Markers + reference

Cleomella

2 species · Cleomaceae · Brassicales

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Species 2
Genome length 154–154 kb
Candidate markers 268
Primer pairs 100

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 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA-trnK-AAA LSC 275 0.0073 1.00 53.7 yes View details
trnR-AGA-atpA LSC 288 0.0316 0.99 71.6 yes View details
rpoC2 LSC 4158 0.0019 1.00 41.6 yes View details
psbM-trnD-GAC LSC 946 0.0064 1.00 55.3 yes View details
trnT-ACC-psbD LSC 1115 0.0027 1.00 59.2 yes View details
psbG LSC 678 0.0029 1.00 46.1 yes View details
clpP LSC 2086 0.0024 1.00 51.4 yes View details
rpl16 LSC 1567 0.0032 0.99 61.5 yes View details
ycf1 IRb 1017 0.0020 1.00 59.9 no View details
rpl32-trnL-CUA SSC 937 0.0128 1.00 52.5 yes View details
psaC SSC 246 0.0041 1.00 46.2 yes View details
ycf1 SSC 5424 0.0031 1.00 44.7 yes View details
ndhD-psaC SSC 138 0.0543 0.93 80.9 yes View details
psbG-ndhC LSC 52 0.0385 1.00 74.6 yes View details
rps12-clpP LSC 194 0.0361 1.00 73.2 yes View details
rpl2-trnH-CAC IRa 165 0.0000 1.00 71.2 no View details
rpl22-rps19 LSC 54 0.0185 1.00 63.1 yes View details
atpH-atpI LSC 731 0.0055 1.00 61.9 yes View details
trnS-AGC-trnG-GGA LSC 706 0.0043 1.00 61.5 yes View details
atpA-atpF LSC 64 0.0156 1.00 61.5 yes View details
ndhC-trnV-GUA LSC 703 0.0043 1.00 61.2 yes View details
cemA LSC 690 0.0043 1.00 61.2 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbA-trnK-AAA_p1 psbA-trnK-AAA TTTTCCGTGCTGGTTATCCA CGGTTTGGGGAGGGATTTTT 445 1.000 72.9
psbA-trnK-AAA_p2 psbA-trnK-AAA TACAGAAGCGACCCCATAGG CGGTTTGGGGAGGGATTTTT 423 1.000 72.8
psbA-trnK-AAA_p3 psbA-trnK-AAA TTTTCCGTGCTGGTTATCCA AAAATGCAAGCACGGTTTGG 457 1.000 72.4
psbA-trnK-AAA_p4 psbA-trnK-AAA TACAGAAGCGACCCCATAGG AAAATGCAAGCACGGTTTGG 435 1.000 72.3
psbA-trnK-AAA_p5 psbA-trnK-AAA ATCCAGTTACAGAAGCGACC CGGTTTGGGGAGGGATTTTT 430 1.000 72.1
trnS-AGC-trnG-GGA_p1 trnS-AGC-trnG-GGA CCAACGCTTTAGTCCACTCA TGAATCAAACCGAGAGACCC 814–816 1.000 73.1
trnS-AGC-trnG-GGA_p2 trnS-AGC-trnG-GGA AACGCTTTAGTCCACTCAGC TGAATCAAACCGAGAGACCC 812–814 1.000 72.8
trnS-AGC-trnG-GGA_p3 trnS-AGC-trnG-GGA GCTTTAGTCCACTCAGCCAT TGAATCAAACCGAGAGACCC 809–811 1.000 71.1
trnS-AGC-trnG-GGA_p4 trnS-AGC-trnG-GGA TCCAACGCTTTAGTCCACTC TGAATCAAACCGAGAGACCC 815–817 1.000 70.8
trnS-AGC-trnG-GGA_p5 trnS-AGC-trnG-GGA CCAACGCTTTAGTCCACTCA GAATCAAACCGAGAGACCCT 813–815 1.000 70.7
trnR-AGA-atpA_p1 trnR-AGA-atpA GGTTCAAATCCTATTGGACGC TCACCGAAGAAGCAGAAAGC 387–390 1.000 65.0
trnR-AGA-atpA_p2 trnR-AGA-atpA GGTTCAAATCCTATTGGACGC ACATTCACCGAAGAAGCAGA 391–394 1.000 62.2
trnR-AGA-atpA_p3 trnR-AGA-atpA GGTTCAAATCCTATTGGACGC AGACATTCACCGAAGAAGCA 393–396 1.000 62.2
trnR-AGA-atpA_p4 trnR-AGA-atpA TGGATAGGACAGAGGTCTTCT TCACCGAAGAAGCAGAAAGC 422–425 1.000 62.0
trnR-AGA-atpA_p5 trnR-AGA-atpA GGTTCAAATCCTATTGGACGC AGAGCAACTGGAACGTTTTCT 347–350 1.000 60.6
atpA-atpF_p1 atpA-atpF CACTTGAAGTACGGTACCGG ACAAGGAGCTATAGGAACCCT 278 1.000 68.8
atpA-atpF_p2 atpA-atpF CCACTTGAAGTACGGTACCG ACAAGGAGCTATAGGAACCCT 279 1.000 68.8
atpA-atpF_p3 atpA-atpF GCCCACTTGAAGTACGGTAC ACAAGGAGCTATAGGAACCCT 281 1.000 66.6
atpA-atpF_p4 atpA-atpF GATACCATCGCCCACTTGAA ACAAGGAGCTATAGGAACCCT 290 1.000 66.3
atpA-atpF_p5 atpA-atpF ATACCATCGCCCACTTGAAG ACAAGGAGCTATAGGAACCCT 289 1.000 66.2
atpH-atpI_p1 atpH-atpI CAGGTCCAATGGAAGCAAGT TAGCTGCGGCGTATATAGGT 848 1.000 78.3
atpH-atpI_p2 atpH-atpI AACCGAAGCAGCAGAAATCA TAGCTGCGGCGTATATAGGT 805 1.000 78.2
atpH-atpI_p3 atpH-atpI CAGGTCCAATGGAAGCAAGT CGTTAGCTGCGGCGTATATA 851 1.000 77.7
atpH-atpI_p4 atpH-atpI AACCGAAGCAGCAGAAATCA CGTTAGCTGCGGCGTATATA 808 1.000 77.6
atpH-atpI_p5 atpH-atpI GGAAGCAAGTCCAACAGCTA TAGCTGCGGCGTATATAGGT 838 1.000 77.5
rpoC2_p1 rpoC2 CGATTTCTTCGCCTCTTTGC ACCCTTTCTTTCCGTCGAAA 222 1.000 74.4
rpoC2_p2 rpoC2 CGATTTCTTCGCCTCTTTGC ACATACCCTTTCTTTCCGTCG 226 1.000 71.1
rpoC2_p3 rpoC2 CGATTTCTTCGCCTCTTTGC CATACCCTTTCTTTCCGTCGA 225 1.000 69.5
rpoC2_p4 rpoC2 CGATTTCTTCGCCTCTTTGC TACCCTTTCTTTCCGTCGAA 223 1.000 67.4
rpoC2_p5 rpoC2 TTCTTCGCCTCTTTGCTACT ACCCTTTCTTTCCGTCGAAA 218 1.000 66.7

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
Cleomella lutea NC_049613.1 154124 View on NCBI ↗
Cleomella serrulata NC_088033.1 154226 View on NCBI ↗