Markers + reference

Erythrostemon

2 species · Fabaceae · Fabales

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Species 2
Genome length 155–156 kb
Candidate markers 267
Primer pairs 120

Genome-wide nucleotide diversity

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

Candidate markers

16 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 343 0.0712 0.94 75.8 yes View details
trnK-UUU-rps16 LSC 707 0.0500 0.96 79.0 yes View details
rps16-trnQ-UUG LSC 635 0.0390 0.61 66.5 yes View details
psbK-psbI LSC 412 0.0385 0.95 67.1 yes View details
psbZ-trnG-GCC LSC 450 0.0742 0.96 86.5 yes View details
trnT-UGU-trnL-UAA LSC 1322 0.0532 0.80 75.6 yes View details
trnL-UAA-trnF-GAA LSC 415 0.0392 0.98 71.5 yes View details
ndhC-trnV-UAC LSC 510 0.0627 0.72 71.5 yes View details
accD-psaI LSC 276 0.0698 0.78 67.6 yes View details
rpl33-rps18 LSC 203 0.0985 1.00 81.6 yes View details
rpl36-rps8 LSC 475 0.0422 1.00 67.0 yes View details
rpl16 LSC 1490 0.0290 0.99 64.2 yes View details
rps3-rps19 LSC 655 0.0642 0.98 89.5 yes View details
ycf1 IRb 772 0.0066 0.98 51.0 no View details
ndhF-rpl32 SSC 923 0.0328 0.96 68.3 yes View details
ycf1 SSC 5400 0.0259 1.00 52.9 yes View details
atpF-atpH LSC 471 0.0495 0.90 81.1 yes View details
psbI-trnS-GCU LSC 75 0.0933 1.00 80.8 yes View details
ndhD-psaC SSC 125 0.0732 0.98 78.6 yes View details
trnW-CCA-trnP-UGG LSC 225 0.0734 0.97 77.7 yes View details
trnG-GCC-trnfM-CAU LSC 191 0.0492 0.96 76.0 yes View details
rps11-rpl36 LSC 220 0.0735 0.93 76.0 yes View details
trnG-UCC-trnR-UCU LSC 368 0.0424 0.90 75.9 yes View details
rps19-trnH-GUG LSC 4 0.3333 0.75 74.6 no View details
rps4-trnT-UGU LSC 349 0.0511 0.95 74.5 yes View details
rps2-rpoC2 LSC 221 0.0588 1.00 73.4 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 120 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 TGTGGTTGAGGCTCCATCTA 395–424 1.000 87.0
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCCTCTAGACCTAGCTGTGG 410–439 1.000 84.7
trnH-GUG-psbA_p3 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCGAGCTAACCTTGGTATGG 461–490 1.000 84.3
trnH-GUG-psbA_p4 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCTCTAGACCTAGCTGTGGT 409–438 1.000 83.5
trnH-GUG-psbA_p5 trnH-GUG-psbA CCTTGATCCACTTGGCTACA TGTGGTTGAGGCTCCATCTA 399–428 1.000 81.6
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCGATGGTATGGACGAATCC TGGAACTTTGTCCTAATCAACA 830–839 1.000 49.7
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCGATGGTATGGACGAATCC TGGAACTTTGTCCTAATCAACAA 830–839 1.000 47.6
trnK-UUU-rps16_p3 trnK-UUU-rps16 TGGAGTCGCACTTAAAAGCC TGGAACTTTGTCCTAATCAACA 784–793 1.000 46.9
trnK-UUU-rps16_p4 trnK-UUU-rps16 AGTCGCACTTAAAAGCCGAG TGGAACTTTGTCCTAATCAACA 781–790 1.000 46.2
trnK-UUU-rps16_p5 trnK-UUU-rps16 CCGATGGTATGGACGAATCC ATGGAACTTTGTCCTAATCAACA 831–840 1.000 46.0
rps16-trnQ-UUG_p1 rps16-trnQ-UUG GTCTTTCAAGTCGCACGTTG GTCGAATAGAAATGGGGCGT 528–775 1.000 85.4
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GTCTTTCAAGTCGCACGTTG TCGAATAGAAATGGGGCGTG 527–774 1.000 85.4
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GTCTTTCAAGTCGCACGTTG TGTCGAATAGAAATGGGGCG 529–776 1.000 85.4
rps16-trnQ-UUG_p4 rps16-trnQ-UUG GTCTTTCAAGTCGCACGTTG GAGGTTCGAATCCTTCCGTC 468–715 1.000 85.4
rps16-trnQ-UUG_p5 rps16-trnQ-UUG ATGTCTTTCAAGTCGCACGT GTCGAATAGAAATGGGGCGT 530–777 1.000 84.4
psbK-psbI_p1 psbK-psbI ACGCCCCATTTCTATTCGAC TGGACTAAAGCGTCGGATTG 1337–1414 1.000 84.8
psbK-psbI_p2 psbK-psbI CACGCCCCATTTCTATTCGA TGGACTAAAGCGTCGGATTG 1338–1415 1.000 84.8
psbK-psbI_p3 psbK-psbI CGCCCCATTTCTATTCGACA TGGACTAAAGCGTCGGATTG 1336–1413 1.000 84.8
psbK-psbI_p4 psbK-psbI ACGCCCCATTTCTATTCGAC GTGGACTAAAGCGTCGGATT 1338–1415 1.000 84.8
psbK-psbI_p5 psbK-psbI CGCCCCATTTCTATTCGACA GTGGACTAAAGCGTCGGATT 1337–1414 1.000 84.8
psbI-trnS-GCU_p1 psbI-trnS-GCU CCTATCTAACGATCCAGGACG TGGACTAAAGCGTCGGATTG 191–310 1.000 67.5
psbI-trnS-GCU_p2 psbI-trnS-GCU CCTATCTAACGATCCAGGACG GTGGACTAAAGCGTCGGATT 192–311 1.000 67.5
psbI-trnS-GCU_p3 psbI-trnS-GCU CCTATCTAACGATCCAGGACG TTTTTCGTACCGAGGGTTCG 154–273 1.000 66.2
psbI-trnS-GCU_p4 psbI-trnS-GCU CCTATCTAACGATCCAGGACG CAATTGGGGAGAGATGGCTG 213–332 1.000 64.9
psbI-trnS-GCU_p5 psbI-trnS-GCU CCTATCTAACGATCCAGGACG GACTAAAGCGTCGGATTGCT 189–308 1.000 64.7
trnG-UCC-trnR-UCU_p1 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 420–448 1.000 69.9
trnG-UCC-trnR-UCU_p2 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 423–451 1.000 69.7
trnG-UCC-trnR-UCU_p3 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 426–454 1.000 69.2
trnG-UCC-trnR-UCU_p4 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 429–457 1.000 69.0
trnG-UCC-trnR-UCU_p5 trnG-UCC-trnR-UCU ACCAAAGTTTCACGTTCGGT AGAAGACCTCTGTCCTATCCA 490–518 1.000 67.7

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
Erythrostemon calycinus NC_047361.1 156190 View on NCBI ↗
Erythrostemon pannosus MZ441397.1 154726 View on NCBI ↗