Markers + reference

Erythrophleum

4 species · Fabaceae · Fabales

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Species 4
Genome length 160–160 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

10 hotspot labels from the diversity plot in genomic order, plus the top 10 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 1357 0.0194 0.80 66.1 yes View details
rps16-trnQ-UUG LSC 694 0.0255 0.72 63.3 yes View details
trnS-GCU-trnG-UCC LSC 765 0.0379 0.94 82.8 yes View details
trnR-UCU-atpA LSC 411 0.0359 0.98 72.2 yes View details
rbcL-accD LSC 1000 0.0269 0.97 80.8 yes View details
accD-psaI LSC 409 0.0338 0.95 66.1 yes View details
ycf4-cemA LSC 455 0.0420 0.92 74.0 yes View details
rps3-rps19 LSC 685 0.0327 0.97 74.6 yes View details
ndhF SSC 2241 0.0055 1.00 46.4 yes View details
ndhG-ndhI SSC 457 0.0387 0.95 76.4 yes View details
ycf1-ndhF SSC 77 0.1645 0.95 77.0 yes View details
trnQ-UUG-psbK LSC 599 0.0248 0.95 74.4 yes View details
atpH-atpI LSC 1395 0.0135 0.98 73.1 yes View details
psbZ-trnG-GCC LSC 529 0.0140 0.99 70.3 yes View details
petA-psbJ LSC 1169 0.0153 1.00 70.2 yes View details
ndhC-trnV-UAC LSC 670 0.0226 0.86 69.6 yes View details
trnT-UGU-trnL-UAA LSC 1450 0.0098 0.94 68.7 yes View details
rps8-rpl14 LSC 230 0.0348 0.89 65.7 yes View details
petD-rpoA LSC 215 0.0159 0.97 64.9 yes View details
ndhF-rpl32 SSC 936 0.0160 0.99 64.3 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 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 CCGATGGTATGGACGAATCC AAAAAGGCGCTCAACCTACA 1312–1584 1.000 85.6
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCGATGGTATGGACGAATCC CCTTGAAAAAGGCGCTCAAC 1317–1589 1.000 84.0
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCGATGGTATGGACGAATCC CTTGAAAAAGGCGCTCAACC 1316–1588 1.000 84.0
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCGATGGTATGGACGAATCC TGAAAAAGGCGCTCAACCTA 1314–1586 1.000 83.7
trnK-UUU-rps16_p5 trnK-UUU-rps16 CCGATGGTATGGACGAATCC TCCTTGAAAAAGGCGCTCAA 1318–1590 1.000 83.3
rps16-trnQ-UUG_p1 rps16-trnQ-UUG GTCTTTCAAGTCGCACGTTG GAGGTTCGAATCCTTCCGTC 583–803 1.000 85.9
rps16-trnQ-UUG_p2 rps16-trnQ-UUG ATGTCTTTCAAGTCGCACGT GAGGTTCGAATCCTTCCGTC 585–805 1.000 84.9
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GCACGTTGCTTTTTACCACA GAGGTTCGAATCCTTCCGTC 571–791 1.000 84.4
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CATGTCTTTCAAGTCGCACG GAGGTTCGAATCCTTCCGTC 586–806 1.000 84.2
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TGTCTTTCAAGTCGCACGTT GAGGTTCGAATCCTTCCGTC 584–804 1.000 83.1
trnQ-UUG-psbK_p1 trnQ-UUG-psbK GATATGCTCTGGGACGGAAG AGGCTTCAGGTAATTTCGCG 719–767 1.000 78.2
trnQ-UUG-psbK_p2 trnQ-UUG-psbK GATATGCTCTGGGACGGAAG GGCTTCAGGTAATTTCGCGA 718–766 1.000 78.2
trnQ-UUG-psbK_p3 trnQ-UUG-psbK GACCAAAACCCGTTGCCTTA AGGCTTCAGGTAATTTCGCG 677–725 1.000 76.5
trnQ-UUG-psbK_p4 trnQ-UUG-psbK GACCAAAACCCGTTGCCTTA GGCTTCAGGTAATTTCGCGA 676–724 1.000 76.5
trnQ-UUG-psbK_p5 trnQ-UUG-psbK AATGGATATGCTCTGGGACG AGGCTTCAGGTAATTTCGCG 723–771 1.000 75.0
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA TGAATCAAACGAGGGATCCC 813–877 1.000 82.8
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC TGAATCAAACGAGGGATCCC 812–876 1.000 82.8
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA TGAATCAAACGAGGGATCCC 867–931 1.000 81.4
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA GGATCCATAGAACGAATCGCA 781–845 1.000 80.5
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC GGATCCATAGAACGAATCGCA 780–844 1.000 80.5
trnR-UCU-atpA_p1 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC CGGGAAGCTGAAGTCCTTTT 517–564 1.000 73.2
trnR-UCU-atpA_p2 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC CATTCACTCGGGAAGCTGAA 525–572 1.000 73.1
trnR-UCU-atpA_p3 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC AAGACATTCACTCGGGAAGC 529–576 1.000 73.1
trnR-UCU-atpA_p4 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC ATTCACTCGGGAAGCTGAAG 524–571 1.000 70.8
trnR-UCU-atpA_p5 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC CCAAGACATTCACTCGGGAA 531–578 1.000 70.1
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTGCAACTTTAGCTGCAGC 1429–1481 1.000 84.2
atpH-atpI_p2 atpH-atpI AATAACGGAAGCGGCAGAAA TTTGCAACTTTAGCTGCAGC 1430–1482 1.000 83.0
atpH-atpI_p3 atpH-atpI CCTTCTACAGCTTGACCTGC TTTGCAACTTTAGCTGCAGC 1510–1562 1.000 82.1
atpH-atpI_p4 atpH-atpI TCCCTTCTACAGCTTGACCT TTTGCAACTTTAGCTGCAGC 1512–1564 1.000 81.6
atpH-atpI_p5 atpH-atpI CCCTTCTACAGCTTGACCTG TTTGCAACTTTAGCTGCAGC 1511–1563 1.000 81.1

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (4)

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

Species Accession Length (bp) Link
Erythrophleum africanum MZ274090.1 160235 View on NCBI ↗
Erythrophleum fordii NC_041164.1 160116 View on NCBI ↗
Erythrophleum ivorense MZ274091.1 160135 View on NCBI ↗
Erythrophleum suaveolens NC_047374.1 160344 View on NCBI ↗