Markers + reference

Jasminum

14 species · Oleaceae · Lamiales

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Species 14
Genome length 144–164 kb
Candidate markers 270
Primer pairs 80

Genome-wide nucleotide diversity

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

Candidate markers

7 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
rps2-rpoC2 LSC 1218 0.1984 0.94 81.9 yes View details
psaI-trnI-CAU LSC 1789 0.0937 0.98 83.5 yes View details
trnV-UAC-ndhC LSC 1523 0.0289 0.66 65.3 yes View details
psaJ-rpl33 LSC 1051 0.0413 0.93 80.5 yes View details
ycf1 IRb 5910 0.0294 0.99 69.2 no View details
rps15-ycf1 SSC 415 0.0661 0.98 85.0 yes View details
ycf1 IRa 5910 0.0297 1.00 69.8 yes View details
trnG-UCC-trnR-UCU LSC 178 0.0625 0.99 84.7 yes View details
trnL-UAA-trnT-UGU LSC 686 0.0151 1.00 80.7 yes View details
ycf3-cemA LSC 924 0.0192 1.00 78.4 yes View details
trnG-GCC-trnfM-CAU LSC 188 0.0535 0.99 78.1 yes View details
trnS-GGA-ycf3 LSC 820 0.0127 1.00 77.6 yes View details
trnH-GUG-psbA LSC 461 0.0353 1.00 76.9 yes View details
ndhF-rpl32 SSC 494 0.0360 0.97 76.7 yes View details
psbZ-trnG-GCC LSC 402 0.0327 0.96 74.2 yes View details
trnI-CAU-ycf2 IRb 152 0.0711 1.00 74.2 yes View details
rps19 LSC 351 0.0316 1.00 72.7 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 80 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA AATCCACTGCCTTAATCCGC GAAGCTCCATCTACAAATGG 506–535 1.000 55.5
trnH-GUG-psbA_p2 trnH-GUG-psbA CCTTAATCCGCTTGGCTACA GAAGCTCCATCTACAAATGG 497–526 1.000 55.5
trnH-GUG-psbA_p3 trnH-GUG-psbA ATGAGTTATGGGCGAACGAC GAAGCTCCATCTACAAATGG 80–585 0.929 54.7
trnH-GUG-psbA_p4 trnH-GUG-psbA CGCATGGTGGATTCACAATC GAAGCTCCATCTACAAATGG 522–551 1.000 54.2
trnH-GUG-psbA_p5 trnH-GUG-psbA TAATCCGCTTGGCTACATCC GAAGCTCCATCTACAAATGG 494–523 1.000 53.7
trnG-UCC-trnR-UCU_p1 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG TGGAAAGAAATTGCGTCCAA 295–318 1.000 77.0
trnG-UCC-trnR-UCU_p2 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG TGGAAAGAAATTGCGTCCAA 298–321 1.000 76.8
trnG-UCC-trnR-UCU_p3 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 248–271 1.000 75.3
trnG-UCC-trnR-UCU_p4 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG ATGGAAAGAAATTGCGTCCA 296–319 1.000 75.1
trnG-UCC-trnR-UCU_p5 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 251–274 1.000 75.1
rps2-rpoC2_p1 rps2-rpoC2 CTTCGTGCTGATCAACGAGA GATTGGTTGAAGGGCCTGAA 1767–2190 0.929 88.4
rps2-rpoC2_p2 rps2-rpoC2 TCTTCGTGCTGATCAACGAG GATTGGTTGAAGGGCCTGAA 1768–2191 0.929 88.4
rps2-rpoC2_p3 rps2-rpoC2 CTTCGTGCTGATCAACGAGA GGGTCGAATCGATTGGTTGA 1777–2200 0.786 83.1
rps2-rpoC2_p4 rps2-rpoC2 TCTTCGTGCTGATCAACGAG GGGTCGAATCGATTGGTTGA 1778–2201 0.786 83.1
rps2-rpoC2_p5 rps2-rpoC2 CTTATCGCAGCCCGTACTAC GGGTCGAATCGATTGGTTGA 1529–1982 0.786 82.9
psbZ-trnG-GCC_p1 psbZ-trnG-GCC GGGTTAGTCTTTCTGGTGGG AATCGAACCCGCATCTTCTC 463–513 1.000 87.6
psbZ-trnG-GCC_p2 psbZ-trnG-GCC GGGTTAGTCTTTCTGGTGGG GAATCGAACCCGCATCTTCT 464–514 1.000 87.6
psbZ-trnG-GCC_p3 psbZ-trnG-GCC GGGTTAGTCTTTCTGGTGGG GAACCCGCATCTTCTCCTTG 459–509 1.000 83.1
psbZ-trnG-GCC_p4 psbZ-trnG-GCC AGTCTTTCTGGTGGGTATCCT AATCGAACCCGCATCTTCTC 458–508 1.000 81.9
psbZ-trnG-GCC_p5 psbZ-trnG-GCC AGTCTTTCTGGTGGGTATCCT GAATCGAACCCGCATCTTCT 459–509 1.000 81.9
trnG-GCC-trnfM-CAU_p1 trnG-GCC-trnfM-CAU AGAAGATGCGGGTTCGATTC GTTCAAATCCTGTCTCCGCA 232–241 1.000 90.0
trnG-GCC-trnfM-CAU_p2 trnG-GCC-trnfM-CAU GAGAAGATGCGGGTTCGATT GTTCAAATCCTGTCTCCGCA 233–242 1.000 90.0
trnG-GCC-trnfM-CAU_p3 trnG-GCC-trnfM-CAU AGAAGATGCGGGTTCGATTC GTAGCTCGCAAGGCTCATAA 266–275 1.000 89.7
trnG-GCC-trnfM-CAU_p4 trnG-GCC-trnfM-CAU AGAAGATGCGGGTTCGATTC TAGCTCGCAAGGCTCATAAC 265–274 1.000 89.7
trnG-GCC-trnfM-CAU_p5 trnG-GCC-trnfM-CAU GAGAAGATGCGGGTTCGATT TAGCTCGCAAGGCTCATAAC 266–275 1.000 89.7
psaI-trnI-CAU_p1 psaI-trnI-CAU ACAGATGAGATTGGGTCCCA GGGGAGTGACATTGATCCAC 1941–2824 0.643 77.1
psaI-trnI-CAU_p2 psaI-trnI-CAU TTTTAGCCATCCAGCGATCC GGGGAGTGACATTGATCCAC 2153–2996 0.571 74.2
psaI-trnI-CAU_p3 psaI-trnI-CAU GCCATTGCAATTGTCGGAAA GTTGGGCGCTTTAACCATTC 80–2939 0.500 71.3
psaI-trnI-CAU_p4 psaI-trnI-CAU ACAGATGAGATTGGGTCCCA GTTGGGCGCTTTAACCATTC 1941–2868 0.357 66.0
psaI-trnI-CAU_p5 psaI-trnI-CAU TTTTAGCCATCCAGCGATCC GTTGGGCGCTTTAACCATTC 2145–2672 0.357 66.0

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (14)

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

Species Accession Length (bp) Link
Jasminum angulare OR605726.1 162628 View on NCBI ↗
Jasminum auriculatum NC_085215.1 161735 View on NCBI ↗
Jasminum beesianum OR605724.1 163845 View on NCBI ↗
Jasminum dallachyi OR605727.1 161316 View on NCBI ↗
Jasminum dichotomum NC_085216.1 162855 View on NCBI ↗
Jasminum dispermum OR605725.1 162495 View on NCBI ↗
Jasminum fluminense NC_042272.1 160789 View on NCBI ↗
Jasminum kedahense OR605728.1 162276 View on NCBI ↗
Jasminum lanceolarium PX412911.1 163015 View on NCBI ↗
Jasminum multiflorum NC_085217.1 162801 View on NCBI ↗
Jasminum nervosum NC_085477.1 163248 View on NCBI ↗
Jasminum polyanthum NC_042273.1 143735 View on NCBI ↗
Jasminum sambac NC_034694.1 163186 View on NCBI ↗
Jasminum tortuosum NC_034691.1 162080 View on NCBI ↗