Markers + reference

Psychotria

2 species · Rubiaceae · Gentianales

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Species 2
Genome length 155–155 kb
Candidate markers 265
Primer pairs 95

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 10 remaining regions by MarkerSeek score (out of 265 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 949 0.0368 0.97 73.7 yes View details
trnS-GCU-trnS-CGA LSC 795 0.0556 0.93 78.8 yes View details
rpoB-trnC-GCA LSC 1079 0.0356 0.96 74.7 yes View details
psbM-trnD-GUC LSC 755 0.0443 0.96 76.7 yes View details
trnF-GAA-ndhJ LSC 2065 0.0655 0.99 75.7 yes View details
psaJ-rps18 LSC 781 0.0439 0.99 74.1 yes View details
rpl16 LSC 1453 0.0346 0.90 74.4 yes View details
rpl32-trnL-UAG SSC 675 0.0609 0.95 80.7 yes View details
ndhA SSC 2336 0.0235 1.00 56.2 yes View details
trnT-UGU-trnL-UAA LSC 718 0.0358 0.93 79.4 yes View details
rpl36-rps8 LSC 514 0.0368 0.95 75.0 yes View details
trnV-UAC-trnM-CAU LSC 240 0.0468 0.98 74.4 yes View details
trnH-GUG-psbA LSC 328 0.0588 0.93 72.6 yes View details
ycf3-trnS-GGA LSC 326 0.0460 1.00 71.4 yes View details
rpoA-rps11 LSC 80 0.0375 1.00 71.1 yes View details
rps8-rpl14 LSC 156 0.0467 0.96 69.8 yes View details
trnR-UCU-atpA LSC 121 0.0413 1.00 69.7 yes View details
ndhC-trnV-UAC LSC 437 0.0359 0.89 69.5 yes View details
accD-psaI LSC 781 0.0279 0.92 69.4 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 TCAGTGCTATGCATGGTTCC 780–814 1.000 83.2
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG GTTATACAACGGCGGTCCTT 1097–1131 1.000 82.2
trnH-GUG-psbA_p3 trnH-GUG-psbA CAATCCACTGCCTTGATCCA GTTATACAACGGCGGTCCTT 1111–1145 1.000 82.2
trnH-GUG-psbA_p4 trnH-GUG-psbA AATCCACTGCCTTGATCCAC GTTATACAACGGCGGTCCTT 1110–1144 1.000 82.1
trnH-GUG-psbA_p5 trnH-GUG-psbA ACAATCCACTGCCTTGATCC GTTATACAACGGCGGTCCTT 1112–1146 1.000 82.1
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1022–1034 1.000 82.9
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGATCTAAATGGGGCGTGG 1080–1092 1.000 82.4
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CACAATGGATCGGGACCTTC GAGGTTCGAATCCTTCCGTC 1042–1054 1.000 81.3
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CACAATGGATCGGGACCTTC GAGATCTAAATGGGGCGTGG 1100–1112 1.000 80.8
rps16-trnQ-UUG_p5 rps16-trnQ-UUG ATGGATCGGGACCTTCAAGT GAGGTTCGAATCCTTCCGTC 1038–1050 1.000 80.7
trnS-GCU-trnS-CGA_p1 trnS-GCU-trnS-CGA AGTCCACTCAGCCATCTCTC ACCACTAAACTATACCCGCC 782–836 1.000 73.6
trnS-GCU-trnS-CGA_p2 trnS-GCU-trnS-CGA TAGTCCACTCAGCCATCTCT ACCACTAAACTATACCCGCC 783–837 1.000 71.1
trnS-GCU-trnS-CGA_p3 trnS-GCU-trnS-CGA TCCACTCAGCCATCTCTCC ACCACTAAACTATACCCGCC 780–834 1.000 69.0
trnS-GCU-trnS-CGA_p4 trnS-GCU-trnS-CGA TTAGTCCACTCAGCCATCTCT ACCACTAAACTATACCCGCC 784–838 1.000 68.9
trnS-GCU-trnS-CGA_p5 trnS-GCU-trnS-CGA TAGTCCACTCAGCCATCTCTC ACCACTAAACTATACCCGCC 783–837 1.000 67.0
trnR-UCU-atpA_p1 trnR-UCU-atpA AAAGCGCCCATCGTCTAATG AGGAGCAAATGGACCGTTTT 237 1.000 76.0
trnR-UCU-atpA_p2 trnR-UCU-atpA CAAAGCGCCCATCGTCTAAT AGGAGCAAATGGACCGTTTT 238 1.000 76.0
trnR-UCU-atpA_p3 trnR-UCU-atpA AAAGCGCCCATCGTCTAATG ATTCAGGAGCAAATGGACCG 241 1.000 74.1
trnR-UCU-atpA_p4 trnR-UCU-atpA CAAAGCGCCCATCGTCTAAT ATTCAGGAGCAAATGGACCG 242 1.000 74.1
trnR-UCU-atpA_p5 trnR-UCU-atpA AAAGCGCCCATCGTCTAATG AGACATTTACCGAGGAAGCG 282 1.000 73.5
rpoB-trnC-GCA_p1 rpoB-trnC-GCA GTTCTTCCGTCAAACCCTGA CCGGATTTGAACTGGGGAAA 1212–1244 1.000 82.3
rpoB-trnC-GCA_p2 rpoB-trnC-GCA AGTTCTTCCGTCAAACCCTG CCGGATTTGAACTGGGGAAA 1213–1245 1.000 82.2
rpoB-trnC-GCA_p3 rpoB-trnC-GCA CTTCCGTCAAACCCTGATCA CCGGATTTGAACTGGGGAAA 1209–1241 1.000 80.5
rpoB-trnC-GCA_p4 rpoB-trnC-GCA GTTCTTCCGTCAAACCCTGA AAAAGGATTTGCAGTCCCCC 1194–1226 1.000 80.2
rpoB-trnC-GCA_p5 rpoB-trnC-GCA AGTTCTTCCGTCAAACCCTG AAAAGGATTTGCAGTCCCCC 1195–1227 1.000 80.1
psbM-trnD-GUC_p1 psbM-trnD-GUC AGAATGAATAGCGCAGTAGCA TTCAATTGGTCAGAGCACCG 866–869 1.000 70.4
psbM-trnD-GUC_p2 psbM-trnD-GUC GAATGAATAGCGCAGTAGCA TTCAATTGGTCAGAGCACCG 865–868 1.000 66.3
psbM-trnD-GUC_p3 psbM-trnD-GUC AGAATGAATAGCGCAGTAGCA GTTCAATTGGTCAGAGCACC 867–870 1.000 66.2
psbM-trnD-GUC_p4 psbM-trnD-GUC AGAATGAATAGCGCAGTAGCAA TTCAATTGGTCAGAGCACCG 866–869 1.000 64.5
psbM-trnD-GUC_p5 psbM-trnD-GUC AGAATGAATAGCGCAGTAGCA TCAATTGGTCAGAGCACCG 865–868 1.000 64.4

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
Psychotria rubra NC_067767.1 154584 View on NCBI ↗
Psychotria serpens NC_069807.1 154972 View on NCBI ↗