Markers + reference

Stegnosperma

2 species · Stegnospermataceae · Caryophyllales

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Species 2
Genome length 155–155 kb
Candidate markers 262
Primer pairs 80

Genome-wide nucleotide diversity

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

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 262 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 709 0.0183 0.93 63.9 yes View details
psbE-petL LSC 1154 0.0078 1.00 52.4 yes View details
rrn4.5-rrn5 IRb 256 0.0508 1.00 68.1 yes View details
rrn5-trnR-ACG IRb 256 0.0898 1.00 71.5 yes View details
ccsA SSC 975 0.0031 1.00 52.2 yes View details
rps15-ycf1 SSC 293 0.0444 1.00 78.0 yes View details
trnR-ACG-rrn5 IRa 256 0.0898 1.00 71.5 yes View details
rrn5-rrn4.5 IRa 256 0.0508 1.00 68.1 yes View details
ccsA-ndhD SSC 195 0.0564 1.00 73.8 yes View details
rpoC1-rpoB LSC 32 0.0312 1.00 70.5 yes View details
rrn5 IRb 120 0.0750 1.00 69.4 yes View details
rrn5 IRa 120 0.0750 1.00 69.4 yes View details
trnR-ACG IRb 74 0.0676 1.00 68.7 yes View details
trnR-ACG IRa 74 0.0676 1.00 68.7 yes View details
rpl22-rps19 LSC 36 0.0278 1.00 68.5 yes View details
trnP-UGG-psaJ LSC 437 0.0048 0.95 62.9 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 80 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps16-trnQ-UUG_p1 rps16-trnQ-UUG GTTCTTCAAGTCGCACGTTG GAGGTTCGAATCCTTCCGTC 744–789 1.000 84.6
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GTTCTTCAAGTCGCACGTTG TAAGGCATCGGGTTTTGGTC 774–819 1.000 83.8
rps16-trnQ-UUG_p3 rps16-trnQ-UUG ATGTTCTTCAAGTCGCACGT GAGGTTCGAATCCTTCCGTC 746–791 1.000 83.6
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 737–782 1.000 83.5
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CATGTTCTTCAAGTCGCACG GAGGTTCGAATCCTTCCGTC 747–792 1.000 82.9
rpoC1-rpoB_p1 rpoC1-rpoB TGGCCCAAGCACTTATTTGT ACGATCTTTGGCTCTGGAAC 181 1.000 79.6
rpoC1-rpoB_p2 rpoC1-rpoB TGTGGCCCAAGCACTTATTT ACGATCTTTGGCTCTGGAAC 183 1.000 79.6
rpoC1-rpoB_p3 rpoC1-rpoB TTGTGGCCCAAGCACTTATT ACGATCTTTGGCTCTGGAAC 184 1.000 79.6
rpoC1-rpoB_p4 rpoC1-rpoB TTTGTGGCCCAAGCACTTAT ACGATCTTTGGCTCTGGAAC 185 1.000 79.6
rpoC1-rpoB_p5 rpoC1-rpoB GGTAGGATTTTTGTGGCCCA ACGATCTTTGGCTCTGGAAC 194 1.000 79.1
psbE-petL_p1 psbE-petL CAACCCGCAATGAATAGGGA GAGGTTATAGTTAAAGCCGCT 1314–1319 1.000 52.1
psbE-petL_p2 psbE-petL AGAACGTTCTCCTGTGCTTC GAGGTTATAGTTAAAGCCGCT 1237–1242 1.000 51.3
psbE-petL_p3 psbE-petL ACGAATAACCAACCCGCAAT GAGGTTATAGTTAAAGCCGCT 1323–1328 1.000 51.1
psbE-petL_p4 psbE-petL TGCTGACGAATAACCAACCC GAGGTTATAGTTAAAGCCGCT 1328–1333 1.000 51.0
psbE-petL_p5 psbE-petL CGAATAACCAACCCGCAATG GAGGTTATAGTTAAAGCCGCT 1322–1327 1.000 51.0
trnP-UGG-psaJ_p1 trnP-UGG-psaJ ACCCGTGACATTTTGTACCC TGTCAACGCATCTGGGAAAA 585–606 1.000 82.2
trnP-UGG-psaJ_p2 trnP-UGG-psaJ CCCGTGACATTTTGTACCCA TGTCAACGCATCTGGGAAAA 584–605 1.000 82.2
trnP-UGG-psaJ_p3 trnP-UGG-psaJ ACAGGATTTGAACCCGTGAC TGTCAACGCATCTGGGAAAA 596–617 1.000 82.1
trnP-UGG-psaJ_p4 trnP-UGG-psaJ CAGGATTTGAACCCGTGACA TGTCAACGCATCTGGGAAAA 595–616 1.000 82.1
trnP-UGG-psaJ_p5 trnP-UGG-psaJ TGACAGGATTTGAACCCGTG TGTCAACGCATCTGGGAAAA 598–619 1.000 82.1
rpl22-rps19_p1 rpl22-rps19 TACTCGTCGTGCTTTGTGAG CACCGACTCTAAACTTCCGG 197 1.000 80.0
rpl22-rps19_p2 rpl22-rps19 TACTCGTCGTGCTTTGTGAG GGAGAATTTGCACCGACTCT 207 1.000 79.2
rpl22-rps19_p3 rpl22-rps19 TACTCGTCGTGCTTTGTGAG ACGGATCGTATGGTAGGTCA 234 1.000 77.1
rpl22-rps19_p4 rpl22-rps19 TACTCGTCGTGCTTTGTGAG TGCACCGACTCTAAACTTCC 199 1.000 76.4
rpl22-rps19_p5 rpl22-rps19 TTACTCGTCGTGCTTTGTGA CACCGACTCTAAACTTCCGG 198 1.000 76.4
rrn4.5-rrn5_p1 rrn4.5-rrn5 CCTAACAGACCGATAGACTTGA ACGCCTAGGACACCAGAATA 300 1.000 56.2
rrn4.5-rrn5_p2 rrn4.5-rrn5 CCTAACAGACCGATAGACTTGA TACGCCTAGGACACCAGAAT 301 1.000 56.2
rrn4.5-rrn5_p3 rrn4.5-rrn5 CCTAACAGACCGATAGACTTGA GTTCCTCTACGCCTAGGACA 308 1.000 55.5
rrn4.5-rrn5_p4 rrn4.5-rrn5 CCTAACAGACCGATAGACTTGA TTCCTCTACGCCTAGGACAC 307 1.000 55.5
rrn4.5-rrn5_p5 rrn4.5-rrn5 ACAGACCGATAGACTTGAAC ACGCCTAGGACACCAGAATA 296 1.000 54.6

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
Stegnosperma cubense NC_040942.1 155272 View on NCBI ↗
Stegnosperma halimifolium NC_041235.1 155485 View on NCBI ↗