Markers + reference

Neotorularia

2 species · Brassicaceae · Brassicales

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Species 2
Genome length 155–155 kb
Candidate markers 266
Primer pairs 110

Genome-wide nucleotide diversity

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

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 10 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 325 0.1294 0.88 80.2 yes View details
trnK-AAA-rps16 LSC 652 0.0612 0.98 76.9 yes View details
psbM-trnD-GAC LSC 1029 0.0498 0.92 86.0 yes View details
trnE-GAA-trnT-ACC LSC 827 0.0524 0.95 84.0 yes View details
trnT-ACA-trnL-UUA LSC 817 0.0659 0.91 84.8 yes View details
trnL-UUA-trnF-UUC LSC 691 0.1478 1.00 81.3 yes View details
ndhC-trnV-GUA LSC 866 0.0607 0.99 77.5 yes View details
petA-psbJ LSC 908 0.0656 0.99 76.5 yes View details
psbE-petL LSC 1285 0.0479 0.97 76.1 yes View details
rpl16 LSC 1500 0.0376 0.99 66.4 yes View details
ndhF-rpl32 SSC 835 0.0570 0.95 81.2 yes View details
rpl32-trnL-CUA SSC 785 0.0859 0.96 80.5 yes View details
trnS-AGC-trnG-GGA LSC 630 0.0641 0.97 86.0 yes View details
petN-psbM LSC 531 0.0550 0.99 80.6 yes View details
psaJ-rpl33 LSC 416 0.0605 0.99 77.5 yes View details
trnP-CCA-psaJ LSC 354 0.0484 0.99 77.3 yes View details
trnS-UCA-psbZ LSC 346 0.0551 1.00 76.7 yes View details
petL-petG LSC 185 0.0919 1.00 76.1 yes View details
atpF-atpH LSC 465 0.0495 0.95 75.8 yes View details
trnR-AGA-atpA LSC 307 0.0570 0.97 75.7 yes View details
rps16-trnQ-CAA LSC 367 0.0656 1.00 75.5 yes View details
trnG-GGA-trnR-AGA LSC 161 0.0807 1.00 75.4 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-CAC-psbA_p1 trnH-CAC-psbA CTGCCTTAATCCACTTGGCT GCTGTTGAGGCTCCATCTAC 354–383 1.000 90.5
trnH-CAC-psbA_p2 trnH-CAC-psbA ACTGCCTTAATCCACTTGGC GCTGTTGAGGCTCCATCTAC 355–384 1.000 90.3
trnH-CAC-psbA_p3 trnH-CAC-psbA CTGCCTTAATCCACTTGGCT CCTCTAGACCTAGCTGCTGT 369–398 1.000 90.1
trnH-CAC-psbA_p4 trnH-CAC-psbA CTGCCTTAATCCACTTGGCT TTCCCTCTAGACCTAGCTGC 372–401 1.000 90.0
trnH-CAC-psbA_p5 trnH-CAC-psbA ACTGCCTTAATCCACTTGGC CCTCTAGACCTAGCTGCTGT 370–399 1.000 89.9
trnK-AAA-rps16_p1 trnK-AAA-rps16 CCTTTCAGGATCAGTCGTGG CCCAATGAGCCGTTTATCGA 1014–1037 1.000 83.9
trnK-AAA-rps16_p2 trnK-AAA-rps16 CCTTTCAGGATCAGTCGTGG TCCCAATGAGCCGTTTATCG 1015–1038 1.000 83.9
trnK-AAA-rps16_p3 trnK-AAA-rps16 TCAGGATCAGTCGTGGTCTT CCCAATGAGCCGTTTATCGA 1010–1033 1.000 83.4
trnK-AAA-rps16_p4 trnK-AAA-rps16 TCAGGATCAGTCGTGGTCTT TCCCAATGAGCCGTTTATCG 1011–1034 1.000 83.4
trnK-AAA-rps16_p5 trnK-AAA-rps16 TTCAGGATCAGTCGTGGTCT CCCAATGAGCCGTTTATCGA 1011–1034 1.000 83.4
rps16-trnQ-CAA_p1 rps16-trnQ-CAA AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 439–440 1.000 82.8
rps16-trnQ-CAA_p2 rps16-trnQ-CAA CCTTCAATTCAAGTCGCACG GAGGTTCGAATCCTTCCGTC 449–450 1.000 82.0
rps16-trnQ-CAA_p3 rps16-trnQ-CAA CCACAGCAGATCATGTCCTT GAGGTTCGAATCCTTCCGTC 465–466 1.000 80.4
rps16-trnQ-CAA_p4 rps16-trnQ-CAA TCCACAGCAGATCATGTCCT GAGGTTCGAATCCTTCCGTC 466–467 1.000 80.3
rps16-trnQ-CAA_p5 rps16-trnQ-CAA ATCCACAGCAGATCATGTCC GAGGTTCGAATCCTTCCGTC 467–468 1.000 78.6
trnS-AGC-trnG-GGA_p1 trnS-AGC-trnG-GGA CCAACGCTTTAGTCCACTCA TGAATCAAACCGAGAGACCC 740–744 1.000 79.2
trnS-AGC-trnG-GGA_p2 trnS-AGC-trnG-GGA AACGCTTTAGTCCACTCAGC TGAATCAAACCGAGAGACCC 738–742 1.000 78.9
trnS-AGC-trnG-GGA_p3 trnS-AGC-trnG-GGA GCTTTAGTCCACTCAGCCAT TGAATCAAACCGAGAGACCC 735–739 1.000 77.2
trnS-AGC-trnG-GGA_p4 trnS-AGC-trnG-GGA TCCAACGCTTTAGTCCACTC TGAATCAAACCGAGAGACCC 741–745 1.000 76.9
trnS-AGC-trnG-GGA_p5 trnS-AGC-trnG-GGA CCAACGCTTTAGTCCACTCA GAATCAAACCGAGAGACCCT 739–743 1.000 76.8
trnG-GGA-trnR-AGA_p1 trnG-GGA-trnR-AGA AGCCTTCCAAGCTAACGATG TGATATTGCGTCCAATAGGA 283–290 1.000 50.8
trnG-GGA-trnR-AGA_p2 trnG-GGA-trnR-AGA ACCCTTAGCCTTCCAAGCTA TGATATTGCGTCCAATAGGA 289–296 1.000 50.7
trnG-GGA-trnR-AGA_p3 trnG-GGA-trnR-AGA CGACGTCGACTAAAACCCTT TGATATTGCGTCCAATAGGA 303–310 1.000 50.3
trnG-GGA-trnR-AGA_p4 trnG-GGA-trnR-AGA AAACCCTTAGCCTTCCAAGC TGATATTGCGTCCAATAGGA 291–298 1.000 50.3
trnG-GGA-trnR-AGA_p5 trnG-GGA-trnR-AGA AGCCTTCCAAGCTAACGATG TTGATATTGCGTCCAATAGGA 284–291 1.000 49.8
trnR-AGA-atpA_p1 trnR-AGA-atpA GGTTCAAATCCTATTGGACGC ACATTAACCGCTGAAGCAGA 409–413 1.000 67.7
trnR-AGA-atpA_p2 trnR-AGA-atpA GGTTCAAATCCTATTGGACGC AGACATTAACCGCTGAAGCA 411–415 1.000 67.7
trnR-AGA-atpA_p3 trnR-AGA-atpA GGTTCAAATCCTATTGGACGC GACATTAACCGCTGAAGCAG 410–414 1.000 65.0
trnR-AGA-atpA_p4 trnR-AGA-atpA GGTTCAAATCCTATTGGACGC TAACCGCTGAAGCAGAAAGC 405–409 1.000 64.8
trnR-AGA-atpA_p5 trnR-AGA-atpA GGTTCAAATCCTATTGGACGC ACCAAGACATTAACCGCTGA 415–419 1.000 64.6

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
Neotorularia rossica NC_053337.1 154598 View on NCBI ↗
Neotorularia torulosa NC_049683.1 154893 View on NCBI ↗