Markers + reference

Dichocarpum

3 species · Ranunculaceae · Ranunculales

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Species 3
Genome length 153–155 kb
Candidate markers 268
Primer pairs 100

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 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 466 0.0378 0.98 72.0 yes View details
petN-psbM LSC 1164 0.0283 0.99 70.7 yes View details
trnE-UUC-trnT-GGU LSC 690 0.0324 0.98 73.5 yes View details
psbE-petL LSC 1005 0.0285 0.98 67.3 yes View details
infA-rps8 LSC 189 0.0353 1.00 60.8 yes View details
ycf1 IRb 1071 0.0112 1.00 51.3 no View details
ndhF SSC 2184 0.0249 1.00 58.7 yes View details
ndhF-trnL-UAG SSC 1082 0.0553 0.97 86.2 yes View details
ndhD SSC 1161 0.0098 1.00 50.9 yes View details
ndhD-psaC SSC 482 0.0363 0.99 66.6 yes View details
rps15-ycf1 SSC 403 0.0377 0.99 68.6 yes View details
ycf1 SSC 5709 0.0248 1.00 53.7 yes View details
trnK-UUU-rps16 LSC 686 0.0392 0.99 76.9 yes View details
atpA-atpF LSC 66 0.0404 1.00 72.6 yes View details
ycf3-trnS-GGA LSC 545 0.0281 1.00 72.5 yes View details
ccsA-ndhD SSC 182 0.0659 1.00 72.2 yes View details
psbT-psbN LSC 94 0.0507 0.98 71.9 yes View details
trnG-UCC-trnR-UCU LSC 197 0.0400 0.89 70.5 yes View details
rpl14-rpl16 LSC 137 0.0245 0.99 70.4 yes View details
trnT-UGU-trnL-UAA LSC 740 0.0267 1.00 70.3 yes View details
infA LSC 129 0.0517 1.00 69.6 yes View details
rps19-trnH-GUG LSC 20 0.0500 1.00 67.2 no 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT CCTTGAAAAAGGCGCTCAAC 769–823 1.000 84.5
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT CTTGAAAAAGGCGCTCAACC 768–822 1.000 84.5
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT CCTTGAAAAAGGCGCTCAAC 768–822 1.000 84.5
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT CTTGAAAAAGGCGCTCAACC 767–821 1.000 84.5
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TGAAAAAGGCGCTCAACCTA 765–819 1.000 84.2
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 535–759 1.000 83.3
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CTCGGAGGTTCGAATCCTTC 539–763 1.000 82.1
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA ACTCGGAGGTTCGAATCCTT 540–764 1.000 80.3
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA AGAAATCTAAGTGGGGCGTG 594–818 1.000 80.2
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAAATCTAAGTGGGGCGTGG 593–817 1.000 78.5
trnG-UCC-trnR-UCU_p1 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 274–278 1.000 70.2
trnG-UCC-trnR-UCU_p2 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 277–281 1.000 70.0
trnG-UCC-trnR-UCU_p3 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 280–284 1.000 69.5
trnG-UCC-trnR-UCU_p4 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 283–287 1.000 69.3
trnG-UCC-trnR-UCU_p5 trnG-UCC-trnR-UCU ATGATGAATTGGCGTCGACT AGAAGACCTCTGTCCTATCCA 303–307 1.000 67.7
atpA-atpF_p1 atpA-atpF CTGCTCAATACGTTCACGGA TGTTTGGGGCCATGAAAGAA 155 1.000 81.2
atpA-atpF_p2 atpA-atpF CCTACTTGAAGTACGGTGCC TGTTTGGGGCCATGAAAGAA 205 1.000 80.8
atpA-atpF_p3 atpA-atpF CTGCTCAATACGTTCACGGA GGTATGTTTGGGGCCATGAA 159 1.000 80.8
atpA-atpF_p4 atpA-atpF CCTACTTGAAGTACGGTGCC GGTATGTTTGGGGCCATGAA 209 1.000 80.4
atpA-atpF_p5 atpA-atpF CCTACTTGAAGTACGGTGCC ATGTTTGGGGCCATGAAAGA 206 1.000 78.9
petN-psbM_p1 petN-psbM TCTTGCTTGGGCTGCTTTAA TGCTACTGCACTGTTCATTCT 1306–1326 1.000 72.9
petN-psbM_p2 petN-psbM AGTAAGTCTTGCTTGGGCTG TGCTACTGCACTGTTCATTCT 1312–1332 1.000 71.4
petN-psbM_p3 petN-psbM ATGGGGAAGAAGTGGACTCT TGCTACTGCACTGTTCATTCT 1252–1272 1.000 70.3
petN-psbM_p4 petN-psbM TCTTGCTTGGGCTGCTTTAA TGCTACTGCACTGTTCATTC 1306–1326 1.000 68.7
petN-psbM_p5 petN-psbM AGTAAGTCTTGCTTGGGCTG TGCTACTGCACTGTTCATTC 1312–1332 1.000 67.2
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC GAACCGATGACTTACGCCTT 831–862 1.000 83.2
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG GAACCGATGACTTACGCCTT 793–824 1.000 82.6
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC CCGATGACTTACGCCTTACC 828–859 1.000 82.1
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC TGGAAAAAGCCCCTTATCGG 855–886 1.000 82.0
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG TGGAAAAAGCCCCTTATCGG 817–848 1.000 81.4

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

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

Species Accession Length (bp) Link
Dichocarpum dalzielii PV546614.1 153727 View on NCBI ↗
Dichocarpum fargesii NC_041478.1 153134 View on NCBI ↗
Dichocarpum sutchuenense MK253458.1 155390 View on NCBI ↗