Markers + reference

Cymbaria

2 species · Orobanchaceae · Lamiales

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Species 2
Genome length 149–152 kb
Candidate markers 254
Primer pairs 75

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 254 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ycf3-psaA LSC 677 0.0726 0.98 79.0 yes View details
trnK-UUU-accD LSC 1689 0.1965 0.94 86.3 yes View details
accD LSC 2397 0.0415 0.86 68.1 yes View details
rrn5S-trnR-ACG SSC 239 0.1378 0.94 77.7 yes View details
trnR-ACG-trnN-GUU SSC 563 0.0716 0.99 80.7 yes View details
ycf1-rrn5S SSC 3601 0.0629 0.75 67.7 yes View details
rps16-trnK-UUU LSC 1080 0.0475 0.96 77.6 yes View details
trnN-GUU-ndhF SSC 2114 0.0572 0.97 77.6 yes View details
rpl32-trnL-UAG SSC 746 0.0615 0.96 77.6 yes View details
psaJ-rpl33 LSC 489 0.0641 0.96 76.5 yes View details
trnM-CAU-ycf2 IRb 2307 0.0240 0.94 75.2 yes View details
ycf2-trnM-CAU IRa 2307 0.0240 0.94 75.2 yes View details
ndhD SSC 858 0.0527 1.00 74.4 yes View details
rps18 LSC 444 0.0463 0.92 72.9 yes View details
psbB-psbT LSC 197 0.0406 1.00 72.6 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 75 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
ycf3-psaA_p1 ycf3-psaA TCACGAGGCGTTTCGAATAA TGAGAAATGACCCGGTTTGG 796–817 1.000 82.8
ycf3-psaA_p2 ycf3-psaA TCACGAGGCGTTTCGAATAA CCCAGTTCTCGAAAGACGTT 776–797 1.000 82.5
ycf3-psaA_p3 ycf3-psaA ATCACGAGGCGTTTCGAATA TGAGAAATGACCCGGTTTGG 797–818 1.000 81.0
ycf3-psaA_p4 ycf3-psaA ATCACGAGGCGTTTCGAATA CCCAGTTCTCGAAAGACGTT 777–798 1.000 80.7
ycf3-psaA_p5 ycf3-psaA TCACGAGGCGTTTCGAATAA TTTGGCCCAGTTCTCGAAAG 781–802 1.000 80.5
rps16-trnK-UUU_p1 rps16-trnK-UUU GAACTTCCGTCTAATCAAATGA AAAGCCGAGTACTCTACCGT 1147–1151 1.000 46.8
rps16-trnK-UUU_p2 rps16-trnK-UUU GAACTTCCGTCTAATCAAATGA AAGCCGAGTACTCTACCGTT 1146–1150 1.000 46.8
rps16-trnK-UUU_p3 rps16-trnK-UUU GAACTTCCGTCTAATCAAATGA TCTAGCCGCACTTAAAAGCC 1161–1165 1.000 46.7
rps16-trnK-UUU_p4 rps16-trnK-UUU GAACTTCCGTCTAATCAAATGA TCAGTCGTGGTCTTCCAAAC 1232–1236 1.000 46.3
rps16-trnK-UUU_p5 rps16-trnK-UUU GAACTTCCGTCTAATCAAATGA CAGTCGTGGTCTTCCAAACT 1231–1235 1.000 46.3
trnK-UUU-accD_p1 trnK-UUU-accD CTAGTTCCGGGTTCGAATCC CCTCATGTTTAGGAGTTTTTGACA 1746–2631 1.000 53.0
trnK-UUU-accD_p2 trnK-UUU-accD CTAGTTCCGGGTTCGAATCC TCCTCATGTTTAGGAGTTTTTGAC 1747–2632 1.000 51.9
trnK-UUU-accD_p3 trnK-UUU-accD ACTCCATCCGACTAGTTCCG CCTCATGTTTAGGAGTTTTTGACA 1757–2642 1.000 51.9
trnK-UUU-accD_p4 trnK-UUU-accD CTAGTTCCGGGTTCGAATCC CCTCATGTTTAGGAGTTTTTGACAT 1746–2631 1.000 51.9
trnK-UUU-accD_p5 trnK-UUU-accD CTAGTTCCGGGTTCGAATCC TCCTCATGTTTAGGAGTTTTTGA 1747–2632 1.000 51.9
accD_p1 accD GATCTCTTACACAACGCGGT AGATCGTTTTCTGCAGGCAT 2718–2977 1.000 85.8
accD_p2 accD TGATCTCTTACACAACGCGG AGATCGTTTTCTGCAGGCAT 2719–2978 1.000 85.8
accD_p3 accD GATCTCTTACACAACGCGGT TTGCAATGGCCGGAAATACT 2531–2785 1.000 85.6
accD_p4 accD TGATCTCTTACACAACGCGG TTGCAATGGCCGGAAATACT 2532–2786 1.000 85.6
accD_p5 accD GATCTCTTACACAACGCGGT ACCACAGATCGTTTTCTGCA 2982 0.500 57.9
psaJ-rpl33_p1 psaJ-rpl33 CGCTATGGTTCGGGGTTTTA TGCCCCTTGGTACCTTCTTA 657–666 1.000 85.7
psaJ-rpl33_p2 psaJ-rpl33 TCGGGGTTTTAGCAGGTCTA TGCCCCTTGGTACCTTCTTA 648–657 1.000 85.5
psaJ-rpl33_p3 psaJ-rpl33 CGCTATGGTTCGGGGTTTTA ACAATCAATTCGATCCCCCG 1027–1034 1.000 85.3
psaJ-rpl33_p4 psaJ-rpl33 TCGGGGTTTTAGCAGGTCTA ACAATCAATTCGATCCCCCG 1018–1025 1.000 85.1
psaJ-rpl33_p5 psaJ-rpl33 CGCTATGGTTCGGGGTTTTA GGGACAAAGGCCTACGAAAA 998–1005 1.000 84.9
rps18_p1 rps18 AGAAATAAACTAAACAAACAAACC TGAATAAAGAATAAGCCTCCCT 479–495 1.000 47.1
rps18_p2 rps18 AGAAATAAACTAAACAAACAAACC ATGAATAAAGAATAAGCCTCCCT 480–496 1.000 47.1
rps18_p3 rps18 AGAAATAAACTAAACAAACAAACC TGAATAAAGAATAAGCCTCCC 479–495 1.000 47.1
rps18_p4 rps18 AGAAATAAACTAAACAAACAAACC AATGAATAAAGAATAAGCCTCCCT 481–497 1.000 47.1
rps18_p5 rps18 AGAAATAAACTAAACAAACAAACC TCAAATGAATAAAGAATAAGCCTCCC 484–500 1.000 47.1

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
Cymbaria daurica NC_064104.1 151545 View on NCBI ↗
Cymbaria mongolica NC_064388.1 149431 View on NCBI ↗