Markers + reference

Dischidia

6 species · Apocynaceae · Gentianales

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Species 6
Genome length 175–177 kb
Candidate markers 292
Primer pairs 100

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 292 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 1374 0.0180 0.96 55.8 yes View details
rps2-rpoC2 LSC 4926 0.0135 0.99 49.3 yes View details
trnE-UUC-trnT-GGU LSC 986 0.0369 0.95 71.7 yes View details
psaA-ycf3 LSC 835 0.0230 1.00 67.0 yes View details
ndhC-trnV-UAC LSC 1524 0.0232 0.99 64.2 yes View details
accD LSC 2040 0.0313 0.93 61.4 yes View details
ycf4 LSC 567 0.0359 1.00 70.3 yes View details
clpP LSC 2266 0.0219 0.99 58.5 yes View details
rpl16 LSC 1605 0.0166 1.00 54.6 yes View details
ndhF-rpl32 IRa 576 0.0262 1.00 59.0 yes View details
trnS-GCU-trnG-UCC LSC 658 0.0232 0.98 68.2 yes View details
trnT-UGU-trnL-UAA LSC 810 0.0170 1.00 64.9 yes View details
ndhI-ndhG IRb 539 0.0102 0.99 64.3 yes View details
ndhG-ndhI IRa 539 0.0102 0.99 64.3 yes View details
rbcL-accD LSC 824 0.0190 0.95 61.1 yes View details
trnG-UCC-trnR-UCU LSC 167 0.0236 0.99 61.0 yes View details
trnK-UUU-rps16 LSC 845 0.0169 1.00 59.2 yes View details
accD-psaI LSC 303 0.0312 1.00 59.1 yes View details
ycf1-trnN-GUU IRa 415 0.0169 0.92 58.7 yes View details
rps19-rpl2 IRb 67 0.0259 1.00 57.7 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 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 AAGGGTGGGGGTTTTTAAGG 905–980 1.000 81.5
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AAGGGTGGGGGTTTTTAAGG 904–979 1.000 81.5
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AGGGTGGGGGTTTTTAAGGA 903–978 1.000 81.2
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GGGTGGGGGTTTTTAAGGAA 902–977 0.833 74.8
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT GGGTGGGGGTTTTTAAGGAA 903–978 0.833 74.7
rps16-trnQ-UUG_p1 rps16-trnQ-UUG TTCTACTCGAGCTCCATCGT AGCAGCTTGCCAAACAAAAG 2102–2270 1.000 86.2
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TTCTACTCGAGCTCCATCGT CTTACAGCAGCTTGCCAAAC 2107–2275 1.000 86.2
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AACTTGCTCGAATGGGATCC AGCAGCTTGCCAAACAAAAG 2218–2386 1.000 86.0
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AACTTGCTCGAATGGGATCC CTTACAGCAGCTTGCCAAAC 2223–2391 1.000 86.0
rps16-trnQ-UUG_p5 rps16-trnQ-UUG GATTCCCGCGTGATACACTT AGCAGCTTGCCAAACAAAAG 2288–2456 1.000 85.7
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA TCAAACCGAAAACAAAGACCC 703–864 1.000 73.3
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA CAAACCGAAAACAAAGACCCT 702–863 1.000 73.2
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA CAAACCGAAAACAAAGACCCTT 702–863 1.000 70.6
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC GCTTTAGTCCACTCAGCCAT TCAAACCGAAAACAAAGACCC 689–850 1.000 70.4
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC GCTTTAGTCCACTCAGCCAT CAAACCGAAAACAAAGACCCT 688–849 1.000 70.3
trnG-UCC-trnR-UCU_p1 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG GAAGACCCCTGTCCTATCCA 235–247 1.000 85.2
trnG-UCC-trnR-UCU_p2 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG GAAGACCCCTGTCCTATCCA 238–250 1.000 84.9
trnG-UCC-trnR-UCU_p3 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCCCTGTCCTATCC 236–248 1.000 82.8
trnG-UCC-trnR-UCU_p4 trnG-UCC-trnR-UCU CCCTAGCCTTCCAAGCTAAC GAAGACCCCTGTCCTATCCA 239–251 1.000 82.7
trnG-UCC-trnR-UCU_p5 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCCCTGTCCTATCC 239–251 1.000 82.5
rps2-rpoC2_p1 rps2-rpoC2 CTTAGCATACCAAGGGGCTG CGGCATTCTGTTCTACAGCT 689–838 1.000 89.3
rps2-rpoC2_p2 rps2-rpoC2 CTTAGCATACCAAGGGGCTG CTCCGGGGGCTATTAGAGAA 1156–1305 1.000 87.9
rps2-rpoC2_p3 rps2-rpoC2 CTTAGCATACCAAGGGGCTG TCCGGGGGCTATTAGAGAAG 1155–1304 1.000 87.9
rps2-rpoC2_p4 rps2-rpoC2 CTTAGCATACCAAGGGGCTG AGAGAAGGAGCTTCGTTCCT 1142–1291 1.000 87.4
rps2-rpoC2_p5 rps2-rpoC2 CTTAGCATACCAAGGGGCTG CGGGGGCTATTAGAGAAGGA 1168–1213 0.500 63.3
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU AGGGAGATGTCCTGAACCTC GAACCGATGACTTACGCCTT 1029–1106 1.000 88.7
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU GGGAGATGTCCTGAACCTCT GAACCGATGACTTACGCCTT 1028–1105 1.000 88.7
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU AGGGAGATGTCCTGAACCTC TACCGCTGAGTTAAAAGGGC 994–1071 1.000 88.1
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU GGGAGATGTCCTGAACCTCT TACCGCTGAGTTAAAAGGGC 993–1070 1.000 88.1
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU TGAACCTCTAGACGATGGGG GAACCGATGACTTACGCCTT 1017–1094 1.000 88.0

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (6)

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

Species Accession Length (bp) Link
Dischidia australis NC_067885.1 176733 View on NCBI ↗
Dischidia griffithii NC_067965.1 176733 View on NCBI ↗
Dischidia milnei MW719059.1 175405 View on NCBI ↗
Dischidia nummularia NC_069567.1 175529 View on NCBI ↗
Dischidia parasita MW719057.1 177089 View on NCBI ↗
Dischidia ruscifolia NC_067966.1 175887 View on NCBI ↗