Markers + reference

Physaria

2 species · Brassicaceae · Brassicales

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Species 2
Genome length 154–154 kb
Candidate markers 263
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 7 remaining regions by MarkerSeek score (out of 263 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-psbA LSC 277 0.0247 0.88 69.1 yes View details
psbA LSC 1062 0.0019 1.00 49.3 yes View details
rps16 LSC 1138 0.0088 1.00 54.1 yes View details
trnQ-psbK LSC 330 0.0152 1.00 61.8 yes View details
psbM-trnD LSC 1022 0.0020 1.00 58.3 yes View details
trnD-trnY LSC 423 0.0143 1.00 63.7 yes View details
accD-psaI LSC 668 0.0061 0.99 52.4 yes View details
rpl20-rps12 LSC 776 0.0052 1.00 61.7 yes View details
ndhF-rpl32 SSC 858 0.0129 1.00 66.5 yes View details
rpl32-trnL SSC 898 0.0146 0.99 67.8 yes View details
ndhA SSC 2169 0.0032 1.00 44.5 yes View details
trnM-atpE LSC 139 0.0382 0.94 78.8 yes View details
rps12-clpP LSC 183 0.0383 1.00 70.9 yes View details
petN-psbM LSC 527 0.0078 0.98 63.7 yes View details
trnL-trnF LSC 596 0.0084 1.00 63.5 yes View details
psbZ-trnG LSC 492 0.0042 0.96 62.7 yes View details
ndhI-ndhA SSC 84 0.0238 1.00 62.6 yes View details
trnS-trnG LSC 674 0.0015 0.97 62.1 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-psbA_p1 trnH-psbA CTGCCTTAATCCACTTGGCT GCTGTTGAGGCTCCATCTAC 302–335 1.000 84.0
trnH-psbA_p2 trnH-psbA CTGCCTTAATCCACTTGGCT CCTCTAGACCTAGCTGCTGT 317–350 1.000 83.8
trnH-psbA_p3 trnH-psbA CTGCCTTAATCCACTTGGCT TTCCCTCTAGACCTAGCTGC 320–353 1.000 83.8
trnH-psbA_p4 trnH-psbA ACTGCCTTAATCCACTTGGC GCTGTTGAGGCTCCATCTAC 303–336 1.000 83.8
trnH-psbA_p5 trnH-psbA ACTGCCTTAATCCACTTGGC CCTCTAGACCTAGCTGCTGT 318–351 1.000 83.6
psbA_p1 psbA AGAAGGCTCATATTGCTCGT ATTTGTGTGCTTGGGAGTCC 1168 1.000 66.8
psbA_p2 psbA AAGAAGGCTCATATTGCTCGT ATTTGTGTGCTTGGGAGTCC 1169 1.000 64.7
psbA_p3 psbA AGAAGGCTCATATTGCTCGTT ATTTGTGTGCTTGGGAGTCC 1168 1.000 64.7
psbA_p4 psbA AGAAGGCTCATATTGCTCGT AGAATTTGTGTGCTTGGGAGT 1171 1.000 61.4
psbA_p5 psbA AGAAGGCTCATATTGCTCGT TTTGTGTGCTTGGGAGTCC 1167 1.000 60.9
rps16_p1 rps16 CGAAGCGAAAGAGGAGGAAA ACTGACTGAACTATGACTATTCATGA 1309–1310 1.000 40.7
rps16_p2 rps16 GATCGAAGCGAAAGAGGAGG ACTGACTGAACTATGACTATTCATGA 1312–1313 1.000 40.7
rps16_p3 rps16 CGAAGCGAAAGAGGAGGAAA ACTGACTGAACTATGACTATTCA 1309–1310 1.000 40.7
rps16_p4 rps16 GATCGAAGCGAAAGAGGAGG ACTGACTGAACTATGACTATTCA 1312–1313 1.000 40.7
rps16_p5 rps16 CGAAGCGAAAGAGGAGGAAA TGAATTACACAAACTAGAGGAATGT 1270–1271 1.000 40.7
trnQ-psbK_p1 trnQ-psbK AACTGTACTCTGGGACGGAA TGCGACTAAAAAGGTGCTTG 483 1.000 72.3
trnQ-psbK_p2 trnQ-psbK AACTGTACTCTGGGACGGAA ACGATTGGATTCAAAAAGGCG 521 1.000 71.0
trnQ-psbK_p3 trnQ-psbK AACTGTACTCTGGGACGGAA CGATTGGATTCAAAAAGGCGT 520 1.000 71.0
trnQ-psbK_p4 trnQ-psbK GTACTCTGGGACGGAAGGAT TGCGACTAAAAAGGTGCTTG 479 1.000 70.6
trnQ-psbK_p5 trnQ-psbK AACTGTACTCTGGGACGGAA GCGACTAAAAAGGTGCTTGA 482 1.000 70.0
trnS-trnG_p1 trnS-trnG CCAACGCTTTAGTCCACTCA TGAATCAAACCGAGAGACCC 769–784 1.000 74.4
trnS-trnG_p2 trnS-trnG AACGCTTTAGTCCACTCAGC TGAATCAAACCGAGAGACCC 767–782 1.000 74.1
trnS-trnG_p3 trnS-trnG GCTTTAGTCCACTCAGCCAT TGAATCAAACCGAGAGACCC 764–779 1.000 72.5
trnS-trnG_p4 trnS-trnG TCCAACGCTTTAGTCCACTC TGAATCAAACCGAGAGACCC 770–785 1.000 72.1
trnS-trnG_p5 trnS-trnG CCAACGCTTTAGTCCACTCA GAATCAAACCGAGAGACCCT 768–783 1.000 72.1
petN-psbM_p1 petN-psbM CGTGGGCTGCTTTAATGGTA TGCTACTGCACTCTTCATTCT 666–677 1.000 64.0
petN-psbM_p2 petN-psbM CGTGGGCTGCTTTAATGGTA TGCACTCTTCATTCTTGTTCCT 660–671 1.000 63.0
petN-psbM_p3 petN-psbM TAGTGTGGGGAAGAAGTGGA TGCTACTGCACTCTTCATTCT 621–632 1.000 62.9
petN-psbM_p4 petN-psbM GTAGTGTGGGGAAGAAGTGG TGCTACTGCACTCTTCATTCT 622–633 1.000 62.4
petN-psbM_p5 petN-psbM TAGTGTGGGGAAGAAGTGGA TGCACTCTTCATTCTTGTTCCT 615–626 1.000 61.9

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
Physaria fendleri BK063463.1 154223 View on NCBI ↗
Physaria pinetorum MK637778.1 154449 View on NCBI ↗