Markers + reference

Hesperis

4 species · Brassicaceae · Brassicales

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Species 4
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

9 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 311 0.1548 0.81 74.0 yes View details
trnK-UUU-rps16 LSC 702 0.0283 0.88 64.0 yes View details
trnS-GCU-trnG LSC 749 0.0437 0.85 85.0 yes View details
rpoB-trnC-GCA LSC 1068 0.0401 1.00 70.1 yes View details
trnL-UAA-trnF-GAA LSC 331 0.1256 0.69 76.3 yes View details
rbcL-accD LSC 693 0.0413 0.97 75.6 yes View details
psbE-petL LSC 1354 0.0161 0.99 61.8 yes View details
rpl32-trnL-UAG SSC 631 0.0625 0.99 88.8 yes View details
rps15-trnN-GUU SSC 5875 0.0136 1.00 56.1 yes View details
ndhK-ndhC LSC 64 0.0317 0.95 65.6 yes View details
lhbA-trnG-UCC LSC 470 0.0142 0.94 64.4 yes View details
rps16 LSC 1143 0.0175 1.00 63.4 yes View details
trnR-ACG-trnN-GUU SSC 642 0.0034 0.99 62.9 yes View details
trnM-CAU-atpE LSC 134 0.0188 0.98 61.9 yes View details
accD-psaI LSC 644 0.0119 1.00 61.3 yes View details
trnF-GAA-ndhJ LSC 426 0.0282 0.54 61.2 yes View details
trnT-GGU-psbD LSC 1223 0.0117 0.90 60.9 yes View details
rps12-trnV-GAC IRb 1902 0.0040 1.00 60.9 yes View details
trnV-GAC-rps12 IRa 1902 0.0040 1.00 60.9 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-GUG-psbA_p1 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT GCGCTAACCTTGGTATGGAA 370–467 1.000 90.7
trnH-GUG-psbA_p2 trnH-GUG-psbA ACTGCCTTAATCCACTTGGC GCGCTAACCTTGGTATGGAA 371–468 1.000 90.5
trnH-GUG-psbA_p3 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT CCTCTAGACCTAGCTGCTGT 320–417 1.000 90.4
trnH-GUG-psbA_p4 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT TTCCCTCTAGACCTAGCTGC 323–420 1.000 90.3
trnH-GUG-psbA_p5 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT GGTGTAGCTGGTGTATTCGG 737–834 1.000 89.7
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG CCCAATGAGCCGTTTATCGA 977–1066 1.000 86.1
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG TCCCAATGAGCCGTTTATCG 978–1067 1.000 86.1
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCAGGATCAGTCGTGGTCTT CCCAATGAGCCGTTTATCGA 973–1062 1.000 85.7
trnK-UUU-rps16_p4 trnK-UUU-rps16 TCAGGATCAGTCGTGGTCTT TCCCAATGAGCCGTTTATCG 974–1063 1.000 85.7
trnK-UUU-rps16_p5 trnK-UUU-rps16 TTCAGGATCAGTCGTGGTCT CCCAATGAGCCGTTTATCGA 974–1063 1.000 85.7
rps16_p1 rps16 GATGGAAGCGAAAGAGGAGG ACGATATACTGACTGAACTATGACT 1306–1312 1.000 42.3
rps16_p2 rps16 GATGGAAGCGAAAGAGGAGG ACTGACTGAACTATGACTATTCATGA 1299–1305 1.000 42.3
rps16_p3 rps16 GATGGAAGCGAAAGAGGAGG ACGATATACTGACTGAACTATGAC 1306–1312 1.000 42.3
rps16_p4 rps16 ATGGAAGCGAAAGAGGAGGA ACGATATACTGACTGAACTATGACT 1305–1311 1.000 42.3
rps16_p5 rps16 GATGGAAGCGAAAGAGGAGG ACTGACTGAACTATGACTATTCA 1299–1305 1.000 42.3
trnS-GCU-trnG_p1 trnS-GCU-trnG CCAACGCTTTAGTCCACTCA TGAATCAAACCGAGAGACCC 657–859 1.000 81.2
trnS-GCU-trnG_p2 trnS-GCU-trnG AACGCTTTAGTCCACTCAGC TGAATCAAACCGAGAGACCC 655–857 1.000 80.9
trnS-GCU-trnG_p3 trnS-GCU-trnG GCTTTAGTCCACTCAGCCAT TGAATCAAACCGAGAGACCC 652–854 1.000 79.3
trnS-GCU-trnG_p4 trnS-GCU-trnG TCCAACGCTTTAGTCCACTC TGAATCAAACCGAGAGACCC 658–860 1.000 78.9
trnS-GCU-trnG_p5 trnS-GCU-trnG CCAACGCTTTAGTCCACTCA GAATCAAACCGAGAGACCCT 656–858 1.000 78.8
rpoB-trnC-GCA_p1 rpoB-trnC-GCA ATTGGATCCCCACCTACACA CCGGATTTGAACTGGGGAAA 1843–1867 1.000 82.6
rpoB-trnC-GCA_p2 rpoB-trnC-GCA ATTGGATCCCCACCTACACA AGCGTCTGTTCCTACGTTTG 1902–1917 0.500 58.5
rpoB-trnC-GCA_p3 rpoB-trnC-GCA ATTGGATCCCCACCTACACA CAAGCGTCTGTTCCTACGTT 1904–1919 0.500 58.5
rpoB-trnC-GCA_p4 rpoB-trnC-GCA ATTGGATCCCCACCTACACA ACGGATTTCCCTCCACTACT 2015–2030 0.500 58.2
rpoB-trnC-GCA_p5 rpoB-trnC-GCA ATTGGATCCCCACCTACACA ATCAAGCGTCTGTTCCTACG 1906–1921 0.500 58.0
trnT-GGU-psbD_p1 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG TCCCTCCGTAACCAGTCATC 1242–1358 1.000 80.8
trnT-GGU-psbD_p2 trnT-GGU-psbD TCAGTGGTAGAGTAACGCCA TCCCTCCGTAACCAGTCATC 1245–1361 1.000 80.6
trnT-GGU-psbD_p3 trnT-GGU-psbD CCAAGACGGCCCTTTTAACT TCCCTCCGTAACCAGTCATC 1264–1380 1.000 80.6
trnT-GGU-psbD_p4 trnT-GGU-psbD ACGGCCCTTTTAACTCAGTG TCCCTCCGTAACCAGTCATC 1259–1375 1.000 80.4
trnT-GGU-psbD_p5 trnT-GGU-psbD GACGGCCCTTTTAACTCAGT TCCCTCCGTAACCAGTCATC 1260–1376 1.000 79.9

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (4)

One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.

Species Accession Length (bp) Link
Hesperis matronalis NC_035511.1 153907 View on NCBI ↗
Hesperis persica NC_049649.1 153383 View on NCBI ↗
Hesperis sylvestris NC_035512.1 154415 View on NCBI ↗
Hesperis tristis NC_049653.1 152683 View on NCBI ↗