Markers + reference

Cynanchum

8 species · Apocynaceae · Gentianales

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Species 8
Genome length 158–161 kb
Candidate markers 273
Primer pairs 70

Genome-wide nucleotide diversity

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

Candidate markers

6 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 273 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnQ-UUG-psbK LSC 666 0.1043 0.74 81.0 yes View details
ndhC-trnV-UAC LSC 1571 0.0520 0.80 77.2 yes View details
rpl20-rps12 LSC 1147 0.0536 0.86 81.0 yes View details
Ycf1 IRb 532 0.0735 0.90 75.9 yes View details
Ycf1-ndhF SSC 308 0.1721 0.91 65.9 yes View details
Ycf1 SSC 6057 0.0678 0.95 77.8 yes View details
ndhF-rpl32 SSC 692 0.0579 0.92 83.4 yes View details
rpl32-trnL-UAG SSC 988 0.0604 0.87 82.4 yes View details
trnK-UUU-rps16 LSC 719 0.0399 0.97 80.5 yes View details
trnH-GUG-psbA LSC 222 0.0871 0.98 77.4 yes View details
rpl2-trnH-GUG IRa 84 0.1336 0.79 77.0 no View details
rpoB-trnC-GCA LSC 1147 0.0340 0.94 76.7 yes View details
trnE-UUC-trnT-GGU LSC 1081 0.0404 0.87 76.6 yes View details
Ycf1-trnN-GUU IRa 769 0.0396 0.97 76.6 yes View details
trnL-UAA-trnF-GAA LSC 318 0.0446 0.96 75.6 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 70 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA AATGGTAAATGGGCGAACGA GCCGGTAGTAGGTATCTGGT 537 0.125 44.0
trnH-GUG-psbA_p2 trnH-GUG-psbA AATGGTAAATGGGCGAACGA TGGCCGGTAGTAGGTATCTG 539 0.125 44.0
trnH-GUG-psbA_p3 trnH-GUG-psbA AATGGTAAATGGGCGAACGA GAGCTTAGTTTCCGTCTGGG 977 0.125 44.0
trnH-GUG-psbA_p4 trnH-GUG-psbA AATGGTAAATGGGCGAACGA GGAGCTTAGTTTCCGTCTGG 978 0.125 44.0
trnH-GUG-psbA_p5 trnH-GUG-psbA AATGGTAAATGGGCGAACGA GGGAGCTTAGTTTCCGTCTG 979 0.125 44.0
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT ATCCTAATCAAACGAAATTCAA 725–891 1.000 50.9
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TCCTAATCAAACGAAATTCAAT 724–890 1.000 50.9
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT ATCCTAATCAAACGAAATTCAA 724–890 1.000 50.9
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TCCTAATCAAACGAAATTCAAT 723–889 1.000 50.9
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TCCTAATCAAACGAAATTCAATT 723–889 1.000 50.9
trnQ-UUG-psbK_p1 trnQ-UUG-psbK GACCAAAACCCGTTGCCTTA AGGCAGAATTAAGACAGATACAGA 553–750 1.000 52.0
trnQ-UUG-psbK_p2 trnQ-UUG-psbK GACCAAAACCCGTTGCCTTA GGGCAATTTTCCGAAGAAA 588–794 1.000 52.0
trnQ-UUG-psbK_p3 trnQ-UUG-psbK AAAACCCGTTGCCTTACCAC AGGCAGAATTAAGACAGATACAGA 549–746 1.000 52.0
trnQ-UUG-psbK_p4 trnQ-UUG-psbK ACCAAAACCCGTTGCCTTAC AGGCAGAATTAAGACAGATACAGA 552–749 1.000 52.0
trnQ-UUG-psbK_p5 trnQ-UUG-psbK CAAAACCCGTTGCCTTACCA AGGCAGAATTAAGACAGATACAGA 550–747 1.000 52.0
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CTCATTTCCATCCACGAGCA CCGGATTTGAACTGGGGAAA 1230–1351 1.000 89.2
rpoB-trnC-GCA_p2 rpoB-trnC-GCA CCCTCATTTCCATCCACGAG CCGGATTTGAACTGGGGAAA 1232–1353 1.000 89.1
rpoB-trnC-GCA_p3 rpoB-trnC-GCA CTCATTTCCATCCACGAGCA AAAAGGATTTGCAGTCCCCC 1212–1333 1.000 87.1
rpoB-trnC-GCA_p4 rpoB-trnC-GCA CCCTCATTTCCATCCACGAG AAAAGGATTTGCAGTCCCCC 1214–1335 1.000 87.0
rpoB-trnC-GCA_p5 rpoB-trnC-GCA TTCCCTCATTTCCATCCACG CCGGATTTGAACTGGGGAAA 1234–1355 1.000 86.1
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU AGAGATGTCCTGAACCGCTA GAACCGATGACTTACGCCTT 1040–1201 1.000 90.4
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU AGATGTCCTGAACCGCTAGA GAACCGATGACTTACGCCTT 1038–1199 1.000 90.4
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU GATGTCCTGAACCGCTAGAC GAACCGATGACTTACGCCTT 1037–1198 1.000 89.9
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU CTTGCTTTCCTAGTCCACCC GAACCGATGACTTACGCCTT 1170–1257 0.375 62.4
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU CTTGCTTTCCTAGTCCACCC TACCGCTGAGTTAAAAGGGC 1135–1222 0.375 61.7
trnL-UAA-trnF-GAA_p1 trnL-UAA-trnF-GAA AATCGTGAGGGTTCAAGTCC TCTACCAGCTGAGCTATCCC 367–392 1.000 87.4
trnL-UAA-trnF-GAA_p2 trnL-UAA-trnF-GAA AATCGTGAGGGTTCAAGTCC TTTGAACTGGTGACACGAGG 403–428 1.000 86.4
trnL-UAA-trnF-GAA_p3 trnL-UAA-trnF-GAA AATCGTGAGGGTTCAAGTCC TCAGTCCTCTGCTCTACCAG 379–404 1.000 86.1
trnL-UAA-trnF-GAA_p4 trnL-UAA-trnF-GAA TTCAAGTCCCTCTATCCCCA TCTACCAGCTGAGCTATCCC 356–381 1.000 83.7
trnL-UAA-trnF-GAA_p5 trnL-UAA-trnF-GAA AATCGTGAGGGTTCAAGTCC GAACTGGTGACACGAGGATT 400–425 1.000 83.2

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (8)

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

Species Accession Length (bp) Link
Cynanchum acutum PV364606.1 159241 View on NCBI ↗
Cynanchum bungei OK271106.1 160572 View on NCBI ↗
Cynanchum chinense NC_057432.1 158615 View on NCBI ↗
Cynanchum otophyllum NC_077575.1 160874 View on NCBI ↗
Cynanchum rostellatum NC_063665.1 160641 View on NCBI ↗
Cynanchum sibiricum OQ390041.2 158283 View on NCBI ↗
Cynanchum wallichii NC_081903.1 159808 View on NCBI ↗
Cynanchum wilfordii NC_029459.1 161241 View on NCBI ↗