Markers + reference

Hibiscus

9 species · Malvaceae · Malvales

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Species 9
Genome length 160–163 kb
Candidate markers 265
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

9 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
trnK-UUU-rps16 LSC 850 0.0491 0.96 77.8 yes View details
rps4-trnT-UGU LSC 641 0.0656 0.88 79.3 yes View details
trnT-UGU-trnL-UAA LSC 919 0.0444 0.91 74.6 yes View details
ndhC-trnV-UAC LSC 1346 0.0461 0.95 82.1 yes View details
atpB-rbcL LSC 1139 0.0391 0.94 77.4 yes View details
petA-psbJ LSC 1085 0.0552 0.92 80.6 yes View details
trnN-GUU-ndhF IRb 1605 0.0816 0.85 77.4 yes View details
ndhF-rpl32 SSC 1176 0.0769 0.77 76.3 yes View details
rpl2-psbA LSC 550 0.0829 0.74 76.2 no View details
rps16-trnQ-UUG LSC 584 0.0470 0.95 85.5 yes View details
psbZ-trnG-GCC LSC 599 0.0524 0.93 85.3 yes View details
trnS-GCU-trnG-UCC LSC 925 0.0426 0.97 81.5 yes View details
psbK-psbI LSC 439 0.0343 0.99 78.8 yes View details
trnR-UCU-atpA LSC 159 0.0710 0.99 78.7 yes View details
ccsA-ndhD SSC 306 0.0602 0.97 77.7 yes View details
rpl32-trnL-UAG SSC 1170 0.0401 0.96 77.4 yes View details
trnD-GUC-trnY-GUA LSC 512 0.0265 0.97 74.0 yes View details
rpl33-rps18 LSC 473 0.0458 0.81 73.4 yes View details
psaA-pafI LSC 911 0.0271 0.98 73.2 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 ATCCACCCCTTTCAGGATCA CCCAATGAGCCGTTTATCGA 1058–1293 1.000 91.5
trnK-UUU-rps16_p2 trnK-UUU-rps16 ATCCACCCCTTTCAGGATCA TCCCAATGAGCCGTTTATCG 1059–1294 1.000 91.5
trnK-UUU-rps16_p3 trnK-UUU-rps16 ATCCACCCCTTTCAGGATCA AAAAGGAGCTCAACCCACAG 919–1154 0.778 82.8
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCCTTTCAGGATCAGTCGTG AAAAGGAGCTCAACCCACAG 913–1148 0.778 82.8
trnK-UUU-rps16_p5 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG AAAAGGAGCTCAACCCACAG 912–1147 0.778 82.8
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CAGCCGATCATGTCCTTCAA GAGGTTCGAATCCTTCCGTC 579–693 1.000 91.2
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GCCGATCATGTCCTTCAAGT GAGGTTCGAATCCTTCCGTC 577–691 1.000 91.2
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 561–675 1.000 90.3
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 572–686 1.000 89.8
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AGCCGATCATGTCCTTCAAG GAGGTTCGAATCCTTCCGTC 578–692 1.000 88.8
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG GGATTACGTCCCGGATCATT 559–581 1.000 81.7
psbK-psbI_p2 psbK-psbI GTTTGGCAAGCTGCTGTAAG TTTTTATTCTTCGCGCCCAG 578–600 1.000 80.9
psbK-psbI_p3 psbK-psbI GTTTGGCAAGCTGCTGTAAG TTTTATTCTTCGCGCCCAGG 577–599 1.000 80.8
psbK-psbI_p4 psbK-psbI TGGCAAGCTGCTGTAAGTTT GGATTACGTCCCGGATCATT 556–578 1.000 79.7
psbK-psbI_p5 psbK-psbI TTGGCAAGCTGCTGTAAGTT GGATTACGTCCCGGATCATT 557–579 1.000 79.7
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA TACCACTAAACTATACCCGC 935–1032 1.000 59.9
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC TACCACTAAACTATACCCGC 934–1031 1.000 59.9
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA TTACCACTAAACTATACCCGC 936–1033 1.000 58.8
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC TTACCACTAAACTATACCCGC 935–1032 1.000 58.8
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA TTTACCACTAAACTATACCCGC 937–1034 1.000 57.1
trnR-UCU-atpA_p1 trnR-UCU-atpA AGCCTTCCAAGCTAACGATG CCAGGTCGTGAAGCTTATCC 1148–1244 1.000 85.8
trnR-UCU-atpA_p2 trnR-UCU-atpA AGCCTTCCAAGCTAACGATG GGTCGTGAAGCTTATCCAGG 1145–1241 1.000 85.8
trnR-UCU-atpA_p3 trnR-UCU-atpA CCTAGCCTTCCAAGCTAACG CCAGGTCGTGAAGCTTATCC 1151–1247 1.000 85.6
trnR-UCU-atpA_p4 trnR-UCU-atpA CCTAGCCTTCCAAGCTAACG GGTCGTGAAGCTTATCCAGG 1148–1244 1.000 85.5
trnR-UCU-atpA_p5 trnR-UCU-atpA AGCCTTCCAAGCTAACGATG GCTTTTGCGCAATTTGCTTC 809–905 0.778 78.0
trnD-GUC-trnY-GUA_p1 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA TGGCAATATGTCTACGCTGG 559–598 1.000 84.0
trnD-GUC-trnY-GUA_p2 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA GGCAATATGTCTACGCTGGT 558–597 1.000 84.0
trnD-GUC-trnY-GUA_p3 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA GGGGACGGACTGTAAATTCG 580–619 1.000 82.9
trnD-GUC-trnY-GUA_p4 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA GGGACGGACTGTAAATTCGT 579–618 1.000 82.7
trnD-GUC-trnY-GUA_p5 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA GATTCTTCCTGGGTCGATGC 613–652 1.000 82.1

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (9)

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

Species Accession Length (bp) Link
Hibiscus acetosella PX694240.1 163023 View on NCBI ↗
Hibiscus aridicola PX694256.1 160068 View on NCBI ↗
Hibiscus coccineus PX694236.1 160280 View on NCBI ↗
Hibiscus glanduliferus PX694248.1 161856 View on NCBI ↗
Hibiscus heterophyllus PX694268.1 160223 View on NCBI ↗
Hibiscus lobatus PX694241.1 161061 View on NCBI ↗
Hibiscus macilwraithensis PX694243.1 160549 View on NCBI ↗
Hibiscus sabdariffa PX694237.1 163121 View on NCBI ↗
Hibiscus surattensis PX694249.1 162256 View on NCBI ↗