Markers + reference

Corymbia

6 species · Myrtaceae · Myrtales

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Species 6
Genome length 160–160 kb
Candidate markers 256
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 256 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 475 0.0107 1.00 58.5 yes View details
trnS-GCU-trnR-UCU LSC 1873 0.0030 0.99 48.3 yes View details
trnR-UCU-atpA LSC 340 0.0098 1.00 61.4 yes View details
trnS-UGA-psbZ LSC 347 0.0044 1.00 45.7 yes View details
psbZ-trnG-UCC LSC 966 0.0061 0.98 61.8 yes View details
ndhC-trnV-UAC LSC 318 0.0113 1.00 54.0 yes View details
ndhF SSC 2253 0.0024 1.00 46.2 yes View details
ndhF-rpl32 SSC 942 0.0054 1.00 54.6 yes View details
rpl32-trnL-UAG SSC 765 0.0073 1.00 52.0 yes View details
ycf1 SSC 5670 0.0037 1.00 44.9 yes View details
psaA-ycf3 LSC 883 0.0026 1.00 56.9 yes View details
rpoB-trnC-GCA LSC 1254 0.0029 1.00 54.6 yes View details
accD-psaI LSC 680 0.0020 1.00 54.3 yes View details
atpH-atpI LSC 1127 0.0010 1.00 53.5 yes View details
matK LSC 1518 0.0025 1.00 52.0 yes View details
psbE-petL LSC 1267 0.0009 1.00 51.5 yes View details
rps19-rpl2 IRb 56 0.0155 1.00 51.4 yes View details
trnC-GCA-petN LSC 882 0.0019 1.00 51.2 yes View details
atpB-rbcL LSC 798 0.0019 1.00 51.0 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 539–543 1.000 80.5
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCTCTAGACCTAGCTGCTGT 553–557 1.000 80.4
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCTCTAGACCTAGCTGCTGT 552–556 1.000 80.4
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCTCTAGACCTAGCTGCTGT 554–558 1.000 80.4
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 542–546 1.000 80.4
matK_p1 matK TTCCATGATCTCATAGCCAA CCTTGTTTTGACTGTATCGCA 1628–1631 1.000 40.6
matK_p2 matK TTTCCATGATCTCATAGCCA CCTTGTTTTGACTGTATCGCA 1629–1632 1.000 40.6
matK_p3 matK TTCCATGATCTCATAGCCAA ACCTTGTTTTGACTGTATCGC 1629–1632 1.000 40.6
matK_p4 matK TTTCCATGATCTCATAGCCA ACCTTGTTTTGACTGTATCGC 1630–1633 1.000 40.6
matK_p5 matK TTCCATGATCTCATAGCCAA CCTTGTTTTGACTGTATCGCAC 1628–1631 1.000 40.6
trnS-GCU-trnR-UCU_p1 trnS-GCU-trnR-UCU CAATCCGACGCTTTAGTCCA AGAAGACCTCTGTCCTATCCA 1920–1944 1.000 65.2
trnS-GCU-trnR-UCU_p2 trnS-GCU-trnR-UCU AATCCGACGCTTTAGTCCAC AGAAGACCTCTGTCCTATCCA 1919–1943 1.000 65.2
trnS-GCU-trnR-UCU_p3 trnS-GCU-trnR-UCU CAATCCGACGCTTTAGTCCA AGGTTTAGAAGACCTCTGTCCT 1926–1950 1.000 64.5
trnS-GCU-trnR-UCU_p4 trnS-GCU-trnR-UCU AATCCGACGCTTTAGTCCAC AGGTTTAGAAGACCTCTGTCCT 1925–1949 1.000 64.5
trnS-GCU-trnR-UCU_p5 trnS-GCU-trnR-UCU ACGGAAAGAGAGGGATTCGA AGAAGACCTCTGTCCTATCCA 1974–1998 1.000 64.0
trnR-UCU-atpA_p1 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC GAGGAAGCAGAAGCCCTTTT 436–439 1.000 67.6
trnR-UCU-atpA_p2 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC CAGGAACAGAAGGAACGCTT 403–406 1.000 67.5
trnR-UCU-atpA_p3 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC AGGAAGCAGAAGCCCTTTTG 435–438 1.000 65.3
trnR-UCU-atpA_p4 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC GGAAGCAGAAGCCCTTTTGA 434–437 1.000 65.3
trnR-UCU-atpA_p5 trnR-UCU-atpA TGGATAGGACAGAGGTCTTCT GAGGAAGCAGAAGCCCTTTT 471–474 1.000 64.6
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT CGAATCCATGGAGGGTCATC 1183–1206 1.000 78.6
atpH-atpI_p2 atpH-atpI TACCTTGACCAACTCCAGGT CGAATCCATGGAGGGTCATC 1239–1262 1.000 78.0
atpH-atpI_p3 atpH-atpI AATAGAAGCAAGCCCCACAG CGAATCCATGGAGGGTCATC 1217–1240 1.000 77.8
atpH-atpI_p4 atpH-atpI CAATAGAAGCAAGCCCCACA CGAATCCATGGAGGGTCATC 1218–1241 1.000 77.6
atpH-atpI_p5 atpH-atpI AATAACGGAAGCGGCAGAAA CGAATCCATGGAGGGTCATC 1184–1207 1.000 77.5
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CCTCATCATTTCCATCCCCG CCGGATTTGAACTGGGGAAA 1341 1.000 79.0
rpoB-trnC-GCA_p2 rpoB-trnC-GCA CCTCATCATTTCCATCCCCG TTTCTTGATCAGGCGACACC 1360 1.000 78.2
rpoB-trnC-GCA_p3 rpoB-trnC-GCA CCCTCATCATTTCCATCCCC CCGGATTTGAACTGGGGAAA 1342 1.000 77.4
rpoB-trnC-GCA_p4 rpoB-trnC-GCA CCTCATCATTTCCATCCCCG AAAAGGATTTGCAGTCCCCC 1323 1.000 76.9
rpoB-trnC-GCA_p5 rpoB-trnC-GCA CCCTCATCATTTCCATCCCC TTTCTTGATCAGGCGACACC 1361 1.000 76.5

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (6)

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

Species Accession Length (bp) Link
Corymbia citriodora subsp. citriodora KP015029.1 159995 View on NCBI ↗
Corymbia eximia NC_022409.1 160012 View on NCBI ↗
Corymbia henryi NC_028409.1 160095 View on NCBI ↗
Corymbia maculata NC_022408.1 160045 View on NCBI ↗
Corymbia tessellaris NC_022410.1 160127 View on NCBI ↗
Corymbia torelliana NC_028410.1 159994 View on NCBI ↗