Markers + reference

Dictamnus

2 species · Rutaceae · Sapindales

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Species 2
Genome length 157–157 kb
Candidate markers 276
Primer pairs 105

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 8 remaining regions by MarkerSeek score (out of 276 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 372 0.0081 1.00 58.6 yes View details
trnK-UUU-rps16 LSC 550 0.0055 1.00 60.8 yes View details
psaA-ycf3 LSC 702 0.0057 1.00 62.0 yes View details
rps4 LSC 606 0.0050 1.00 61.6 yes View details
trnL-UAA-trnF-GAA LSC 370 0.0054 1.00 46.7 yes View details
psaJ-rpl33 LSC 494 0.0061 1.00 60.4 yes View details
ycf15-trnL-CAA IRb 725 0.0055 1.00 61.9 yes View details
ndhB IRb 2214 0.0014 1.00 58.0 yes View details
rps7-ndhB IRa 322 0.0000 1.00 21.0 yes View details
ndhB IRa 2214 0.0014 1.00 58.0 no View details
ndhB-trnL-CAA IRa 591 0.0000 1.00 35.5 yes View details
trnL-CAA-ycf15 IRa 725 0.0055 1.00 61.9 yes View details
psbZ-trnG-GCC LSC 552 0.0037 0.97 62.7 yes View details
trnT-UGU-trnL-UAA LSC 952 0.0000 0.98 61.0 yes View details
atpH-atpI LSC 783 0.0026 1.00 60.2 yes View details
matK-trnK-UUU LSC 717 0.0028 1.00 60.1 yes View details
ndhC-trnV-UAC LSC 926 0.0022 1.00 60.1 yes View details
trnE-UUC-trnT-GGU LSC 833 0.0000 0.99 60.0 yes View details
rpl32-trnL-UAG SSC 1014 0.0020 1.00 60.0 yes View details
ndhH SSC 1182 0.0017 1.00 59.7 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 105 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 TTCCCTCTAGACCTAGCTGC 441 1.000 78.9
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TTCCCTCTAGACCTAGCTGC 455 1.000 78.9
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TTCCCTCTAGACCTAGCTGC 454 1.000 78.9
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TTCCCTCTAGACCTAGCTGC 456 1.000 78.9
trnH-GUG-psbA_p5 trnH-GUG-psbA CGCATGGTGGATTCACAATC TTCCCTCTAGACCTAGCTGC 470 1.000 76.1
trnK-UUU_p1 trnK-UUU TCTCGATTCAGATATTCAGATTCAGA TGCTTCGAGTTCTTGCTAGT 2813 1.000 40.2
trnK-UUU_p2 trnK-UUU CTCGATTCAGATATTCAGATTCAGA TGCTTCGAGTTCTTGCTAGT 2812 1.000 40.2
trnK-UUU_p3 trnK-UUU TCTCGATTCAGATATTCAGATTCAG TGCTTCGAGTTCTTGCTAGT 2813 1.000 40.2
trnK-UUU_p4 trnK-UUU TCTCGATTCAGATATTCAGATTCAGA TGCTTCGAGTTCTTGCTAGTT 2813 1.000 40.2
trnK-UUU_p5 trnK-UUU TCTCGATTCAGATATTCAGATTCAGA TTGCTTCGAGTTCTTGCTAGT 2814 1.000 40.2
matK-trnK-UUU_p1 matK-trnK-UUU ACTCCCGAAAAAGAAGTGGG AACGGTAGAGTACTCGGCTT 820 1.000 76.7
matK-trnK-UUU_p2 matK-trnK-UUU ACTCCCGAAAAAGAAGTGGG ACGGTAGAGTACTCGGCTTT 819 1.000 76.7
matK-trnK-UUU_p3 matK-trnK-UUU CTCCCGAAAAAGAAGTGGGT AACGGTAGAGTACTCGGCTT 819 1.000 76.7
matK-trnK-UUU_p4 matK-trnK-UUU CTCCCGAAAAAGAAGTGGGT ACGGTAGAGTACTCGGCTTT 818 1.000 76.7
matK-trnK-UUU_p5 matK-trnK-UUU CTCCCGAAAAAGAAGTGGGT GGGTTGCTAACTCAACGGTA 832 1.000 74.3
trnK-UUU-rps16_p1 trnK-UUU-rps16 AGCCGTACTTAAAAGCCGAG ATTTCAAAGAAAGCGGGGGT 655–656 1.000 80.2
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT ATTTCAAAGAAAGCGGGGGT 644–645 1.000 78.9
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT ATTTCAAAGAAAGCGGGGGT 643–644 1.000 78.9
trnK-UUU-rps16_p4 trnK-UUU-rps16 AGCCGTACTTAAAAGCCGAG CCAACCTACAGGAACCGTTC 680–681 1.000 78.7
trnK-UUU-rps16_p5 trnK-UUU-rps16 AGCCGTACTTAAAAGCCGAG TCAAAGAAAGCGGGGGTTTT 652–653 1.000 78.6
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTGCAACTTTAGCTGCGG 870 1.000 78.8
atpH-atpI_p2 atpH-atpI GATCCCTTCTACTGCTTGGC TTTTGCAACTTTAGCTGCGG 955 1.000 78.8
atpH-atpI_p3 atpH-atpI GTACCTTGACCAACACCAGG TTTTGCAACTTTAGCTGCGG 927 1.000 78.2
atpH-atpI_p4 atpH-atpI GTCCAATAGAAGCAAGCCCA TTTTGCAACTTTAGCTGCGG 908 1.000 78.1
atpH-atpI_p5 atpH-atpI AACGGAAGCGGCAGAAATAA TTTTGCAACTTTAGCTGCGG 868 1.000 77.7
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG GAACCGATGACTTACGCCTT 927–938 1.000 78.8
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA GAACCGATGACTTACGCCTT 906–917 1.000 78.7
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU TTCCTAGTACCCTACCCCCA GAACCGATGACTTACGCCTT 964–975 1.000 78.5
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG CCAAAAAGCCCCTTATCGGA 950–961 1.000 77.7
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG CCGATGACTTACGCCTTACC 924–935 1.000 77.6

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
Dictamnus albus PP335056.1 157051 View on NCBI ↗
Dictamnus dasycarpus NC_063821.1 157036 View on NCBI ↗