Markers + reference

Stenopetalum

4 species · Brassicaceae · Brassicales

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Species 4
Genome length 154–155 kb
Candidate markers 265
Primer pairs 100

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 10 remaining regions by MarkerSeek score (out of 265 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-psbA LSC 273 0.0374 1.00 67.6 yes View details
trnR-atpA LSC 274 0.0217 0.92 58.3 yes View details
psbM-trnD LSC 996 0.0148 1.00 61.2 yes View details
trnT-trnL LSC 854 0.0158 0.93 68.9 yes View details
trnL-trnF LSC 306 0.0349 1.00 67.0 yes View details
rbcL-accD LSC 673 0.0183 1.00 57.5 yes View details
ycf10/cemA LSC 690 0.0157 1.00 54.7 yes View details
petA-psbJ LSC 1000 0.0153 0.99 62.8 yes View details
rpl16 LSC 1557 0.0186 0.96 61.1 yes View details
ycf1 IRb 1032 0.0023 1.00 53.0 no View details
ycf1 SSC 5355 0.0130 1.00 49.5 yes View details
trnT-trnR LSC 179 0.0419 0.98 77.4 yes View details
psbG-ndhC LSC 66 0.0505 0.98 77.4 yes View details
rps18-rpl20 LSC 300 0.0339 1.00 69.3 yes View details
atpF-atpH LSC 463 0.0166 1.00 67.9 yes View details
psaA-ycf3 LSC 727 0.0149 0.99 66.9 yes View details
rpl32-trnL SSC 797 0.0147 0.99 64.9 yes View details
trnK-rps16 LSC 665 0.0176 0.98 64.2 yes View details
trnD-trnY LSC 426 0.0184 1.00 63.7 yes View details
orf77-trnL IRb 546 0.0018 1.00 63.6 yes View details
trnL-orf77 IRa 546 0.0018 1.00 63.6 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-psbA_p1 trnH-psbA CTGCCTTAATCCACTTGGCT GCTGTTGAGGCTCCATCTAC 330–332 1.000 83.6
trnH-psbA_p2 trnH-psbA ACTGCCTTAATCCACTTGGC GCTGTTGAGGCTCCATCTAC 331–333 1.000 83.3
trnH-psbA_p3 trnH-psbA CTGCCTTAATCCACTTGGCT CCTCTAGACCTAGCTGCTGT 345–347 1.000 83.2
trnH-psbA_p4 trnH-psbA CTGCCTTAATCCACTTGGCT TTCCCTCTAGACCTAGCTGC 348–350 1.000 83.1
trnH-psbA_p5 trnH-psbA ACTGCCTTAATCCACTTGGC CCTCTAGACCTAGCTGCTGT 346–348 1.000 83.0
trnK-rps16_p1 trnK-rps16 AAAGCCGAGTACTCTACCGT GGGATTTTTACGGAATTAAGTCT 744 0.250 10.0
trnK-rps16_p2 trnK-rps16 AAGCCGAGTACTCTACCGTT GGGATTTTTACGGAATTAAGTCT 743 0.250 10.0
trnK-rps16_p3 trnK-rps16 AAAGCCGAGTACTCTACCGT GGGATTTTTACGGAATTAAGTCTT 744 0.250 10.0
trnK-rps16_p4 trnK-rps16 AAGCCGAGTACTCTACCGTT GGGATTTTTACGGAATTAAGTCTT 743 0.250 10.0
trnK-rps16_p5 trnK-rps16 TACCGTTGAGTTAGCAACCC GGGATTTTTACGGAATTAAGTCT 730 0.250 10.0
trnT-trnR_p1 trnT-trnR AGCCTTCCAAGCTAACGATG TGATATTGCGTCCAATAGGA 282–324 1.000 54.9
trnT-trnR_p2 trnT-trnR ACCCTTAGCCTTCCAAGCTA TGATATTGCGTCCAATAGGA 288–330 1.000 54.8
trnT-trnR_p3 trnT-trnR CGACGTCGACTAAAACCCTT TGATATTGCGTCCAATAGGA 302–344 1.000 54.4
trnT-trnR_p4 trnT-trnR AAACCCTTAGCCTTCCAAGC TGATATTGCGTCCAATAGGA 290–332 1.000 54.4
trnT-trnR_p5 trnT-trnR AGCCTTCCAAGCTAACGATG TTGATATTGCGTCCAATAGGA 283–325 1.000 53.9
trnR-atpA_p1 trnR-atpA GGTTCAAATCCTATTGGACGC TGGAACGTTTTCTACTTCAGGA 301–357 1.000 51.8
trnR-atpA_p2 trnR-atpA GGTTCAAATCCTATTGGACGC CTGGAACGTTTTCTACTTCAGG 302–358 1.000 49.2
trnR-atpA_p3 trnR-atpA GGTTCAAATCCTATTGGACGC GGAACGTTTTCTACTTCAGGAGA 300–356 1.000 48.2
trnR-atpA_p4 trnR-atpA GGTTCAAATCCTATTGGACGC TGGAACGTTTTCTACTTCAGG 301–357 1.000 47.9
trnR-atpA_p5 trnR-atpA GGTTCAAATCCTATTGGACGC GGAACGTTTTCTACTTCAGGAG 300–356 1.000 47.2
atpF-atpH_p1 atpF-atpH ATTAAACCCGAAACTCCCGG TGGCCTGGTTGTAGCATTAG 580–581 1.000 78.0
atpF-atpH_p2 atpF-atpH CCAGTGACCCAAGTAAACGA TGGCCTGGTTGTAGCATTAG 553–554 1.000 74.8
atpF-atpH_p3 atpF-atpH ATTAAACCCGAAACTCCCGG TTTATGGCCTGGTTGTAGCA 584–585 1.000 74.3
atpF-atpH_p4 atpF-atpH ATTAAACCCGAAACTCCCGG GGCCTGGTTGTAGCATTAGC 579–580 1.000 73.6
atpF-atpH_p5 atpF-atpH GGCCAGTGACCCAAGTAAAC TGGCCTGGTTGTAGCATTAG 555–556 1.000 73.1
psbM-trnD_p1 psbM-trnD AGGAACGAGAATGAAGAGTGC TTCAATTGGTCAGAGCACCG 1116–1119 1.000 70.5
psbM-trnD_p2 psbM-trnD ACGAGAATGAAGAGTGCAGT TTCAATTGGTCAGAGCACCG 1112–1115 1.000 69.8
psbM-trnD_p3 psbM-trnD GGAACGAGAATGAAGAGTGCA TTCAATTGGTCAGAGCACCG 1115–1118 1.000 68.3
psbM-trnD_p4 psbM-trnD AACGAGAATGAAGAGTGCAGT TTCAATTGGTCAGAGCACCG 1113–1116 1.000 67.6
psbM-trnD_p5 psbM-trnD GGAACGAGAATGAAGAGTGC TTCAATTGGTCAGAGCACCG 1115–1118 1.000 67.1

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
Stenopetalum decipiens NC_069350.1 154423 View on NCBI ↗
Stenopetalum lineare MK637800.1 154508 View on NCBI ↗
Stenopetalum nutans NC_069360.1 153821 View on NCBI ↗
Stenopetalum velutinum NC_069340.1 154373 View on NCBI ↗