Markers + reference

Conringia

2 species · Brassicaceae · Brassicales

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Species 2
Genome length 153–153 kb
Candidate markers 270
Primer pairs 80

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-AAA-rps16 LSC 646 0.0669 0.97 77.2 yes View details
trnL-UUA-trnF-UUC LSC 497 0.1064 0.91 82.2 yes View details
trnF-UUC-ndhJ LSC 570 0.0626 0.95 83.1 yes View details
accD LSC 1458 0.0344 1.00 65.5 yes View details
ycf1 IRb 1035 0.0039 1.00 46.4 no View details
ndhF-rpl32 SSC 833 0.0506 0.97 77.4 yes View details
rpl32-trnL-CUA SSC 960 0.0840 0.84 82.9 yes View details
rps15-ycf1 SSC 2266 0.0438 1.00 68.1 yes View details
ycf1 SSC 3399 0.0330 1.00 62.1 yes View details
petA-psbJ LSC 612 0.0447 0.99 81.2 yes View details
trnS-UCC-rps4 LSC 275 0.0582 1.00 77.5 yes View details
atpH-atpI LSC 479 0.0369 0.96 76.2 yes View details
psbK-psbI LSC 393 0.0663 0.88 75.3 yes View details
trnL-CUA-ccsA SSC 118 0.0619 0.96 75.0 yes View details
trnS-AGC-trnG-GGA LSC 593 0.0497 0.98 74.9 yes View details
psbA-trnK-AAA LSC 279 0.0430 0.92 74.6 yes View details
atpF-atpH LSC 495 0.0498 0.97 74.5 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 80 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbA-trnK-AAA_p1 psbA-trnK-AAA ACGGTTTTCAGTGCTGGTTA AAAATGCAAGCACGGTTTGG 449–470 1.000 79.9
psbA-trnK-AAA_p2 psbA-trnK-AAA ACGGTTTTCAGTGCTGGTTA ACTCCATCCGACTAGTTCCG 379–402 1.000 78.7
psbA-trnK-AAA_p3 psbA-trnK-AAA ACGGTTTTCAGTGCTGGTTA TGAAAAATGCAAGCACGGTT 452–473 1.000 78.5
psbA-trnK-AAA_p4 psbA-trnK-AAA TACAGAAGCGACCCCATAGG AAAATGCAAGCACGGTTTGG 423–444 1.000 78.0
psbA-trnK-AAA_p5 psbA-trnK-AAA ATCCAGTTACAGAAGCGACC AAAATGCAAGCACGGTTTGG 430–451 1.000 77.2
trnK-AAA-rps16_p1 trnK-AAA-rps16 CCTTTCAGGATCAGTCGTGG CCCAATGAGCCGTTTATCGA 981–1045 1.000 84.4
trnK-AAA-rps16_p2 trnK-AAA-rps16 CCTTTCAGGATCAGTCGTGG TCCCAATGAGCCGTTTATCG 982–1046 1.000 84.4
trnK-AAA-rps16_p3 trnK-AAA-rps16 CCTTTCAGGATCAGTCGTGG ATGCGTGAATCAAGCGTTTG 1486–1571 1.000 83.9
trnK-AAA-rps16_p4 trnK-AAA-rps16 CCTTTCAGGATCAGTCGTGG CATGCGTGAATCAAGCGTTT 1487–1572 1.000 83.9
trnK-AAA-rps16_p5 trnK-AAA-rps16 TCAGGATCAGTCGTGGTCTT ATGCGTGAATCAAGCGTTTG 1482–1567 1.000 83.4
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCAGCTGTAAG ACAAAAAGTTTGAGAGTAAGCA 411–446 1.000 48.3
psbK-psbI_p2 psbK-psbI TGGCAAGCAGCTGTAAGTTT ACAAAAAGTTTGAGAGTAAGCA 408–443 1.000 48.3
psbK-psbI_p3 psbK-psbI TTGGCAAGCAGCTGTAAGTT ACAAAAAGTTTGAGAGTAAGCA 409–444 1.000 48.3
psbK-psbI_p4 psbK-psbI TTTGGCAAGCAGCTGTAAGT ACAAAAAGTTTGAGAGTAAGCA 410–445 1.000 48.3
psbK-psbI_p5 psbK-psbI GTTTGGCAAGCAGCTGTAAG ACAAAAAGTTTGAGAGTAAGCAT 411–446 1.000 48.3
trnS-AGC-trnG-GGA_p1 trnS-AGC-trnG-GGA GTTTGGCAAGCAGCTGTAAG TGGTTTCATTCGGCTCCTTT 1984–2021 1.000 83.1
trnS-AGC-trnG-GGA_p2 trnS-AGC-trnG-GGA GTTTGGCAAGCAGCTGTAAG TTGGTTTCATTCGGCTCCTT 1985–2022 1.000 83.1
trnS-AGC-trnG-GGA_p3 trnS-AGC-trnG-GGA GTTTGGCAAGCAGCTGTAAG TTTGGTTTCATTCGGCTCCT 1986–2023 1.000 83.1
trnS-AGC-trnG-GGA_p4 trnS-AGC-trnG-GGA CCAACGCTTTAGTCCACTCA TGGTTTCATTCGGCTCCTTT 1298 0.500 56.4
trnS-AGC-trnG-GGA_p5 trnS-AGC-trnG-GGA CCAACGCTTTAGTCCACTCA TTGGTTTCATTCGGCTCCTT 1299 0.500 56.4
atpF-atpH_p1 atpF-atpH GAAAGAATCGGTTAAATTTTTCA TGGCCTGGTTGTAGCATTAG 565–568 1.000 45.2
atpF-atpH_p2 atpF-atpH GAAAGAATCGGTTAAATTTTTCAT TGGCCTGGTTGTAGCATTAG 565–568 1.000 45.2
atpF-atpH_p3 atpF-atpH GAAAGAATCGGTTAAATTTTTCA TTTATGGCCTGGTTGTAGCA 569–572 1.000 45.2
atpF-atpH_p4 atpF-atpH GAAAGAATCGGTTAAATTTTTCA GGCCTGGTTGTAGCATTAGC 564–567 1.000 45.2
atpF-atpH_p5 atpF-atpH GAAAGAATCGGTTAAATTTTTCA ATGGCCTGGTTGTAGCATTAG 566–569 1.000 45.2
atpH-atpI_p1 atpH-atpI AATAGAAGCAAGCCCGACAG TACAAGCGGGATTCAAGCTC 624–625 1.000 84.1
atpH-atpI_p2 atpH-atpI AACCGAAGCAGCAGAAATCA TACAAGCGGGATTCAAGCTC 588–589 1.000 83.7
atpH-atpI_p3 atpH-atpI AATAGAAGCAAGCCCGACAG TTTTTGCCACTTTAGCTGCG 601–602 1.000 83.4
atpH-atpI_p4 atpH-atpI TACCTTGACCAACTCCAGGT TACAAGCGGGATTCAAGCTC 646–647 1.000 83.2
atpH-atpI_p5 atpH-atpI GCTGTACCTTGACCAACTCC TACAAGCGGGATTCAAGCTC 650–651 1.000 82.6

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
Conringia clavata MK637822.1 153220 View on NCBI ↗
Conringia orientalis NC_049615.1 153445 View on NCBI ↗