Markers + reference

Tetracme

2 species · Brassicaceae · Brassicales

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Species 2
Genome length 154–155 kb
Candidate markers 266
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

11 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-CAC-psbA LSC 315 0.0795 0.84 75.9 yes View details
trnS-AGC-trnG-GGA LSC 649 0.0302 0.97 72.3 yes View details
trnR-AGA-atpA LSC 295 0.0455 0.97 75.5 yes View details
trnT-ACA-trnL-UUA LSC 824 0.0311 0.98 69.6 yes View details
trnL-UUA-trnF-UUC LSC 566 0.0421 0.92 73.3 yes View details
trnF-UUC-ndhJ LSC 577 0.0208 1.00 55.7 yes View details
psaJ-rpl33 LSC 407 0.0304 0.97 69.3 yes View details
rpl33-rps18 LSC 225 0.0667 1.00 70.7 yes View details
ycf1 IRb 1035 0.0019 1.00 46.9 no View details
ndhF-rpl32 SSC 850 0.0287 0.82 63.0 yes View details
ycf1 SSC 5361 0.0168 1.00 47.6 yes View details
psbI-trnS-AGC LSC 92 0.0769 0.99 81.7 yes View details
ndhK-ndhC LSC 61 0.0656 1.00 77.2 yes View details
rps12-clpP LSC 181 0.0497 1.00 76.6 yes View details
psbC-trnS-UCA LSC 180 0.0556 1.00 74.7 yes View details
psbL-psbF LSC 21 0.0476 1.00 74.3 yes View details
petA-psbJ LSC 938 0.0185 0.98 71.1 yes View details
psaI-ycf4 LSC 431 0.0194 0.96 70.3 yes View details
trnK-AAA-rps16 LSC 650 0.0220 0.98 70.2 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-CAC-psbA_p1 trnH-CAC-psbA CTGCCTTAATCCACTTGGCT GCTGTTGAGGCTCCATCTAC 322–373 1.000 87.3
trnH-CAC-psbA_p2 trnH-CAC-psbA ACTGCCTTAATCCACTTGGC GCTGTTGAGGCTCCATCTAC 323–374 1.000 87.1
trnH-CAC-psbA_p3 trnH-CAC-psbA CTGCCTTAATCCACTTGGCT CCTCTAGACCTAGCTGCTGT 337–388 1.000 87.0
trnH-CAC-psbA_p4 trnH-CAC-psbA CTGCCTTAATCCACTTGGCT TTCCCTCTAGACCTAGCTGC 340–391 1.000 86.9
trnH-CAC-psbA_p5 trnH-CAC-psbA ACTGCCTTAATCCACTTGGC CCTCTAGACCTAGCTGCTGT 338–389 1.000 86.8
trnK-AAA-rps16_p1 trnK-AAA-rps16 CCGTCGATCTGTACGAATCC CGCTCAACCAACAAGAACAG 833–837 1.000 79.2
trnK-AAA-rps16_p2 trnK-AAA-rps16 AAAGCCGAGTACTCTACCGT CGCTCAACCAACAAGAACAG 772–776 1.000 78.3
trnK-AAA-rps16_p3 trnK-AAA-rps16 AAGCCGAGTACTCTACCGTT CGCTCAACCAACAAGAACAG 771–775 1.000 78.3
trnK-AAA-rps16_p4 trnK-AAA-rps16 TACCGTTGAGTTAGCAACCC CGCTCAACCAACAAGAACAG 758–762 1.000 76.0
trnK-AAA-rps16_p5 trnK-AAA-rps16 AGTCGCACTTAAAAGCCGAG CGCTCAACCAACAAGAACAG 783–787 1.000 75.1
psbI-trnS-AGC_p1 psbI-trnS-AGC TCCTATCTAATGATCCAGGACGT TAGGAGAGATGGCTGAGTGG 225–226 1.000 58.2
psbI-trnS-AGC_p2 psbI-trnS-AGC TCCTATCTAATGATCCAGGACGT TGAGTGGACTAAAGCGTTGG 212–213 1.000 57.7
psbI-trnS-AGC_p3 psbI-trnS-AGC TCCTATCTAATGATCCAGGACGT GCTGAGTGGACTAAAGCGTT 214–215 1.000 57.4
psbI-trnS-AGC_p4 psbI-trnS-AGC TCCTATCTAATGATCCAGGACGT CGAGTTAATCGTACCGAGGG 175–176 1.000 56.5
psbI-trnS-AGC_p5 psbI-trnS-AGC TCCTATCTAATGATCCAGGACGT ATGGCTGAGTGGACTAAAGC 217–218 1.000 55.7
trnS-AGC-trnG-GGA_p1 trnS-AGC-trnG-GGA CCAACGCTTTAGTCCACTCA TGAATCAAACCGAGAGACCC 753–759 1.000 76.6
trnS-AGC-trnG-GGA_p2 trnS-AGC-trnG-GGA AACGCTTTAGTCCACTCAGC TGAATCAAACCGAGAGACCC 751–757 1.000 76.3
trnS-AGC-trnG-GGA_p3 trnS-AGC-trnG-GGA GCTTTAGTCCACTCAGCCAT TGAATCAAACCGAGAGACCC 748–754 1.000 74.7
trnS-AGC-trnG-GGA_p4 trnS-AGC-trnG-GGA TCCAACGCTTTAGTCCACTC TGAATCAAACCGAGAGACCC 754–760 1.000 74.3
trnS-AGC-trnG-GGA_p5 trnS-AGC-trnG-GGA CCAACGCTTTAGTCCACTCA GAATCAAACCGAGAGACCCT 752–758 1.000 74.2
trnR-AGA-atpA_p1 trnR-AGA-atpA TCGAAAAGCGTCCATTGTCT ACATTAACCGCTGAAGCAGA 454–458 1.000 78.8
trnR-AGA-atpA_p2 trnR-AGA-atpA TCGAAAAGCGTCCATTGTCT AGACATTAACCGCTGAAGCA 456–460 1.000 78.8
trnR-AGA-atpA_p3 trnR-AGA-atpA TCGAAAAGCGTCCATTGTCT GACATTAACCGCTGAAGCAG 455–459 1.000 76.0
trnR-AGA-atpA_p4 trnR-AGA-atpA TCGAAAAGCGTCCATTGTCT TAACCGCTGAAGCAGAAAGC 450–454 1.000 75.8
trnR-AGA-atpA_p5 trnR-AGA-atpA TCGAAAAGCGTCCATTGTCT ACCAAGACATTAACCGCTGA 460–464 1.000 75.7
psbC-trnS-UCA_p1 psbC-trnS-UCA TCGTGGGTCATTTATGGCAC GATGGCTCCGGTCTTGAAAA 362–378 1.000 78.7
psbC-trnS-UCA_p2 psbC-trnS-UCA TCGTGGGTCATTTATGGCAC GGGTTCGAATCCCTCTCTCT 313–329 1.000 78.7
psbC-trnS-UCA_p3 psbC-trnS-UCA CGGCAGCAGGATTTGAAAAA GGGTTCGAATCCCTCTCTCT 274–290 1.000 77.6
psbC-trnS-UCA_p4 psbC-trnS-UCA CGGCAGCAGGATTTGAAAAA GATGGCTCCGGTCTTGAAAA 323–339 1.000 77.5
psbC-trnS-UCA_p5 psbC-trnS-UCA TTCGTGGGTCATTTATGGCA GATGGCTCCGGTCTTGAAAA 363–379 1.000 76.7

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
Tetracme quadricornis NC_050828.1 154566 View on NCBI ↗
Tetracme recurvata NC_053349.1 154399 View on NCBI ↗