Markers + reference

Chorispora

2 species · Brassicaceae · Brassicales

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Species 2
Genome length 162–163 kb
Candidate markers 262
Primer pairs 65

Genome-wide nucleotide diversity

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

Candidate markers

6 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 262 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rbcL-psaI LSC 4837 0.0094 0.95 62.9 yes View details
psbE-petL LSC 1397 0.0144 1.00 67.4 yes View details
ycf2 IRb 6262 0.0002 1.00 52.6 no View details
ycf1 IRb 5586 0.0014 1.00 49.7 yes View details
ycf1 IRa 5586 0.0014 1.00 49.7 no View details
ycf2 IRa 6237 0.0013 1.00 53.2 yes View details
rpl23-trnH-CAC IRa 119 0.0000 0.99 71.1 no View details
trnK-AAA-rps16 LSC 687 0.0000 0.97 61.7 yes View details
trnS-AGC-trnG-GGA LSC 617 0.0032 1.00 60.6 yes View details
trnN-AAC-ycf1 IRb 1170 0.0011 0.79 59.6 yes View details
ycf1-trnN-AAC IRa 1170 0.0011 0.79 59.6 yes View details
petA-psbJ LSC 838 0.0012 1.00 59.4 yes View details
rpoB-trnC-UGC LSC 1076 0.0009 1.00 59.3 yes View details
matK LSC 1515 0.0007 1.00 59.1 yes View details
rpl2 LSC 1519 0.0007 1.00 59.1 yes View details
ndhD SSC 1521 0.0007 1.00 59.1 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 65 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
matK_p1 matK TGCTAGGTCTCATAACCCAA GACTGTATCGCACTATGTGTCA 1612 1.000 44.1
matK_p2 matK TGCTAGGTCTCATAACCCAA TGACTGTATCGCACTATGTGTC 1613 1.000 44.1
matK_p3 matK TGCTAGGTCTCATAACCCAA ACCTCATTTTGACTGTATCGCA 1622 1.000 43.8
matK_p4 matK GGTATGCTAGGTCTCATAACCC GACTGTATCGCACTATGTGTCA 1616 1.000 43.5
matK_p5 matK GGTATGCTAGGTCTCATAACCC TGACTGTATCGCACTATGTGTC 1617 1.000 43.5
trnK-AAA-rps16_p1 trnK-AAA-rps16 AAAGCCGAGTACTCTACCGT AAAGGCGGGGATTTTTACGT 752–773 1.000 80.2
trnK-AAA-rps16_p2 trnK-AAA-rps16 AAGCCGAGTACTCTACCGTT AAAGGCGGGGATTTTTACGT 751–772 1.000 80.2
trnK-AAA-rps16_p3 trnK-AAA-rps16 TCTACCGCATATCTGGACGA AAAGGCGGGGATTTTTACGT 817–838 1.000 79.2
trnK-AAA-rps16_p4 trnK-AAA-rps16 CCGCATATCTGGACGAATCC AAAGGCGGGGATTTTTACGT 813–834 1.000 79.1
trnK-AAA-rps16_p5 trnK-AAA-rps16 ACCGCATATCTGGACGAATC AAAGGCGGGGATTTTTACGT 814–835 1.000 77.8
trnS-AGC-trnG-GGA_p1 trnS-AGC-trnG-GGA CCACTCAGCCATCTCTCCTA TGAATCAAACCGAGAGACCC 720–738 1.000 73.5
trnS-AGC-trnG-GGA_p2 trnS-AGC-trnG-GGA CCAACGCTTTAGTCCACTCA TGAATCAAACCGAGAGACCC 733–751 1.000 72.8
trnS-AGC-trnG-GGA_p3 trnS-AGC-trnG-GGA AACGCTTTAGTCCACTCAGC TGAATCAAACCGAGAGACCC 731–749 1.000 72.5
trnS-AGC-trnG-GGA_p4 trnS-AGC-trnG-GGA CCACTCAGCCATCTCTCCTA GAATCAAACCGAGAGACCCT 719–737 1.000 71.1
trnS-AGC-trnG-GGA_p5 trnS-AGC-trnG-GGA GCTTTAGTCCACTCAGCCAT TGAATCAAACCGAGAGACCC 728–746 1.000 70.8
rpoB-trnC-UGC_p1 rpoB-trnC-UGC GTTCCCTCTTTTCCATCCCC AGGGGATTTCAAGCCTGTTG 1196–1197 1.000 78.3
rpoB-trnC-UGC_p2 rpoB-trnC-UGC GTTCCCTCTTTTCCATCCCC GGGGATTTCAAGCCTGTTGT 1195–1196 1.000 76.0
rpoB-trnC-UGC_p3 rpoB-trnC-UGC GTTCCCTCTTTTCCATCCCC GTAGGGGATTTCAAGCCTGT 1198–1199 1.000 72.4
rpoB-trnC-UGC_p4 rpoB-trnC-UGC TGTTCCCTCTTTTCCATCCC AGGGGATTTCAAGCCTGTTG 1197–1198 1.000 72.3
rpoB-trnC-UGC_p5 rpoB-trnC-UGC TCTTTTCCATCCCCGAGCAT AGGGGATTTCAAGCCTGTTG 1190–1191 1.000 70.9
rbcL-psaI_p1 rbcL-psaI GCAATTAAACCCGGCTCAAC CTTGATAGCCATTCCCACCC 2361–2368 1.000 84.5
rbcL-psaI_p2 rbcL-psaI GCAATTAAACCCGGCTCAAC TAGCCATTCCCAATGTTCCG 2443–2450 1.000 84.0
rbcL-psaI_p3 rbcL-psaI GCAATTAAACCCGGCTCAAC TTTCCGACGAATCCGAATCC 2483–2490 1.000 83.8
rbcL-psaI_p4 rbcL-psaI ACCTCGACCTCTTTACGGAT TCCGGCTAGAGGTAGTTACC 342–386 1.000 82.2
rbcL-psaI_p5 rbcL-psaI GCAATTAAACCCGGCTCAAC GCTGTTCAAATTCGGCTTCC 2393 0.500 59.8
petA-psbJ_p1 petA-psbJ ACGTGTCCAAGGACTTTTGT GCTGGTATTCCTGTGATCGG 1025 1.000 75.7
petA-psbJ_p2 petA-psbJ TAGGATCGGTTGTTTTGGCA GCTGGTATTCCTGTGATCGG 999 1.000 74.5
petA-psbJ_p3 petA-psbJ TCCATTACGTGTCCAAGGAC GCTGGTATTCCTGTGATCGG 1031 1.000 73.0
petA-psbJ_p4 petA-psbJ CCATTACGTGTCCAAGGACT GCTGGTATTCCTGTGATCGG 1030 1.000 72.9
petA-psbJ_p5 petA-psbJ AGGATCGGTTGTTTTGGCAC GCTGGTATTCCTGTGATCGG 998 1.000 70.7

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
Chorispora sibirica NC_081112.1 162956 View on NCBI ↗
Chorispora songarica NC_081113.1 162326 View on NCBI ↗