Markers + reference

Patrinia

7 species · Caprifoliaceae · Dipsacales

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Species 7
Genome length 151–159 kb
Candidate markers 263
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 263 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 342 0.0865 0.44 61.3 yes View details
petN-psbM LSC 1073 0.0322 0.79 60.8 yes View details
accD LSC 1092 0.0495 0.98 86.2 yes View details
psbE-petL LSC 1270 0.0536 0.71 79.0 yes View details
rpoA LSC 981 0.0566 1.00 69.8 yes View details
rpl23-trnI-CAU IRb 170 0.0034 1.00 26.7 yes View details
trnN-GUU-ndhF SSC 580 0.0987 0.99 78.1 yes View details
rpl32-trnL-UAG SSC 806 0.0364 0.95 77.4 yes View details
ycf1 SSC 4814 0.0240 0.98 56.2 yes View details
trnI-CAU-trnH-GUG IRa 379 0.0858 0.82 70.0 no View details
trnI-CAU-ycf2 IRb 162 0.1247 0.99 72.7 yes View details
rps15-ycf1 SSC 460 0.0391 0.87 71.6 yes View details
clpP LSC 606 0.0388 1.00 71.2 yes View details
ycf2-trnI-CAU IRa 163 0.1024 0.97 71.2 yes View details
accD-psaI LSC 554 0.0345 0.95 70.4 yes View details
trnE-UUC-trnT-GGU LSC 805 0.0172 1.00 69.6 yes View details
rps16-trnQ-UUG LSC 1757 0.0211 0.97 69.4 yes View details
trnT-UGU-trnL-UAA LSC 761 0.0149 0.97 69.1 yes View details
atpF-atpH LSC 383 0.0234 1.00 68.8 yes View details
ycf1-trnN-GUU SSC 456 0.0406 0.84 65.2 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 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 GCAATGGAACCATAGACGGT TTCCCTCTAGACCTAGCTGC 552–553 0.286 56.3
trnH-GUG-psbA_p2 trnH-GUG-psbA GCAATGGAACCATAGACGGT GAGCTTAGTTTCCGTCTGGG 1173–1174 0.286 53.9
trnH-GUG-psbA_p3 trnH-GUG-psbA GCAATGGAACCATAGACGGT GAGTGGGAGCTTAGTTTCCG 1179–1180 0.286 53.9
trnH-GUG-psbA_p4 trnH-GUG-psbA GCAATGGAACCATAGACGGT GGAGCTTAGTTTCCGTCTGG 1174–1175 0.286 53.9
trnH-GUG-psbA_p5 trnH-GUG-psbA GCAATGGAACCATAGACGGT GGGAGCTTAGTTTCCGTCTG 1175–1176 0.286 53.9
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TCGGAGGTTCGAATCCTTTC 1798–1833 1.000 81.3
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TAAGGCAACGGGTTTTGGTC 1825–1860 1.000 81.0
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GGGTTTTGGTCCCGCTATTC 1816–1851 1.000 79.3
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GTAAGGCAACGGGTTTTGGT 1826–1861 1.000 78.7
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GTGGTAAGGCAACGGGTTTT 1829–1864 1.000 78.7
atpF-atpH_p1 atpF-atpH ATTAAACCCGAAACTCCCGG CCGAGGCAGAGGGAAAAATA 568–574 1.000 77.4
atpF-atpH_p2 atpF-atpH ATTAAACCCGAAACTCCCGG GGCTTGGTTGTAGCATTAGC 497–503 1.000 76.9
atpF-atpH_p3 atpF-atpH ATTAAACCCGAAACTCCCGG GCAGAGGGAAAAATACGAGGT 563–569 1.000 75.1
atpF-atpH_p4 atpF-atpH ATTAAACCCGAAACTCCCGG GCTTGGTTGTAGCATTAGCAC 496–502 1.000 74.6
atpF-atpH_p5 atpF-atpH ATTAAACCCGAAACTCCCGG GAGGCAGAGGGAAAAATACGA 566–572 1.000 73.0
petN-psbM_p1 petN-psbM GGGGAAGAAGTGGGCTCTAA CGTAAAAACCATCAGTCAAAGTCA 873–1127 1.000 50.0
petN-psbM_p2 petN-psbM GGGGAAGAAGTGGGCTCTAA ACGTAAAAACCATCAGTCAAAGTC 874–1128 1.000 50.0
petN-psbM_p3 petN-psbM GGGGAAGAAGTGGGCTCTAA ACGTAAAAACCATCAGTCAAAGT 874–1128 1.000 49.8
petN-psbM_p4 petN-psbM TATGGGGAAGAAGTGGGCTC CGTAAAAACCATCAGTCAAAGTCA 876–1130 1.000 49.4
petN-psbM_p5 petN-psbM TATGGGGAAGAAGTGGGCTC ACGTAAAAACCATCAGTCAAAGTC 877–1131 1.000 49.4
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU AGAGATGTCCTGAACCGCTA GAACCGATGACTTACGCCTT 892–952 1.000 85.9
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU AGATGTCCTGAACCGCTAGA GAACCGATGACTTACGCCTT 890–950 1.000 85.9
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU AGAGATGTCCTGAACCGCTA CCATGGCGTTACTCTACCAC 871–931 1.000 85.6
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU AGATGTCCTGAACCGCTAGA CCATGGCGTTACTCTACCAC 869–929 1.000 85.6
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU GATGTCCTGAACCGCTAGAC GAACCGATGACTTACGCCTT 889–949 1.000 85.4
trnT-UGU-trnL-UAA_p1 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG ACCAATTTCGCCATATCCCC 788–811 1.000 84.9
trnT-UGU-trnL-UAA_p2 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG TAGCGTCTACCAATTTCGCC 796–819 1.000 84.3
trnT-UGU-trnL-UAA_p3 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT ACCAATTTCGCCATATCCCC 820–843 1.000 83.8
trnT-UGU-trnL-UAA_p4 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT TAGCGTCTACCAATTTCGCC 828–851 1.000 83.3
trnT-UGU-trnL-UAA_p5 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG AGTCCGTAGCGTCTACCAAT 802–825 1.000 82.9

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (7)

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

Species Accession Length (bp) Link
Patrinia heterophylla NC_045047.1 151964 View on NCBI ↗
Patrinia monandra NC_061006.1 158940 View on NCBI ↗
Patrinia rupestris NC_060729.1 159266 View on NCBI ↗
Patrinia saniculifolia NC_036835.1 153775 View on NCBI ↗
Patrinia scabiosifolia NC_042178.1 158872 View on NCBI ↗
Patrinia scabra NC_045048.1 151267 View on NCBI ↗
Patrinia villosa NC_042190.1 158922 View on NCBI ↗