Markers + reference

Solms-laubachia

21 species · Brassicaceae · Brassicales

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Species 21
Genome length 153–155 kb
Candidate markers 266
Primer pairs 115

Genome-wide nucleotide diversity

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

Candidate markers

14 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 266 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-CAC-psbA LSC 349 0.0821 0.92 86.4 yes View details
trnS-AGC-trnG-GGA LSC 661 0.0606 0.95 89.2 yes View details
trnE-GAA-trnT-ACC LSC 846 0.0306 0.97 80.4 yes View details
trnT-ACC-psbD LSC 1273 0.0300 0.94 79.2 yes View details
ndhC-trnV-GUA LSC 906 0.0301 0.95 78.6 yes View details
rbcL-accD LSC 675 0.0306 0.99 82.9 yes View details
petA-psbJ LSC 947 0.0333 0.96 90.2 yes View details
psbE-petL LSC 1056 0.0253 1.00 78.8 yes View details
trnP-CCA-psaJ LSC 377 0.0318 0.94 74.8 yes View details
psaJ-rpl33 LSC 432 0.0338 1.00 75.1 yes View details
ycf1 IRb 1026 0.0031 1.00 57.7 no View details
ndhF-rpl32 SSC 837 0.0356 0.96 80.3 yes View details
rpl32-trnL-CUA SSC 753 0.0335 1.00 84.9 yes View details
ycf1 SSC 5346 0.0171 1.00 64.0 yes View details
trnK-AAA-rps16 LSC 601 0.0298 1.00 90.6 yes View details
ycf4-cemA LSC 441 0.0396 0.96 90.4 yes View details
trnT-ACA-trnL-UUA LSC 824 0.0288 1.00 89.6 yes View details
atpF-atpH LSC 462 0.0294 0.99 85.6 yes View details
psaA-ycf3 LSC 716 0.0180 1.00 85.3 yes View details
rpoB-trnC-UGC LSC 1106 0.0189 1.00 85.1 yes View details
psbZ-trnG-GGC LSC 511 0.0251 0.97 84.9 yes View details
petN-psbM LSC 533 0.0343 1.00 84.5 yes View details
rpl20-rps12 LSC 766 0.0134 1.00 83.3 yes View details
trnC-UGC-petN LSC 687 0.0268 0.97 80.2 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 115 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 306–456 0.952 88.6
trnH-CAC-psbA_p2 trnH-CAC-psbA CTGCCTTAATCCACTTGGCT TTCCCTCTAGACCTAGCTGC 225–474 0.952 88.4
trnH-CAC-psbA_p3 trnH-CAC-psbA ACTGCCTTAATCCACTTGGC GCTGTTGAGGCTCCATCTAC 307–457 0.952 88.4
trnH-CAC-psbA_p4 trnH-CAC-psbA CTGCCTTAATCCACTTGGCT CCTCTAGACCTAGCTGCTGT 222–471 0.905 86.6
trnH-CAC-psbA_p5 trnH-CAC-psbA ACTGCCTTAATCCACTTGGC CCTCTAGACCTAGCTGCTGT 223–472 0.905 86.4
trnK-AAA-rps16_p1 trnK-AAA-rps16 AAAGCCGAGTACTCTACCGT CGCTCAACCAACAAGAACAG 723–796 1.000 87.5
trnK-AAA-rps16_p2 trnK-AAA-rps16 AAGCCGAGTACTCTACCGTT CGCTCAACCAACAAGAACAG 722–795 1.000 87.5
trnK-AAA-rps16_p3 trnK-AAA-rps16 TACCGTTGAGTTAGCAACCC CGCTCAACCAACAAGAACAG 709–782 1.000 85.2
trnK-AAA-rps16_p4 trnK-AAA-rps16 AGTCGCACTTAAAAGCCGAG CGCTCAACCAACAAGAACAG 734–807 1.000 84.3
trnK-AAA-rps16_p5 trnK-AAA-rps16 TCGCACTTAAAAGCCGAGTA CGCTCAACCAACAAGAACAG 732–805 1.000 83.1
trnS-AGC-trnG-GGA_p1 trnS-AGC-trnG-GGA CCAACGCTTTAGTCCACTCA TCGGAAGATGAATCAAACCGA 534–882 1.000 77.9
trnS-AGC-trnG-GGA_p2 trnS-AGC-trnG-GGA AACGCTTTAGTCCACTCAGC TCGGAAGATGAATCAAACCGA 532–880 1.000 77.6
trnS-AGC-trnG-GGA_p3 trnS-AGC-trnG-GGA GCTTTAGTCCACTCAGCCAT TCGGAAGATGAATCAAACCGA 529–877 1.000 75.9
trnS-AGC-trnG-GGA_p4 trnS-AGC-trnG-GGA TCCAACGCTTTAGTCCACTC TCGGAAGATGAATCAAACCGA 535–883 1.000 75.6
trnS-AGC-trnG-GGA_p5 trnS-AGC-trnG-GGA AGTCCACTCAGCCATCTCTC TCGGAAGATGAATCAAACCGA 524–872 1.000 75.0
atpF-atpH_p1 atpF-atpH ATTAAACCCGAAACTCCCGG TGGCCTGGTTGTAGCATTAG 556–610 1.000 87.7
atpF-atpH_p2 atpF-atpH CCAGTGACCCAAGTAAACGA TGGCCTGGTTGTAGCATTAG 529–583 1.000 84.4
atpF-atpH_p3 atpF-atpH ATTAAACCCGAAACTCCCGG TTTATGGCCTGGTTGTAGCA 560–614 1.000 83.9
atpF-atpH_p4 atpF-atpH ATTAAACCCGAAACTCCCGG GGCCTGGTTGTAGCATTAGC 555–609 1.000 83.3
atpF-atpH_p5 atpF-atpH GGCCAGTGACCCAAGTAAAC TGGCCTGGTTGTAGCATTAG 531–585 1.000 82.6
rpoB-trnC-UGC_p1 rpoB-trnC-UGC GTTCCCTCTTTTCCATCCCC CCGGATTTGAACTGGGGAAA 1174–1238 1.000 90.2
rpoB-trnC-UGC_p2 rpoB-trnC-UGC GTTCCCTCTTTTCCATCCCC AAAAGGATTTGCAGTCCCCC 1156–1220 1.000 88.0
rpoB-trnC-UGC_p3 rpoB-trnC-UGC GTTCCCTCTTTTCCATCCCC TCAAGTCTGTTGTTGAGGCG 1198–1262 1.000 87.5
rpoB-trnC-UGC_p4 rpoB-trnC-UGC TGTTCCCTCTTTTCCATCCC CCGGATTTGAACTGGGGAAA 1175–1239 1.000 84.1
rpoB-trnC-UGC_p5 rpoB-trnC-UGC GTTCCCTCTTTTCCATCCCC AAGTCTGTTGTTGAGGCGG 1196–1260 1.000 82.8
trnC-UGC-petN_p1 trnC-UGC-petN TTTCCCCAGTTCAAATCCGG ACTTCTTCCCCACACTACGA 681–855 0.952 89.4
trnC-UGC-petN_p2 trnC-UGC-petN GTTTCTATCGTTTTGGCGGC ACTTCTTCCCCACACTACGA 737–911 0.952 89.2
trnC-UGC-petN_p3 trnC-UGC-petN TTTCCCCAGTTCAAATCCGG CACTTCTTCCCCACACTACG 682–856 0.952 88.8
trnC-UGC-petN_p4 trnC-UGC-petN GTTTCTATCGTTTTGGCGGC CACTTCTTCCCCACACTACG 738–912 0.952 88.6
trnC-UGC-petN_p5 trnC-UGC-petN TTTCCCCAGTTCAAATCCGG TCTAGAGGCCACTTCTTCCC 691–865 0.952 88.4

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (21)

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

Species Accession Length (bp) Link
Solms-laubachia angustifolia NC_053340.1 154531 View on NCBI ↗
Solms-laubachia baiogoinensis NC_050807.1 154201 View on NCBI ↗
Solms-laubachia calcicola NC_050808.1 153939 View on NCBI ↗
Solms-laubachia eurycarpa NC_034359.1 152895 View on NCBI ↗
Solms-laubachia grandiflora NC_053341.1 154095 View on NCBI ↗
Solms-laubachia himalayensis NC_050809.1 155175 View on NCBI ↗
Solms-laubachia jafrii NC_050810.1 155014 View on NCBI ↗
Solms-laubachia kashgarica NC_050811.1 154164 View on NCBI ↗
Solms-laubachia lanata NC_050812.1 154603 View on NCBI ↗
Solms-laubachia linearifolia NC_050814.1 154626 View on NCBI ↗
Solms-laubachia linearis NC_050813.1 154581 View on NCBI ↗
Solms-laubachia mieheorum NC_053342.1 153561 View on NCBI ↗
Solms-laubachia minor NC_050815.1 153684 View on NCBI ↗
Solms-laubachia platycarpa NC_050816.1 153696 View on NCBI ↗
Solms-laubachia prolifera NC_050817.1 153960 View on NCBI ↗
Solms-laubachia pulcherrima NC_050818.1 154985 View on NCBI ↗
Solms-laubachia retropilosa NC_050819.1 154576 View on NCBI ↗
Solms-laubachia sunhangiana NC_050820.1 154021 View on NCBI ↗
Solms-laubachia villosa NC_050821.1 154212 View on NCBI ↗
Solms-laubachia xerophyta NC_050822.1 155406 View on NCBI ↗
Solms-laubachia zhongdianensis NC_050823.1 155499 View on NCBI ↗