Markers + reference

Embelia

4 species · Primulaceae · Ericales

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Species 4
Genome length 157–157 kb
Candidate markers 268
Primer pairs 110

Genome-wide nucleotide diversity

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

Candidate markers

12 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
trnH-GUG-psbA LSC 417 0.0311 0.97 67.6 yes View details
rps16-trnQ-UUG LSC 1763 0.0177 0.98 63.6 yes View details
petN-psbM LSC 922 0.0219 1.00 73.7 yes View details
trnT-GGU-psbD LSC 1469 0.0107 0.92 61.8 yes View details
ndhC-trnV-UAC LSC 1144 0.0264 0.98 79.0 yes View details
petA-psbJ LSC 1051 0.0188 0.98 67.1 yes View details
psaJ-rpl33 LSC 533 0.0254 0.95 55.8 yes View details
clpP-psbB LSC 454 0.0327 1.00 69.2 yes View details
ycf1 IRb 994 0.0005 1.00 30.0 no View details
ndhF-rpl32 SSC 915 0.0169 0.71 56.7 yes View details
rpl32-trnL-UAG SSC 787 0.0178 0.99 60.7 yes View details
ycf1 SSC 5595 0.0095 1.00 45.8 yes View details
rps4-trnT-UGU LSC 349 0.0239 0.98 66.6 yes View details
trnR-UCU-atpA LSC 128 0.0286 0.99 65.1 yes View details
ycf2-trnL-CAA IRb 716 0.0079 1.00 63.9 yes View details
trnL-CAA-ycf2 IRa 716 0.0079 1.00 63.9 yes View details
psbZ-trnG-GCC LSC 260 0.0310 0.99 63.4 yes View details
psaC-ndhE SSC 283 0.0154 0.99 62.8 yes View details
trnE-UUC-trnT-GGU LSC 874 0.0135 1.00 62.3 yes View details
rbcL-accD LSC 636 0.0162 0.97 61.7 yes View details
trnS-GCU-trnG-UCC LSC 754 0.0140 0.97 61.0 yes View details
accD-psaI LSC 716 0.0156 0.99 60.9 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 110 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA CCACTTGGCTACATCCGC TTCCCTCTAGACCTAGCTGC 483–489 1.000 69.3
trnH-GUG-psbA_p2 trnH-GUG-psbA CCACTTGGCTACATCCGC TAGACCTAGCTGCGGTTGAA 476–482 1.000 66.4
trnH-GUG-psbA_p3 trnH-GUG-psbA CCACTTGGCTACATCCGC CTCTAGACCTAGCTGCGGTT 479–485 1.000 65.1
trnH-GUG-psbA_p4 trnH-GUG-psbA CCACTTGGCTACATCCGC CGGTTGAAGCTCCATCTACA 464–470 1.000 64.8
trnH-GUG-psbA_p5 trnH-GUG-psbA CCACTTGGCTACATCCGC GCGGTTGAAGCTCCATCTAC 465–471 1.000 64.5
rps16-trnQ-UUG_p1 rps16-trnQ-UUG ATCATGTCTTTCAAGCCGCA GAGGTTCGAATCCTTCCGTC 1366–1865 1.000 84.4
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GATCATGTCTTTCAAGCCGC GAGGTTCGAATCCTTCCGTC 1367–1866 1.000 82.1
rps16-trnQ-UUG_p3 rps16-trnQ-UUG ATCATGTCTTTCAAGCCGCA AAATTTAAATGGGGCGTGGC 1423–1922 1.000 81.8
rps16-trnQ-UUG_p4 rps16-trnQ-UUG ATCATGTCTTTCAAGCCGCA GGGTTTTGGTCCCGGTATTC 1387–1886 1.000 80.7
rps16-trnQ-UUG_p5 rps16-trnQ-UUG ATCATGTCTTTCAAGCCGCA TTCGGAGGTTCGAATCCTTC 1370–1869 1.000 79.7
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CTTTCGTCCACTCAGCCATC ACGAATCACACTTTTACCACT 775–813 1.000 52.3
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC CTTTCGTCCACTCAGCCATC AGAACGAATCACACTTTTACCAC 778–816 1.000 51.3
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CTTTCGTCCACTCAGCCATC GAACGAATCACACTTTTACCACT 777–815 1.000 51.3
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CTTTCGTCCACTCAGCCATC AACGAATCACACTTTTACCACT 776–814 1.000 50.4
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC TTTCGTCCACTCAGCCATCT ACGAATCACACTTTTACCACT 774–812 1.000 49.2
trnR-UCU-atpA_p1 trnR-UCU-atpA CGGAATGAATGAAAAGCGTCC CAGGAACAGATGGAACGCTT 256–257 1.000 71.3
trnR-UCU-atpA_p2 trnR-UCU-atpA CGGAATGAATGAAAAGCGTCC TTCAGGAACAGATGGAACGC 258–259 1.000 71.2
trnR-UCU-atpA_p3 trnR-UCU-atpA CCAAACAAGAGGCAAAATCGG CAGGAACAGATGGAACGCTT 274–275 1.000 70.2
trnR-UCU-atpA_p4 trnR-UCU-atpA CCAAACAAGAGGCAAAATCGG TTCAGGAACAGATGGAACGC 276–277 1.000 70.2
trnR-UCU-atpA_p5 trnR-UCU-atpA CGGAATGAATGAAAAGCGTCC AGGAACAGATGGAACGCTTT 255–256 1.000 68.2
petN-psbM_p1 petN-psbM TAGTAAGTCTCGCTTGGGCT TCTCGTGCCTACTGCTTTTC 1067–1141 1.000 85.0
petN-psbM_p2 petN-psbM TAGTAAGTCTCGCTTGGGCT CTCGTGCCTACTGCTTTTCT 1066–1140 1.000 84.9
petN-psbM_p3 petN-psbM TAGTAAGTCTCGCTTGGGCT ACTGCATTGTTCGTTCTCGT 1081–1155 1.000 84.5
petN-psbM_p4 petN-psbM TAGTAAGTCTCGCTTGGGCT GTTCTCGTGCCTACTGCTTT 1069–1143 1.000 84.0
petN-psbM_p5 petN-psbM TAGTAAGTCTCGCTTGGGCT CTGCATTGTTCGTTCTCGTG 1080–1154 1.000 83.8
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC GAACCGATGACTTACGCCTT 1015–1036 1.000 80.8
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC CCATGGCGTTACTCTACCAC 994–1015 1.000 80.4
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC TGGCGTTACTCTACCACTGA 991–1012 1.000 80.2
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC CCGATGACTTACGCCTTACC 1012–1033 1.000 79.6
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC TTGAACCGATGACTTACGCC 1017–1038 1.000 78.6

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
Embelia parviflora NC_085237.1 157452 View on NCBI ↗
Embelia ribes PV608446.1 157186 View on NCBI ↗
Embelia scandens NC_056316.1 157259 View on NCBI ↗
Embelia vestita NC_045113.1 157238 View on NCBI ↗