Markers + reference

Kopsia

3 species · Apocynaceae · Gentianales

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Species 3
Genome length 155–163 kb
Candidate markers 266
Primer pairs 65

Genome-wide nucleotide diversity

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

Candidate markers

3 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 266 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 272 0.0625 1.00 76.5 yes View details
trnS-GCU-trnG-UCC LSC 10164 0.0300 0.34 49.5 yes View details
ycf1 SSC 5541 0.0131 1.00 48.4 yes View details
trnK-UUU LSC 35 0.0381 1.00 69.4 yes View details
ndhF-rpl32 SSC 668 0.0216 1.00 67.6 yes View details
psbM-trnD-GUC LSC 546 0.0208 1.00 66.2 yes View details
ycf3-trnS-GGA LSC 546 0.0110 1.00 64.1 yes View details
psbK-psbI LSC 155 0.0194 1.00 63.3 yes View details
psbE-petL LSC 1049 0.0095 1.00 63.2 yes View details
trnR-ACG-trnN-GUU IRb 549 0.0085 1.00 63.1 yes View details
trnN-GUU-trnR-ACG IRa 549 0.0085 1.00 63.1 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 65 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 290–621 1.000 86.2
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TTCCCTCTAGACCTAGCTGC 304–635 1.000 86.0
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TTCCCTCTAGACCTAGCTGC 303–634 1.000 86.0
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TTCCCTCTAGACCTAGCTGC 305–636 1.000 86.0
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCGTGCTAACCTTGGTATGG 339–670 1.000 83.7
trnK-UUU_p1 trnK-UUU TGCTAGTGTCAACCAATATCGA TGGGGAGGGGTGTTTACTTA 189 1.000 55.5
trnK-UUU_p2 trnK-UUU TGCTAGTGTCAACCAATATCGA TACATAGGGAAAGCCGTGTG 232 1.000 53.4
trnK-UUU_p3 trnK-UUU TGCTAGTGTCAACCAATATCG TGGGGAGGGGTGTTTACTTA 189 1.000 51.7
trnK-UUU_p4 trnK-UUU TGCTAGTGTCAACCAATATCGA CTGGGGAGGGGTGTTTACTT 190 1.000 51.6
trnK-UUU_p5 trnK-UUU TGCTAGTGTCAACCAATATCGAT TGGGGAGGGGTGTTTACTTA 189 1.000 51.1
psbK-psbI_p1 psbK-psbI GCCTGAGGCCTATGCTTTTT AAACCCCTATTCTTCACGCC 376–381 1.000 79.5
psbK-psbI_p2 psbK-psbI CTTTTGTTTGGCAAGCTGCT AAGGGGTTTTTGTTTTCGCG 869–876 0.667 67.8
psbK-psbI_p3 psbK-psbI GTTTGGCAAGCTGCTGTAAG AAGGGGTTTTTGTTTTCGCG 864–871 0.667 67.8
psbK-psbI_p4 psbK-psbI CTTTTGTTTGGCAAGCTGCT TCGAAGCGTTACGACAGAAG 886 0.333 52.6
psbK-psbI_p5 psbK-psbI GTTTGGCAAGCTGCTGTAAG TCGAAGCGTTACGACAGAAG 881 0.333 52.6
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC GCGATCGCATCTCGTTAGAT TTGTTTTGCTCGGTTCTCGA 1738 0.333 52.6
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC TTTCTCATCTCATCAGCCGC TTGTTTTGCTCGGTTCTCGA 2137 0.333 52.4
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC AATGTTTCGTTCCGTCGGAT TTGTTTTGCTCGGTTCTCGA 1648 0.333 52.2
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC TGGTCATTCCAAAGAGAGCG TTGTTTTGCTCGGTTCTCGA 2168 0.333 52.1
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC GGTCATTCCAAAGAGAGCGT TTGTTTTGCTCGGTTCTCGA 2167 0.333 52.1
psbM-trnD-GUC_p1 psbM-trnD-GUC AGGCGGTAGGAACTAGAATGA TTCAATTGGTCAGAGCACCG 667–673 1.000 70.5
psbM-trnD-GUC_p2 psbM-trnD-GUC AGAAAGGCGGTAGGAACTAGA TTCAATTGGTCAGAGCACCG 671–677 1.000 69.9
psbM-trnD-GUC_p3 psbM-trnD-GUC AGTAGAAAGGCGGTAGGAACT TTCAATTGGTCAGAGCACCG 674–680 1.000 69.2
psbM-trnD-GUC_p4 psbM-trnD-GUC AGTAGAAAGGCGGTAGGAAC TTCAATTGGTCAGAGCACCG 674–680 1.000 67.9
psbM-trnD-GUC_p5 psbM-trnD-GUC GTAGAAAGGCGGTAGGAACT TTCAATTGGTCAGAGCACCG 673–679 1.000 67.9
ycf3-trnS-GGA_p1 ycf3-trnS-GGA CTCCCTTTCTCCCGAAGTTG CCCTCGGTAAACAAAAGCCT 714–715 1.000 79.6
ycf3-trnS-GGA_p2 ycf3-trnS-GGA CTCCCTTTCTCCCGAAGTTG ACGGAAAGAGAGGGATTCGA 735–736 1.000 79.1
ycf3-trnS-GGA_p3 ycf3-trnS-GGA CCCTTTCTCCCGAAGTTGTC CCCTCGGTAAACAAAAGCCT 712–713 1.000 78.8
ycf3-trnS-GGA_p4 ycf3-trnS-GGA CTCCCTTTCTCCCGAAGTTG TTCCAATGCTACGCCTTGAA 685–686 1.000 78.8
ycf3-trnS-GGA_p5 ycf3-trnS-GGA CCCTTTCTCCCGAAGTTGTC ACGGAAAGAGAGGGATTCGA 733–734 1.000 78.4

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
Kopsia arborea NC_079607.1 162640 View on NCBI ↗
Kopsia fruticosa NC_079608.1 154630 View on NCBI ↗
Kopsia hainanensis NC_079609.1 156604 View on NCBI ↗