Markers + reference

Sterculia

3 species · Malvaceae · Malvales

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Species 3
Genome length 160–163 kb
Candidate markers 267
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 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 826 0.0262 0.98 55.6 yes View details
trnS-GCU-trnG-UCC LSC 899 0.0379 0.92 63.1 yes View details
trnR-UCU-atpA LSC 298 0.0780 0.69 58.2 yes View details
psbZ-trnG-GCC LSC 1010 0.0448 0.77 64.6 yes View details
trnT-UGU-trnL-UAA LSC 1969 0.0382 0.50 49.3 yes View details
ndhC-trnV-UAC LSC 1389 0.0357 0.85 55.2 yes View details
atpB-rbcL LSC 921 0.0249 0.99 48.8 yes View details
trnN-GUU-ndhF IRb 565 0.1534 0.82 76.5 yes View details
ndhF-rpl32 SSC 1292 0.0270 0.46 44.3 yes View details
rpl2-trnH-GUG IRa 60 0.1111 1.00 68.0 no View details
petG-trnW-CCA LSC 141 0.0492 0.87 63.2 yes View details
pafI-trnS-GGA LSC 1006 0.0227 0.97 61.6 yes View details
rps19-rpl2 IRb 52 0.0897 1.00 61.3 yes View details
atpA-atpF LSC 87 0.0450 0.85 57.5 yes View details
trnD-GUC-trnY-GUA LSC 509 0.0280 0.98 55.7 yes View details
rpl14-rpl16 LSC 119 0.0226 0.99 55.1 yes View details
rpl32-trnL-UAG SSC 1092 0.0247 0.99 55.0 yes View details
ccsA SSC 972 0.0123 1.00 54.9 yes View details
psaI-pafII LSC 420 0.0134 0.95 53.5 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 AAAGCCGAGTACTCTACCGT AAAAGGAGCTCAACCCACAG 954–1047 1.000 82.1
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AAAAGGAGCTCAACCCACAG 953–1046 1.000 82.1
trnK-UUU-rps16_p3 trnK-UUU-rps16 TACCGTTGAGTTAGCAACCC AAAAGGAGCTCAACCCACAG 940–1033 1.000 79.8
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT CGGGGGTTTTTACGGAACTT 907–1000 1.000 79.2
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT CGGGGGTTTTTACGGAACTT 906–999 1.000 79.2
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA ACGAATCACACTTTTACCACT 903–968 1.000 59.7
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC ACGAATCACACTTTTACCACT 902–967 1.000 59.7
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CGCACAACGGATTAGCAATC ACGAATCACACTTTTACCACT 918–983 1.000 59.0
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA AGAACGAATCACACTTTTACCAC 906–971 1.000 58.7
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA GAACGAATCACACTTTTACCACT 905–970 1.000 58.7
trnR-UCU-atpA_p1 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC ACGCTATTCAGGAACAAATGGA 277–370 1.000 60.3
trnR-UCU-atpA_p2 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC TGAAAGACGCTATTCAGGAACA 283–376 1.000 58.4
trnR-UCU-atpA_p3 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC GACGCTATTCAGGAACAAATGG 278–371 1.000 58.4
trnR-UCU-atpA_p4 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC ACGCTATTCAGGAACAAATGG 277–370 1.000 57.5
trnR-UCU-atpA_p5 trnR-UCU-atpA TGGATAGGACAGAGGTCTTCT ACGCTATTCAGGAACAAATGGA 312–405 1.000 56.8
atpA-atpF_p1 atpA-atpF GCCCACTTGAAGTACGGTAC ATTGGCTTGTTTGGGGTGAT 221–234 1.000 83.3
atpA-atpF_p2 atpA-atpF CCCACTTGAAGTACGGTACC ATTGGCTTGTTTGGGGTGAT 220–233 1.000 82.6
atpA-atpF_p3 atpA-atpF TTGCTCAATACGTTCACGGA ATTGGCTTGTTTGGGGTGAT 170–183 1.000 82.5
atpA-atpF_p4 atpA-atpF TGCTCAATACGTTCACGGAT ATTGGCTTGTTTGGGGTGAT 169–182 1.000 80.8
atpA-atpF_p5 atpA-atpF GCCCACTTGAAGTACGGTAC GGCTTGTTTGGGGTGATGAA 218–231 1.000 78.2
trnD-GUC-trnY-GUA_p1 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA TGGCAATATGTCTACGCTGG 573–579 1.000 78.4
trnD-GUC-trnY-GUA_p2 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA GGCAATATGTCTACGCTGGT 572–578 1.000 78.4
trnD-GUC-trnY-GUA_p3 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA GGGGACGGACTGTAAATTCG 594–600 1.000 77.4
trnD-GUC-trnY-GUA_p4 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA GGGACGGACTGTAAATTCGT 593–599 1.000 77.2
trnD-GUC-trnY-GUA_p5 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA CGGACTGTAAATTCGTTGGC 589–595 1.000 76.1
psbZ-trnG-GCC_p1 psbZ-trnG-GCC TTTGCTTCCCCTGATGGTTG CGTCTTCTCCTTGGCAAAGA 964–1168 1.000 83.7
psbZ-trnG-GCC_p2 psbZ-trnG-GCC CTTCCCCTGATGGTTGGTTG CGTCTTCTCCTTGGCAAAGA 960–1164 1.000 83.1
psbZ-trnG-GCC_p3 psbZ-trnG-GCC TTCCCCTGATGGTTGGTTGA CGTCTTCTCCTTGGCAAAGA 959–1163 1.000 79.9
psbZ-trnG-GCC_p4 psbZ-trnG-GCC TTTGCTTCCCCTGATGGTTG TACCATTCGACCATATCCGC 937–1141 1.000 79.3
psbZ-trnG-GCC_p5 psbZ-trnG-GCC CTTCCCCTGATGGTTGGTTG TACCATTCGACCATATCCGC 933–1137 1.000 78.7

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

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

Species Accession Length (bp) Link
Sterculia foetida NC_088097.1 162637 View on NCBI ↗
Sterculia monosperma NC_053571.1 160178 View on NCBI ↗
Sterculia nobilis NC_063575.1 160177 View on NCBI ↗