Markers + reference

Platymiscium

2 species · Fabaceae · Fabales

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Species 2
Genome length 153–157 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

10 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 265 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA-trnK-UUU LSC 428 0.0939 0.92 80.2 yes View details
trnL-UAA-trnT-UGU LSC 1381 0.0645 0.92 84.0 yes View details
trnG-GCC-psbZ LSC 735 0.0801 0.95 81.2 yes View details
atpA-trnR-UCU LSC 264 0.1133 0.97 80.7 yes View details
trnG-UCC-trnS-GCU LSC 803 0.0714 0.80 81.4 yes View details
psbK-trnQ-UUG LSC 559 0.0919 0.97 84.1 yes View details
clpP-psbB LSC 457 0.1221 0.95 87.9 yes View details
ycf1 IRb 467 0.0107 1.00 47.5 no View details
rpl32-trnL-UAG SSC 1008 0.0913 0.76 75.8 yes View details
ycf1 SSC 5268 0.0385 1.00 61.9 yes View details
trnK-UUU-rbcL LSC 573 0.0702 0.94 83.4 yes View details
trnF-GAA-trnL-UAA LSC 437 0.0844 0.89 82.3 yes View details
trnQ-UUG-rps16 LSC 524 0.0594 0.96 81.9 yes View details
petA-psbJ LSC 1304 0.0385 0.94 81.4 yes View details
psbE-petL LSC 1030 0.0462 0.97 79.9 yes View details
atpI-atpH LSC 951 0.0396 0.88 79.2 yes View details
trnT-GGU-trnE-UUC LSC 695 0.0407 0.88 78.6 yes View details
ndhF-rpl32 SSC 594 0.0596 0.93 77.8 yes View details
ndhJ-trnF-GAA LSC 654 0.0472 0.94 77.6 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
psbA-trnK-UUU_p1 psbA-trnK-UUU GCTCTCGCGTCTCTCTAAAA ACTCCATCCGACTAGTTCCG 488–500 1.000 80.7
psbA-trnK-UUU_p2 psbA-trnK-UUU GCTCTCGCGTCTCTCTAAAA ACTAGTTCCGGGTTCGAGTC 478–490 1.000 79.1
psbA-trnK-UUU_p3 psbA-trnK-UUU GCTCTCGCGTCTCTCTAAAA GACTAGTTCCGGGTTCGAGT 479–491 1.000 79.1
psbA-trnK-UUU_p4 psbA-trnK-UUU GCTCTCGCGTCTCTCTAAAA ATCCGACTAGTTCCGGGTTC 483–495 1.000 78.6
psbA-trnK-UUU_p5 psbA-trnK-UUU TCGCGTCTCTCTAAAATTGCA ACTCCATCCGACTAGTTCCG 484–496 1.000 76.8
trnK-UUU_p1 trnK-UUU ACCTTAATTGGAATTCGGTCA TAGACAAAGGGGTGGTCCAT 2933 0.500 29.1
trnK-UUU_p2 trnK-UUU ACCTTAATTGGAATTCGGTCAA TAGACAAAGGGGTGGTCCAT 2933 0.500 27.4
trnK-UUU_p3 trnK-UUU ACCTTAATTGGAATTCGGTCA TCTAGACAAAGGGGTGGTCC 2935 0.500 26.8
trnK-UUU_p4 trnK-UUU ACCTTAATTGGAATTCGGTCA ACCACTCTAGACAAAGGGGT 2940 0.500 26.2
trnK-UUU_p5 trnK-UUU ACCTTAATTGGAATTCGGTCA ACTCTAGACAAAGGGGTGGT 2937 0.500 26.2
trnK-UUU-rbcL_p1 trnK-UUU-rbcL TGGAGTCGCACTTAAAAGCC GAGGCTAGCAAATGGAGTCC 711–746 1.000 83.5
trnK-UUU-rbcL_p2 trnK-UUU-rbcL AGTCGCACTTAAAAGCCGAG GAGGCTAGCAAATGGAGTCC 708–743 1.000 82.8
trnK-UUU-rbcL_p3 trnK-UUU-rbcL GAGTCGCACTTAAAAGCCGA GAGGCTAGCAAATGGAGTCC 709–744 1.000 82.8
trnK-UUU-rbcL_p4 trnK-UUU-rbcL TGGAGTCGCACTTAAAAGCC GAGTCCTGAGTTAGCTGCTG 697–732 1.000 81.7
trnK-UUU-rbcL_p5 trnK-UUU-rbcL TCGCACTTAAAAGCCGAGTA GAGGCTAGCAAATGGAGTCC 706–741 1.000 81.6
ndhJ-trnF-GAA_p1 ndhJ-trnF-GAA CCCCAATTTTTATGAAATACAAGATGC CCTCGTGTCACCAGTTCAAA 690–722 1.000 47.3
ndhJ-trnF-GAA_p2 ndhJ-trnF-GAA CCCCAATTTTTATGAAATACAAGATGC CTGGTAGAGCAGAGGACTGA 714–746 1.000 47.2
ndhJ-trnF-GAA_p3 ndhJ-trnF-GAA CCCCAATTTTTATGAAATACAAGATGC GGGATAGCTCAGCTGGTAGA 726–758 1.000 47.1
ndhJ-trnF-GAA_p4 ndhJ-trnF-GAA CCCCAATTTTTATGAAATACAAGATGC GCGTTAAGAATGGTCGGGAT 741–773 1.000 47.1
ndhJ-trnF-GAA_p5 ndhJ-trnF-GAA CCCCAATTTTTATGAAATACAAGATGC AGAATGGTCGGGATAGCTCA 735–767 1.000 47.1
trnF-GAA-trnL-UAA_p1 trnF-GAA-trnL-UAA TCTACCAGCTGAGCTATCCC AATCGTGAGGGTTCAAGTCC 467–491 1.000 85.7
trnF-GAA-trnL-UAA_p2 trnF-GAA-trnL-UAA TTTGAACTGGTGACACGAGG AATCGTGAGGGTTCAAGTCC 503–527 1.000 84.9
trnF-GAA-trnL-UAA_p3 trnF-GAA-trnL-UAA GTGCCAGGAACCAGATTTGA AATCGTGAGGGTTCAAGTCC 518–542 1.000 84.5
trnF-GAA-trnL-UAA_p4 trnF-GAA-trnL-UAA TCAGTCCTCTGCTCTACCAG AATCGTGAGGGTTCAAGTCC 479–503 1.000 84.5
trnF-GAA-trnL-UAA_p5 trnF-GAA-trnL-UAA CATGTGCCAGGAACCAGATT AATCGTGAGGGTTCAAGTCC 521–545 1.000 83.9
trnL-UAA-trnT-UGU_p1 trnL-UAA-trnT-UGU ACCAATTTCGCCATATCCCC GCGATGCTCTAACCTCTGAG 1385–1431 1.000 87.6
trnL-UAA-trnT-UGU_p2 trnL-UAA-trnT-UGU TAGCGTCTACCAATTTCGCC GCGATGCTCTAACCTCTGAG 1393–1439 1.000 87.0
trnL-UAA-trnT-UGU_p3 trnL-UAA-trnT-UGU ACCAATTTCGCCATATCCCC GGAATCGAACCGATGACCAT 1417–1463 1.000 86.6
trnL-UAA-trnT-UGU_p4 trnL-UAA-trnT-UGU CCCATTGTTAATTCCGGGGT GCGATGCTCTAACCTCTGAG 1478–1524 1.000 86.1
trnL-UAA-trnT-UGU_p5 trnL-UAA-trnT-UGU TAGCGTCTACCAATTTCGCC GGAATCGAACCGATGACCAT 1425–1471 1.000 86.1

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
Platymiscium parviflorum PV870749.1 156518 View on NCBI ↗
Platymiscium pubescens NC_067525.1 152956 View on NCBI ↗