Markers + reference

Eugenia

3 species · Myrtaceae · Myrtales

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Species 3
Genome length 158–159 kb
Candidate markers 267
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 9 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 465 0.0871 0.95 86.4 yes View details
trnK-UUU-rps16 LSC 572 0.0518 0.98 80.6 yes View details
psbK-psbI LSC 386 0.0523 0.94 77.0 yes View details
trnR-UCU-atpA LSC 355 0.0509 0.85 76.2 yes View details
atpH-atpI LSC 1116 0.0319 0.98 69.7 yes View details
psbZ-trnG-GCC LSC 566 0.0521 0.92 77.5 yes View details
accD-psaI LSC 764 0.0433 0.98 75.9 yes View details
ycf1 IRb 762 0.0063 0.98 51.8 no View details
ndhF-rpl32 SSC 925 0.0504 0.99 79.1 yes View details
rpl32-trnL-UAG SSC 732 0.0578 0.97 77.7 yes View details
ycf1 SSC 5607 0.0306 0.99 57.8 yes View details
trnG-UCC-trnR-UCU LSC 256 0.0664 0.96 80.8 yes View details
trnL-UAA-trnF-GAA LSC 174 0.0556 1.00 79.3 yes View details
trnfM-CAU-rps14 LSC 150 0.0556 1.00 78.8 yes View details
petA-psbJ LSC 1017 0.0416 0.96 78.0 yes View details
psbI-trnS-GCU LSC 154 0.0602 0.94 76.7 yes View details
trnG-GCC-trnfM-CAU LSC 178 0.0549 0.96 75.7 yes View details
rps2-rpoC2 LSC 240 0.0505 0.96 74.9 yes View details
rps16-trnQ-UUG LSC 1389 0.0366 0.94 74.3 yes View details
trnD-GUC-trnY-GUA LSC 440 0.0409 1.00 74.0 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 CCTCTAGACCTAGCTGCTGT 532–533 1.000 90.4
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCTCTAGACCTAGCTGCTGT 546–547 1.000 90.4
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCTCTAGACCTAGCTGCTGT 545–546 1.000 90.4
trnH-GUG-psbA_p4 trnH-GUG-psbA GATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 535–536 1.000 90.4
trnH-GUG-psbA_p5 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCTCTAGACCTAGCTGCTGT 547–548 1.000 90.3
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG AAAAAGGCGCTCAACCTACA 775–788 1.000 87.6
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG CCCAATGAGCCGTTTATCGA 913–926 1.000 86.5
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG TCCCAATGAGCCGTTTATCG 914–927 1.000 86.5
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG AAGTGTATCGTGCGGGAATC 1433–1445 1.000 86.0
trnK-UUU-rps16_p5 trnK-UUU-rps16 TTCATGGAAAAGCCCTTCCC AAAAAGGCGCTCAACCTACA 1065–1082 1.000 85.9
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1377–1462 1.000 86.3
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1388–1473 1.000 85.7
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 1381–1466 1.000 81.6
rps16-trnQ-UUG_p4 rps16-trnQ-UUG ATCATGTCCTTCAAGTCGCA GAGGTTCGAATCCTTCCGTC 1389–1474 1.000 81.2
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG GAGGTTCGAATCCTTCCGTC 1369–1454 1.000 81.1
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG ACAAAGAGTTTGAGAGTAAGCA 418–439 1.000 53.7
psbK-psbI_p2 psbK-psbI TGGCAAGCTGCTGTAAGTTT ACAAAGAGTTTGAGAGTAAGCA 415–436 1.000 51.7
psbK-psbI_p3 psbK-psbI TTGGCAAGCTGCTGTAAGTT ACAAAGAGTTTGAGAGTAAGCA 416–437 1.000 51.7
psbK-psbI_p4 psbK-psbI TTTGGCAAGCTGCTGTAAGT ACAAAGAGTTTGAGAGTAAGCA 417–438 1.000 51.7
psbK-psbI_p5 psbK-psbI GTTTGGCAAGCTGCTGTAAG AACAAAGAGTTTGAGAGTAAGCA 419–440 1.000 51.5
psbI-trnS-GCU_p1 psbI-trnS-GCU CGTAATCCTGGACGTGAAGA TTTTTCGTACCGAGGGTTCG 166–214 1.000 79.3
psbI-trnS-GCU_p2 psbI-trnS-GCU CGTAATCCTGGACGTGAAGA ATTGGGAGAGATGGCTGAGT 222–270 1.000 79.2
psbI-trnS-GCU_p3 psbI-trnS-GCU CGTAATCCTGGACGTGAAGA GAGTTTTTCGTACCGAGGGT 169–217 1.000 77.4
psbI-trnS-GCU_p4 psbI-trnS-GCU CGTAATCCTGGACGTGAAGAA TTTTTCGTACCGAGGGTTCG 166–214 1.000 76.9
psbI-trnS-GCU_p5 psbI-trnS-GCU CGTAATCCTGGACGTGAAGAA ATTGGGAGAGATGGCTGAGT 222–270 1.000 76.8
trnG-UCC-trnR-UCU_p1 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 326–336 1.000 72.1
trnG-UCC-trnR-UCU_p2 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 329–339 1.000 71.8
trnG-UCC-trnR-UCU_p3 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 332–342 1.000 71.3
trnG-UCC-trnR-UCU_p4 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 335–345 1.000 71.0
trnG-UCC-trnR-UCU_p5 trnG-UCC-trnR-UCU CCCTAGCCTTCCAAGCTAAC AGAAGACCTCTGTCCTATCCA 330–340 1.000 69.5

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

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

Species Accession Length (bp) Link
Eugenia reinwardtiana NC_084367.1 159112 View on NCBI ↗
Eugenia selloi MN095411.1 157683 View on NCBI ↗
Eugenia uniflora NC_027744.1 158445 View on NCBI ↗