Markers + reference

Gardenia

4 species · Rubiaceae · Gentianales

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Species 4
Genome length 155–155 kb
Candidate markers 270
Primer pairs 105

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 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 1458 0.0051 1.00 43.4 yes View details
psbk-psbI LSC 410 0.0049 1.00 41.4 yes View details
petN-psbM LSC 1158 0.0043 1.00 51.2 yes View details
psbC-trnS-UGA LSC 226 0.0177 1.00 38.8 yes View details
trnT-UGU-trnL-UAA LSC 764 0.0024 1.00 41.7 yes View details
trnF-GAA-ndhJ LSC 514 0.0052 1.00 34.8 yes View details
rbcL-accD LSC 618 0.0032 1.00 38.3 yes View details
accD-psaI LSC 742 0.0052 0.98 45.0 yes View details
petB-petD LSC 874 0.0107 1.00 41.2 yes View details
rpoA LSC 1014 0.0020 1.00 26.6 yes View details
ycf1 IRb 1148 0.0000 1.00 40.1 no View details
ycf1 SSC 5631 0.0020 1.00 44.4 yes View details
rps19-rpl2 IRb 60 0.0083 1.00 54.7 yes View details
ndhC-trnV-UAC LSC 1072 0.0028 1.00 51.2 yes View details
rbcL LSC 1443 0.0022 1.00 50.8 yes View details
trnT-GGU-psbD LSC 1272 0.0016 1.00 50.5 yes View details
trnH-GUG-psbA LSC 236 0.0113 0.99 49.4 yes View details
ycf3 LSC 1964 0.0009 1.00 49.0 yes View details
ndhD SSC 1503 0.0008 1.00 48.1 yes View details
ndhF-rpl32 SSC 807 0.0031 1.00 47.8 yes View details
trnQ-UUG-psbk LSC 338 0.0054 1.00 47.5 yes View details
trnG-GCC-trnfM-CAU LSC 188 0.0062 1.00 47.2 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 105 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 GCGCTAACCTTGGTATGGAA 348–353 1.000 80.8
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 301–306 1.000 80.7
trnH-GUG-psbA_p3 trnH-GUG-psbA CAATCCACTGCCTTGATCCA GCGCTAACCTTGGTATGGAA 362–367 1.000 80.6
trnH-GUG-psbA_p4 trnH-GUG-psbA AATCCACTGCCTTGATCCAC GCGCTAACCTTGGTATGGAA 361–366 1.000 80.6
trnH-GUG-psbA_p5 trnH-GUG-psbA ACAATCCACTGCCTTGATCC GCGCTAACCTTGGTATGGAA 363–368 1.000 80.6
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1531–1532 1.000 78.9
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GGATCGTCTCCTTCAAGTCG GAGGTTCGAATCCTTCCGTC 1545–1546 1.000 78.4
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GATCGTCTCCTTCAAGTCGC GAGGTTCGAATCCTTCCGTC 1544–1545 1.000 76.4
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 1535–1536 1.000 74.2
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TAAGGCAACGGGTTTTGGTC 1561–1562 1.000 74.1
trnQ-UUG-psbk_p1 trnQ-UUG-psbk GATATGCTCTGGGACGGAAG AAAAAGCATAGGCCTCGGG 515 1.000 67.4
trnQ-UUG-psbk_p2 trnQ-UUG-psbk GACCAAAACCCGTTGCCTTA AAAAAGCATAGGCCTCGGG 473 1.000 65.5
trnQ-UUG-psbk_p3 trnQ-UUG-psbk AATGGATATGCTCTGGGACG AAAAAGCATAGGCCTCGGG 519 1.000 64.2
trnQ-UUG-psbk_p4 trnQ-UUG-psbk GAATAGCGGGACCAAAACCC AAAAAGCATAGGCCTCGGG 482 1.000 63.8
trnQ-UUG-psbk_p5 trnQ-UUG-psbk ATATGCTCTGGGACGGAAGG AAAAAGCATAGGCCTCGGG 514 1.000 63.4
psbk-psbI_p1 psbk-psbI CTTTTGTTTGGCAAGCTGCT ACGAAGAGTTTGAGAGTAAGCA 467–468 1.000 59.7
psbk-psbI_p2 psbk-psbI GTTTGGCAAGCTGCTGTAAG ACGAAGAGTTTGAGAGTAAGCA 462–463 1.000 59.7
psbk-psbI_p3 psbk-psbI TGGCAAGCTGCTGTAAGTTT ACGAAGAGTTTGAGAGTAAGCA 459–460 1.000 57.7
psbk-psbI_p4 psbk-psbI TTGGCAAGCTGCTGTAAGTT ACGAAGAGTTTGAGAGTAAGCA 460–461 1.000 57.7
psbk-psbI_p5 psbk-psbI TTTGGCAAGCTGCTGTAAGT ACGAAGAGTTTGAGAGTAAGCA 461–462 1.000 57.7
petN-psbM_p1 petN-psbM TAGTAAGTCTCGCTTGGGCT AGTTCCTACGGCCTTTCTACT 1299 1.000 69.9
petN-psbM_p2 petN-psbM GGGGAAGGAGTGGACTCTAA AGTTCCTACGGCCTTTCTACT 1236 1.000 69.1
petN-psbM_p3 petN-psbM TAGTAAGTCTCGCTTGGGCT AGTTCCTACGGCCTTTCTAC 1299 1.000 68.6
petN-psbM_p4 petN-psbM TAGTAAGTCTCGCTTGGGCT GTTCCTACGGCCTTTCTACT 1298 1.000 68.6
petN-psbM_p5 petN-psbM GGGGGCATAATTCACATGGA AGTTCCTACGGCCTTTCTACT 1321 1.000 68.0
trnT-GGU-psbD_p1 trnT-GGU-psbD GCCCTTTTAACTCAGCGGTA GAAACGGTCCCTACGTAACC 1428–1429 1.000 79.4
trnT-GGU-psbD_p2 trnT-GGU-psbD GCCCTTTTAACTCAGCGGTA GGACCAGCCTACAAAAACGA 1446–1447 1.000 78.5
trnT-GGU-psbD_p3 trnT-GGU-psbD GGCGTAAGTCATCGGTTCAA GAAACGGTCCCTACGTAACC 1391–1392 1.000 77.9
trnT-GGU-psbD_p4 trnT-GGU-psbD GCCCTTTTAACTCAGCGGTA ACAAAAACGAAACGGTCCCT 1436–1437 1.000 77.4
trnT-GGU-psbD_p5 trnT-GGU-psbD GGCGTAAGTCATCGGTTCAA GGACCAGCCTACAAAAACGA 1409–1410 1.000 77.1

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
Gardenia jasminoides NC_057593.1 154921 View on NCBI ↗
Gardenia jasminoides f. longicarpa PP078786.1 154921 View on NCBI ↗
Gardenia jasminoides var. grandiflora MZ151502.1 155098 View on NCBI ↗
Gardenia stenophylla NC_066153.1 155109 View on NCBI ↗