Markers + reference

Goldbachia

2 species · Brassicaceae · Brassicales

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Species 2
Genome length 153–154 kb
Candidate markers 270
Primer pairs 95

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 9 remaining regions by MarkerSeek score (out of 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbK-psbI LSC 432 0.0640 0.98 84.5 yes View details
trnS-AGC-trnG-GGA LSC 703 0.0515 0.97 82.2 yes View details
trnL-UUA-trnF-UUC LSC 433 0.1145 0.83 81.8 yes View details
trnF-UUC-ndhJ LSC 575 0.0524 0.99 78.6 yes View details
ndhC-trnV-GUA LSC 893 0.0453 0.96 76.4 yes View details
accD LSC 1470 0.0636 0.97 79.1 yes View details
petA-psbJ LSC 962 0.0513 0.97 77.4 yes View details
trnP-CCA-psaJ LSC 339 0.0299 0.79 62.6 yes View details
ycf1 IRb 1038 0.0058 0.99 49.0 no View details
ndhF-rpl32 SSC 847 0.0426 0.97 73.7 yes View details
ycf1 SSC 3129 0.0436 1.00 65.8 yes View details
trnH-CAC-psbA LSC 271 0.0889 1.00 83.8 yes View details
ycf4-cemA LSC 468 0.0472 1.00 78.4 yes View details
ndhE-ndhG SSC 253 0.0558 0.99 76.8 yes View details
trnG-GGA-trnR-AGA LSC 164 0.0633 0.96 76.2 yes View details
psbT-psbN LSC 65 0.0769 1.00 73.9 yes View details
trnE-GAA-trnT-ACC LSC 825 0.0309 0.98 72.7 yes View details
psbZ-trnG-GGC LSC 453 0.0442 1.00 72.6 yes View details
rpl36-rps8 LSC 480 0.0426 0.98 72.5 yes View details
trnW-UGG-trnP-CCA LSC 188 0.0428 0.99 72.3 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 95 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 329–346 1.000 84.4
trnH-CAC-psbA_p2 trnH-CAC-psbA ACTGCCTTAATCCACTTGGC GCTGTTGAGGCTCCATCTAC 330–347 1.000 84.2
trnH-CAC-psbA_p3 trnH-CAC-psbA CTGCCTTAATCCACTTGGCT CCTCTAGACCTAGCTGCTGT 344–361 1.000 84.1
trnH-CAC-psbA_p4 trnH-CAC-psbA CTGCCTTAATCCACTTGGCT TTCCCTCTAGACCTAGCTGC 347–364 1.000 83.9
trnH-CAC-psbA_p5 trnH-CAC-psbA ACTGCCTTAATCCACTTGGC CCTCTAGACCTAGCTGCTGT 345–362 1.000 83.8
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCAGCTGTAAG TTCTTCACGTCCCGGATTAC 563–570 1.000 79.5
psbK-psbI_p2 psbK-psbI TGGCAAGCAGCTGTAAGTTT TTCTTCACGTCCCGGATTAC 560–567 1.000 77.5
psbK-psbI_p3 psbK-psbI TTGGCAAGCAGCTGTAAGTT TTCTTCACGTCCCGGATTAC 561–568 1.000 77.5
psbK-psbI_p4 psbK-psbI TTTGGCAAGCAGCTGTAAGT TTCTTCACGTCCCGGATTAC 562–569 1.000 77.5
psbK-psbI_p5 psbK-psbI GTTTGGCAAGCAGCTGTAAG CCGGATTACGTCCTGGATCA 552–559 1.000 77.2
trnS-AGC-trnG-GGA_p1 trnS-AGC-trnG-GGA CCAACGCTTTAGTCCACTCA AATCAAACCGAGAGACCCTT 802–811 1.000 72.1
trnS-AGC-trnG-GGA_p2 trnS-AGC-trnG-GGA CCAACGCTTTAGTCCACTCA ATCAAACCGAGAGACCCTTT 801–810 1.000 72.1
trnS-AGC-trnG-GGA_p3 trnS-AGC-trnG-GGA AACGCTTTAGTCCACTCAGC AATCAAACCGAGAGACCCTT 800–809 1.000 71.8
trnS-AGC-trnG-GGA_p4 trnS-AGC-trnG-GGA AACGCTTTAGTCCACTCAGC ATCAAACCGAGAGACCCTTT 799–808 1.000 71.8
trnS-AGC-trnG-GGA_p5 trnS-AGC-trnG-GGA CCAACGCTTTAGTCCACTCA AATCAAACCGAGAGACCCTTT 802–811 1.000 70.1
trnG-GGA-trnR-AGA_p1 trnG-GGA-trnR-AGA AGCCTTCCAAGCTAACGATG TGATATTGCGTCCAATAGGA 286–288 1.000 51.6
trnG-GGA-trnR-AGA_p2 trnG-GGA-trnR-AGA ACCCTTAGCCTTCCAAGCTA TGATATTGCGTCCAATAGGA 292–294 1.000 51.5
trnG-GGA-trnR-AGA_p3 trnG-GGA-trnR-AGA AAACCCTTAGCCTTCCAAGC TGATATTGCGTCCAATAGGA 294–296 1.000 51.1
trnG-GGA-trnR-AGA_p4 trnG-GGA-trnR-AGA AGCCTTCCAAGCTAACGATG TTGATATTGCGTCCAATAGGA 287–289 1.000 50.6
trnG-GGA-trnR-AGA_p5 trnG-GGA-trnR-AGA ACCCTTAGCCTTCCAAGCTA TTGATATTGCGTCCAATAGGA 293–295 1.000 50.5
trnE-GAA-trnT-ACC_p1 trnE-GAA-trnT-ACC TTTCGTAGTACCCTACCCCC GAACCGATGACTTACGCCTT 966–969 1.000 82.0
trnE-GAA-trnT-ACC_p2 trnE-GAA-trnT-ACC TTTCGTAGTACCCTACCCCC CCATGGCGTTACTCTACCAC 945–948 1.000 81.6
trnE-GAA-trnT-ACC_p3 trnE-GAA-trnT-ACC TTTCGTAGTACCCTACCCCC TGGCGTTACTCTACCACTGA 942–945 1.000 81.4
trnE-GAA-trnT-ACC_p4 trnE-GAA-trnT-ACC GCTGCCTCCTTGAAAGAGAG GAACCGATGACTTACGCCTT 928–931 1.000 81.3
trnE-GAA-trnT-ACC_p5 trnE-GAA-trnT-ACC TGTCCTGAACCACTAGACGA GAACCGATGACTTACGCCTT 907–910 1.000 81.2
psbZ-trnG-GGC_p1 psbZ-trnG-GGC TCCTGATGGTTGGTCGAGTA CGTCTTCTCCTTGGCAAAGA 603–604 1.000 79.5
psbZ-trnG-GGC_p2 psbZ-trnG-GGC TTTGCGTCTCCTGATGGTTG CGTCTTCTCCTTGGCAAAGA 611–612 1.000 77.4
psbZ-trnG-GGC_p3 psbZ-trnG-GGC ATTTGCGTCTCCTGATGGTT CGTCTTCTCCTTGGCAAAGA 612–613 1.000 77.3
psbZ-trnG-GGC_p4 psbZ-trnG-GGC TCTCCTGATGGTTGGTCGAG CGTCTTCTCCTTGGCAAAGA 605–606 1.000 74.8
psbZ-trnG-GGC_p5 psbZ-trnG-GGC CCTGATGGTTGGTCGAGTAA CGTCTTCTCCTTGGCAAAGA 602–603 1.000 72.9

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
Goldbachia laevigata NC_049642.1 153750 View on NCBI ↗
Goldbachia sabulosa NC_081127.1 153454 View on NCBI ↗