Markers + reference

Sterigmostemum

2 species · Brassicaceae · Brassicales

Back to catalogue

Species 2
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

11 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbK-psbI LSC 258 0.0039 1.00 55.1 yes View details
atpA LSC 1524 0.0020 1.00 59.8 yes View details
atpI LSC 750 0.0000 1.00 29.2 yes View details
rpoC2 LSC 4116 0.0010 1.00 54.4 yes View details
rpoB-trnC-UGC LSC 1041 0.0029 0.99 61.1 yes View details
psbM-trnD-GAC LSC 1078 0.0009 1.00 52.5 yes View details
atpB LSC 1497 0.0000 1.00 40.0 yes View details
atpB-rbcL LSC 791 0.0025 1.00 60.2 yes View details
psaJ-rpl33 LSC 410 0.0098 1.00 50.1 yes View details
ndhF-rpl32 SSC 882 0.0000 0.41 50.2 yes View details
rpl32-trnL-CUA SSC 469 0.0171 1.00 65.8 yes View details
rpoA-rps11 LSC 69 0.0145 1.00 60.8 yes View details
rpl36-rps8 LSC 532 0.0000 0.97 60.6 yes View details
ccsA SSC 987 0.0030 1.00 60.5 yes View details
psbE-petL LSC 1082 0.0019 1.00 60.0 yes View details
rpl16 LSC 1396 0.0014 1.00 60.0 yes View details
trnK-AAA-rps16 LSC 599 0.0017 1.00 59.7 yes View details
psaA-ycf3 LSC 701 0.0014 1.00 59.6 yes View details
rps3 LSC 654 0.0015 1.00 59.6 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
trnK-AAA-rps16_p1 trnK-AAA-rps16 AAAGCCGAGTACTCTACCGT CGCTCAACCAACAAGAACAG 703 1.000 75.6
trnK-AAA-rps16_p2 trnK-AAA-rps16 AAGCCGAGTACTCTACCGTT CGCTCAACCAACAAGAACAG 702 1.000 75.6
trnK-AAA-rps16_p3 trnK-AAA-rps16 TACCGTTGAGTTAGCAACCC CGCTCAACCAACAAGAACAG 689 1.000 73.3
trnK-AAA-rps16_p4 trnK-AAA-rps16 AGTCGCACTTAAAAGCCGAG CGCTCAACCAACAAGAACAG 714 1.000 72.4
trnK-AAA-rps16_p5 trnK-AAA-rps16 AAGCCGAGTACTCTACCGTT AGGCAGGGATTTTTACGGAA 664 1.000 71.6
psbK-psbI_p1 psbK-psbI CAAGCGGCTGTAAGTTTTCG TTCTTCACGTCCCGGATTAC 389–390 1.000 74.7
psbK-psbI_p2 psbK-psbI AGCGGCTGTAAGTTTTCGAT TTCTTCACGTCCCGGATTAC 387–388 1.000 74.4
psbK-psbI_p3 psbK-psbI AAGCGGCTGTAAGTTTTCGA TTCTTCACGTCCCGGATTAC 388–389 1.000 74.1
psbK-psbI_p4 psbK-psbI GCGGCTGTAAGTTTTCGATG TTCTTCACGTCCCGGATTAC 386–387 1.000 73.9
psbK-psbI_p5 psbK-psbI GCAAGCGGCTGTAAGTTTTC TTCTTCACGTCCCGGATTAC 390–391 1.000 72.6
atpA_p1 atpA AGCCTTCCAAGCTAACGATG AATCGGGAGAGGATAGGCTC 2729 1.000 79.3
atpA_p2 atpA AGCCTTCCAAGCTAACGATG ATCAGTTTCGCGTGAATGGA 2422 1.000 79.1
atpA_p3 atpA AGCCTTCCAAGCTAACGATG TCAGTTTCGCGTGAATGGAT 2421 1.000 79.1
atpA_p4 atpA AGCCTTCCAAGCTAACGATG TCATGTTTGGTTCGGGAAGG 2619 1.000 79.1
atpA_p5 atpA CCTAGCCTTCCAAGCTAACG AATCGGGAGAGGATAGGCTC 2732 1.000 79.1
atpI_p1 atpI TGGGCTAACCTAAAAACGAA AGTTCTTATTTATGTCAGAGGGCA 809 1.000 40.0
atpI_p2 atpI TTGGGCTAACCTAAAAACGA AGTTCTTATTTATGTCAGAGGGCA 810 1.000 40.0
atpI_p3 atpI TTGGGCTAACCTAAAAACGAA AGTTCTTATTTATGTCAGAGGGCA 810 1.000 40.0
atpI_p4 atpI TGGGCTAACCTAAAAACGAA GTTCTTATTTATGTCAGAGGGCA 808 1.000 40.0
atpI_p5 atpI TTGGGCTAACCTAAAAACGA GTTCTTATTTATGTCAGAGGGCA 809 1.000 40.0
rpoC2_p1 rpoC2 CGTGAACAATGCACCAATCC TATTACGAGCAGAACGGACG 259 1.000 76.5
rpoC2_p2 rpoC2 CCGTGAACAATGCACCAATC TATTACGAGCAGAACGGACG 260 1.000 76.4
rpoC2_p3 rpoC2 TGGTATGTTGCCGTGAACAA TATTACGAGCAGAACGGACG 270 1.000 76.3
rpoC2_p4 rpoC2 TGTTGGTATGTTGCCGTGAA TATTACGAGCAGAACGGACG 273 1.000 76.3
rpoC2_p5 rpoC2 TTGGTATGTTGCCGTGAACA TATTACGAGCAGAACGGACG 271 1.000 76.3
rpoB-trnC-UGC_p1 rpoB-trnC-UGC GTTCCCTCTTTTCCATCCCC CCGGATTTGAACTGGGGAAA 1122–1129 1.000 78.9
rpoB-trnC-UGC_p2 rpoB-trnC-UGC AACCCCTGCTCAATAAACCG CCGGATTTGAACTGGGGAAA 1188–1195 1.000 78.7
rpoB-trnC-UGC_p3 rpoB-trnC-UGC CCCCTGCTCAATAAACCGAT CCGGATTTGAACTGGGGAAA 1186–1193 1.000 77.2
rpoB-trnC-UGC_p4 rpoB-trnC-UGC GTTCCCTCTTTTCCATCCCC AAAAGGATTTGCAGTCCCCC 1104–1111 1.000 76.7
rpoB-trnC-UGC_p5 rpoB-trnC-UGC AACCCCTGCTCAATAAACCG AAAAGGATTTGCAGTCCCCC 1170–1177 1.000 76.5

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
Sterigmostemum caspicum NC_081133.1 153754 View on NCBI ↗
Sterigmostemum violaceum MK637808.1 153274 View on NCBI ↗