Markers + reference

Menonvillea

2 species · Brassicaceae · Brassicales

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Species 2
Genome length 154–154 kb
Candidate markers 258
Primer pairs 110

Genome-wide nucleotide diversity

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

Candidate markers

14 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 258 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0085 1.00 50.5 yes View details
trnK-rps16 LSC 738 0.0323 0.92 73.5 yes View details
atpF-atpH LSC 474 0.0496 0.98 86.5 yes View details
trnD-trnY LSC 435 0.0437 1.00 72.9 yes View details
trnS-ycf9 LSC 347 0.0289 1.00 56.4 yes View details
petA-psbJ LSC 942 0.0244 1.00 63.0 yes View details
rpl36-rps8 LSC 470 0.0384 1.00 68.9 yes View details
ycf1 IRb 1047 0.0019 1.00 59.0 no View details
ndhF-rpl32 SSC 859 0.0381 0.98 69.7 yes View details
rpl32-trnL SSC 732 0.0431 0.95 77.9 yes View details
ndhG-ndhI SSC 335 0.0129 0.93 49.8 yes View details
ndhI SSC 516 0.0564 1.00 72.7 yes View details
ndhH SSC 1176 0.0255 1.00 59.0 yes View details
ycf1 SSC 5337 0.0202 1.00 51.2 yes View details
trnH-psbA LSC 251 0.0840 0.95 78.1 yes View details
psbL-psbF LSC 21 0.0476 1.00 75.3 yes View details
ycf6-psbM LSC 552 0.0275 0.99 74.6 yes View details
trnE-trnT LSC 668 0.0311 0.96 73.6 yes View details
trnL-ycf5 SSC 122 0.0984 1.00 73.3 yes View details
psbT-psbN LSC 65 0.0462 1.00 72.9 yes View details
rpl2-rpl23 IRb 18 0.0556 1.00 71.3 yes View details
rpl23-rpl2 IRa 18 0.0556 1.00 71.3 yes View details
psbK-psbI LSC 407 0.0362 0.95 70.7 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 110 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-psbA_p1 trnH-psbA CTGCCTTAATCCACTTGGCT GCTGTTGAGGCTCCATCTAC 309–372 1.000 86.2
trnH-psbA_p2 trnH-psbA ACTGCCTTAATCCACTTGGC GCTGTTGAGGCTCCATCTAC 310–373 1.000 86.0
trnH-psbA_p3 trnH-psbA CTGCCTTAATCCACTTGGCT CCTCTAGACCTAGCTGCTGT 324–387 1.000 85.8
trnH-psbA_p4 trnH-psbA ACTGCCTTAATCCACTTGGC CCTCTAGACCTAGCTGCTGT 325–388 1.000 85.6
trnH-psbA_p5 trnH-psbA AATCCACTTGGCTACATCCG GCTGTTGAGGCTCCATCTAC 302–365 1.000 84.8
psbA_p1 psbA ACTAGGTTTAGACTAACGCT GATTAAATAAACCAAGGATTTTACC 1113 1.000 40.6
psbA_p2 psbA AACTAGGTTTAGACTAACGCT GATTAAATAAACCAAGGATTTTACC 1114 1.000 40.6
psbA_p3 psbA AAACTAGGTTTAGACTAACGCT GATTAAATAAACCAAGGATTTTACC 1115 1.000 40.6
psbA_p4 psbA AGGTTTAGACTAACGCTAAAGA GATTAAATAAACCAAGGATTTTACC 1110 1.000 40.6
psbA_p5 psbA AACTAGGTTTAGACTAACGC GATTAAATAAACCAAGGATTTTACC 1114 1.000 40.6
trnK-rps16_p1 trnK-rps16 AAAGCCGAGTACTCTACCGT CGCTCAACCAACAAGAACAG 810–860 1.000 81.6
trnK-rps16_p2 trnK-rps16 AAGCCGAGTACTCTACCGTT CGCTCAACCAACAAGAACAG 809–859 1.000 81.6
trnK-rps16_p3 trnK-rps16 CAAACTCTACCGCGGATCTG CGCTCAACCAACAAGAACAG 880–930 1.000 79.3
trnK-rps16_p4 trnK-rps16 TACCGTTGAGTTAGCAACCC CGCTCAACCAACAAGAACAG 796–846 1.000 79.3
trnK-rps16_p5 trnK-rps16 AGTCGCACTTAAAAGCCGAG CGCTCAACCAACAAGAACAG 821–871 1.000 78.4
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCAGCTGTAAG TTCTTCACGTCCCGGATTAC 545–570 1.000 79.1
psbK-psbI_p2 psbK-psbI TGGCAAGCAGCTGTAAGTTT TTCTTCACGTCCCGGATTAC 542–567 1.000 77.2
psbK-psbI_p3 psbK-psbI TTGGCAAGCAGCTGTAAGTT TTCTTCACGTCCCGGATTAC 543–568 1.000 77.1
psbK-psbI_p4 psbK-psbI TTTGGCAAGCAGCTGTAAGT TTCTTCACGTCCCGGATTAC 544–569 1.000 77.1
psbK-psbI_p5 psbK-psbI GTTTGGCAAGCAGCTGTAAG CCGGATTACGTCCTGGATCA 534–559 1.000 76.8
atpF-atpH_p1 atpF-atpH ATTAAACCCGAAACTCCCGG TGGCCTGGTTGTAGCATTAG 582–592 1.000 80.2
atpF-atpH_p2 atpF-atpH CCAGTGACCCAAGTAAACGA TGGCCTGGTTGTAGCATTAG 555–565 1.000 77.1
atpF-atpH_p3 atpF-atpH ATTAAACCCGAAACTCCCGG TTTATGGCCTGGTTGTAGCA 586–596 1.000 76.4
atpF-atpH_p4 atpF-atpH ATTAAACCCGAAACTCCCGG GGCCTGGTTGTAGCATTAGC 581–591 1.000 75.8
atpF-atpH_p5 atpF-atpH GGCCAGTGACCCAAGTAAAC TGGCCTGGTTGTAGCATTAG 557–567 1.000 75.3
ycf6-psbM_p1 ycf6-psbM TCGTAGTGTGGGGAAGAAGT TGCTACTGCACTCTTCATTCT 657–660 1.000 66.8
ycf6-psbM_p2 ycf6-psbM CGTAGTGTGGGGAAGAAGTG TGCTACTGCACTCTTCATTCT 656–659 1.000 66.2
ycf6-psbM_p3 ycf6-psbM CTCTCGTAGTGTGGGGAAGA TGCTACTGCACTCTTCATTCT 660–663 1.000 65.5
ycf6-psbM_p4 ycf6-psbM CTCTCTCGTAGTGTGGGGAA TGCTACTGCACTCTTCATTCT 662–665 1.000 65.5
ycf6-psbM_p5 ycf6-psbM TCTCTCGTAGTGTGGGGAAG TGCTACTGCACTCTTCATTCT 661–664 1.000 65.5

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
Menonvillea cuneata NC_065153.1 154059 View on NCBI ↗
Menonvillea spathulata NC_049679.1 154065 View on NCBI ↗