTGCAGT 276–350 1.000 87.9
trnH-GUG-psbA_p4 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCTCTAGACCTAGCTGCAGT 275–349 1.000 87.9
trnH-GUG-psbA_p5 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCTCTAGACCTAGCTGCAGT 277–351 1.000 87.8
trnK-UUU-rbcL_p1 trnK-UUU-rbcL GAGTTGCCAAGCTCTATCCC AGTCCTGAATTAGCTGCTGC 1101–1153 1.000 86.2
trnK-UUU-rbcL_p2 trnK-UUU-rbcL GAGTTGCCAAGCTCTATCCC AATGAGGGTCGTGATCTTGC 1161–1213 1.000 86.0
trnK-UUU-rbcL_p3 trnK-UUU-rbcL GGAGTTGCCAAGCTCTATCC AATGAGGGTCGTGATCTTGC 1162–1214 1.000 86.0
trnK-UUU-rbcL_p4 trnK-UUU-rbcL GAGTTGCCAAGCTCTATCCC GCCGTAGCTAATCGAGTAGC 1206–1258 1.000 85.7
trnK-UUU-rbcL_p5 trnK-UUU-rbcL GGAGTTGCCAAGCTCTATCC GCCGTAGCTAATCGAGTAGC 1207–1259 1.000 85.7
trnV-UAC-ndhC_p1 trnV-UAC-ndhC AGAAGGTCTACGGTTCGAGT GCTGGATATCATTAGAAATGCCC 395–625 1.000 58.1
trnV-UAC-ndhC_p2 trnV-UAC-ndhC AGAAGGTCTACGGTTCGAGT GGCTGGATATCATTAGAAATGCC 396–626 1.000 58.0
trnV-UAC-ndhC_p3 trnV-UAC-ndhC GAAGGTCTACGGTTCGAGTC GCTGGATATCATTAGAAATGCCC 394–624 1.000 55.3
trnV-UAC-ndhC_p4 trnV-UAC-ndhC GAAGGTCTACGGTTCGAGTC GGCTGGATATCATTAGAAATGCC 395–625 1.000 55.3
trnV-UAC-ndhC_p5 trnV-UAC-ndhC GTTCGAGTCCGTATAGCCCT GCTGGATATCATTAGAAATGCCC 383–613 1.000 54.3
trnL-UAA-trnT-UGU_p1 trnL-UAA-trnT-UGU TAGCGTCTACCAATTTCGCC AAGAGAAAAGCCGGCTATCG 1263–1407 1.000 86.7
trnL-UAA-trnT-UGU_p2 trnL-UAA-trnT-UGU TAGCGTCTACCAATTTCGCC GCGATGCTCTAACCTCTGAG 1212–1356 1.000 86.3
trnL-UAA-trnT-UGU_p3 trnL-UAA-trnT-UGU AGTCCGTAGCGTCTACCAAT AAGAGAAAAGCCGGCTATCG 1269–1413 1.000 85.3
trnL-UAA-trnT-UGU_p4 trnL-UAA-trnT-UGU TAGCGTCTACCAATTTCGCC GGAATCGAACCGATGACCAT 1244–1388 1.000 85.3
trnL-UAA-trnT-UGU_p5 trnL-UAA-trnT-UGU AGTCCGTAGCGTCTACCAAT GCGATGCTCTAACCTCTGAG 1218–1362 1.000 84.9
psbD-trnT-GGU_p1 psbD-trnT-GGU CACAAAAACGAAACGGTCCC GTGGTAGAGTAACGCCATGG 1221–1640 1.000 85.2
psbD-trnT-GGU_p2 psbD-trnT-GGU CCACAAAAACGAAACGGTCC GTGGTAGAGTAACGCCATGG 1222–1641 1.000 85.2
psbD-trnT-GGU_p3 psbD-trnT-GGU CCCACAAAAACGAAACGGTC GTGGTAGAGTAACGCCATGG 1223–1642 1.000 85.2
psbD-trnT-GGU_p4 psbD-trnT-GGU CACAAAAACGAAACGGTCCC TCAGTGGTAGAGTAACGCCA 1224–1643 1.000 85.0
psbD-trnT-GGU_p5 psbD-trnT-GGU CCACAAAAACGAAACGGTCC TCAGTGGTAGAGTAACGCCA 1225–1644 1.000 85.0
atpI-atpH_p1 atpI-atpH TACAAGCGGTATTCAAGCCC ATAACGGAAGCGGCAGAAAT 1152–1472 1.000 88.4
atpI-atpH_p2 atpI-atpH TACAAGCGGTATTCAAGCCC CGCAATCCCTTCTACTGCTT 1240–1560 1.000 88.2
atpI-atpH_p3 atpI-atpH TACAAGCGGTATTCAAGCCC AATAACGGAAGCGGCAGAAA 1153–1473 1.000 87.2
atpI-atpH_p4 atpI-atpH TACAAGCGGTATTCAAGCCC AGGTCCAATAGAAGCAAGCC 1192–1512 1.000 85.1
atpI-atpH_p5 atpI-atpH TACAAGCGGTATTCAAGCCC GTCCAATAGAAGCAAGCCCT 1190–1510 1.000 85.1

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (9)

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

Species Accession Length (bp) Link
Pterocarpus angolensis MZ274114.1 158889 View on NCBI ↗
Pterocarpus erinaceus MZ274115.1 159246 View on NCBI ↗
Pterocarpus indicus NC_049082.1 158107 View on NCBI ↗
Pterocarpus macrocarpus NC_049083.1 157992 View on NCBI ↗
Pterocarpus marsupium NC_049080.1 158451 View on NCBI ↗
Pterocarpus pedatus NC_049081.1 158568 View on NCBI ↗
Pterocarpus santalinus NC_049084.1 158966 View on NCBI ↗
Pterocarpus soyauxii MZ274116.1 159418 View on NCBI ↗
Pterocarpus tinctorius MZ274117.1 159029 View on NCBI ↗