Markers + reference

Gelsemium

2 species · Gelsemiaceae · Gentianales

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Species 2
Genome length 155–155 kb
Candidate markers 273
Primer pairs 85

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 273 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GTG-psbA LSC 459 0.1033 0.86 82.7 yes View details
atpF LSC 1245 0.0088 1.00 55.1 yes View details
atpF-atpH LSC 352 0.0483 1.00 81.4 yes View details
petN-psbM LSC 1181 0.1088 0.97 84.4 yes View details
ndhC-trnV-UAC LSC 1160 0.0380 1.00 71.5 yes View details
trnM-CAU-atpE LSC 205 0.0537 1.00 67.5 yes View details
psbE-petL LSC 1014 0.0684 0.97 90.7 yes View details
ndhF-rpl32 SSC 767 0.0248 1.00 67.9 yes View details
ycf1 SSC 5556 0.0162 1.00 51.2 yes View details
psbL-psbF LSC 23 0.0870 1.00 82.0 yes View details
petB-petD LSC 188 0.0286 0.93 73.0 yes View details
rpl36-infA LSC 60 0.0500 1.00 70.0 yes View details
ndhG-ndhI SSC 221 0.0452 1.00 66.1 yes View details
ndhI-ndhA SSC 98 0.0306 1.00 65.5 yes View details
rpl2-trnH-GTG IRa 118 0.0085 1.00 64.0 no View details
atpB-rbcL LSC 724 0.0097 1.00 63.7 yes View details
petD-rps11 LSC 1265 0.0063 1.00 62.4 yes View details
trnR-ACG-trnN-GUU IRb 572 0.0070 1.00 62.2 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 85 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GTG-psbA_p1 trnH-GTG-psbA GATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 496–528 1.000 88.8
trnH-GTG-psbA_p2 trnH-GTG-psbA CAATCCACTGCCTTGATCCA TTCCCTCTAGACCTAGCTGC 510–542 1.000 88.6
trnH-GTG-psbA_p3 trnH-GTG-psbA AATCCACTGCCTTGATCCAC TTCCCTCTAGACCTAGCTGC 509–541 1.000 88.6
trnH-GTG-psbA_p4 trnH-GTG-psbA ACAATCCACTGCCTTGATCC TTCCCTCTAGACCTAGCTGC 511–543 1.000 88.5
trnH-GTG-psbA_p5 trnH-GTG-psbA CGCATGGTGGATTCACAATC TTCCCTCTAGACCTAGCTGC 525–557 1.000 85.6
atpF_p1 atpF TTTCGTCAGCTCGAATGGTT GGGGGAAGTTATACAAAAAGAACTC 1399 1.000 40.6
atpF_p2 atpF TTTCGTCAGCTCGAATGGTT GGGGGAAGTTATACAAAAAGAACT 1399 1.000 40.6
atpF_p3 atpF TCGTCAGCTCGAATGGTTAC GGGGGAAGTTATACAAAAAGAACTC 1397 1.000 40.6
atpF_p4 atpF TCGTCAGCTCGAATGGTTAC GGGGGAAGTTATACAAAAAGAACT 1397 1.000 40.6
atpF_p5 atpF GTCAGCTCGAATGGTTACCA GGGGGAAGTTATACAAAAAGAACTC 1395 1.000 40.6
atpF-atpH_p1 atpF-atpH TATTAACCCCGAAACTCCCG AGGCAGAGGGAAAAATACGG 538–539 1.000 71.3
atpF-atpH_p2 atpF-atpH GGTATTAACCCCGAAACTCCC AGGCAGAGGGAAAAATACGG 540–541 1.000 70.5
atpF-atpH_p3 atpF-atpH TATTAACCCCGAAACTCCCG GCAGAGGGAAAAATACGGGG 536–537 1.000 69.8
atpF-atpH_p4 atpF-atpH TATTAACCCCGAAACTCCCG GGCAGAGGGAAAAATACGGG 537–538 1.000 69.8
atpF-atpH_p5 atpF-atpH GGTATTAACCCCGAAACTCCC GCAGAGGGAAAAATACGGGG 538–539 1.000 69.0
petN-psbM_p1 petN-psbM ACTCGTAGTGTGGGGAAGAA TCATTCTAGTTCCTACCGCCT 1263–1277 1.000 81.9
petN-psbM_p2 petN-psbM TCGTAGTGTGGGGAAGAAGT TCATTCTAGTTCCTACCGCCT 1261–1275 1.000 81.9
petN-psbM_p3 petN-psbM ACTCGTAGTGTGGGGAAGAA TCTAGTTCCTACCGCCTTTCT 1259–1273 1.000 81.4
petN-psbM_p4 petN-psbM TCGTAGTGTGGGGAAGAAGT TCTAGTTCCTACCGCCTTTCT 1257–1271 1.000 81.4
petN-psbM_p5 petN-psbM CGTAGTGTGGGGAAGAAGTG TCATTCTAGTTCCTACCGCCT 1260–1274 1.000 81.3
ndhC-trnV-UAC_p1 ndhC-trnV-UAC TCATATTCGTAAAGCAGAAACA AGAAGGTCTACGGTTCGAGT 1216–1225 1.000 43.0
ndhC-trnV-UAC_p2 ndhC-trnV-UAC AGCCAAAATAGGAATAAGACTTGA AGAAGGTCTACGGTTCGAGT 1265–1274 1.000 42.9
ndhC-trnV-UAC_p3 ndhC-trnV-UAC AAGCCAAAATAGGAATAAGACTTGA AGAAGGTCTACGGTTCGAGT 1266–1275 1.000 42.9
ndhC-trnV-UAC_p4 ndhC-trnV-UAC AGCCAAAATAGGAATAAGACTTGA GAAGGTCTACGGTTCGAGTC 1264–1273 1.000 42.9
ndhC-trnV-UAC_p5 ndhC-trnV-UAC GCCAAAATAGGAATAAGACTTGA AGAAGGTCTACGGTTCGAGT 1264–1273 1.000 42.9
trnM-CAU-atpE_p1 trnM-CAU-atpE GCTCCATGTGCTCTGATTCA AGAGGCTATCAGTGGGGTTT 960–965 1.000 81.0
trnM-CAU-atpE_p2 trnM-CAU-atpE TCTATTTGCGCGGTATTGCT TACGCCTTAACGACCAATGG 632–637 1.000 81.0
trnM-CAU-atpE_p3 trnM-CAU-atpE TGCGCGGTATTGCTTAGATT TACGCCTTAACGACCAATGG 626–631 1.000 81.0
trnM-CAU-atpE_p4 trnM-CAU-atpE TTGCGCGGTATTGCTTAGAT TACGCCTTAACGACCAATGG 627–632 1.000 81.0
trnM-CAU-atpE_p5 trnM-CAU-atpE GCTCCATGTGCTCTGATTCA TACGCCTTAACGACCAATGG 1186–1191 1.000 80.8

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (2)

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

Species Accession Length (bp) Link
Gelsemium elegans NC_065471.1 154993 View on NCBI ↗
Gelsemium sempervirens NC_065472.1 155022 View on NCBI ↗