Markers + reference

Adansonia

9 species · Malvaceae · Malvales

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Species 9
Genome length 160–161 kb
Candidate markers 272
Primer pairs 95

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 9 remaining regions by MarkerSeek score (out of 272 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 507 0.0146 1.00 58.6 yes View details
trnS-GCU-trnG-GCC LSC 803 0.0103 1.00 65.0 yes View details
trnG-GCC-trnR-UCU LSC 184 0.0245 1.00 48.0 yes View details
psbZ-trnG-UCC LSC 847 0.0131 0.93 64.6 yes View details
atpB-rbcL LSC 1032 0.0079 0.99 55.1 yes View details
accD-psaI LSC 742 0.0072 1.00 42.7 yes View details
clpP LSC 2163 0.0059 0.99 60.4 yes View details
rpl32-trnL-UAG SSC 846 0.0071 1.00 56.8 yes View details
ccsA-ndhD SSC 297 0.0232 1.00 47.5 yes View details
ycf1-ndhF SSC 67 0.0506 1.00 79.1 yes View details
trnT-UGU-trnL-UAA LSC 987 0.0053 1.00 66.4 yes View details
petA-psbJ LSC 1057 0.0043 1.00 61.1 yes View details
ycf4-cemA LSC 984 0.0033 1.00 59.9 yes View details
ycf3-trnS-GGA LSC 967 0.0040 0.99 59.8 yes View details
ndhC-trnV-UAC LSC 1226 0.0080 0.98 58.9 yes View details
rps19-rpl2 IRb 90 0.0133 0.98 56.0 yes View details
atpH-atpI LSC 1203 0.0036 1.00 54.4 yes View details
ndhF-rpl32 SSC 1230 0.0056 0.99 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 573–597 1.000 83.9
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TTCCCTCTAGACCTAGCTGC 587–611 1.000 83.7
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TTCCCTCTAGACCTAGCTGC 586–610 1.000 83.7
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TTCCCTCTAGACCTAGCTGC 588–612 1.000 83.7
trnH-GUG-psbA_p5 trnH-GUG-psbA CGCATGGTGGATTCACAATC TTCCCTCTAGACCTAGCTGC 602–626 1.000 80.8
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA ATGAATCAAACCGAGGGACC 736–919 1.000 83.7
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC ATGAATCAAACCGAGGGACC 735–918 1.000 83.7
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC CGCACAACGGATTAGCAATC ATGAATCAAACCGAGGGACC 751–934 1.000 83.0
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC ACGGAAAGAGAGGGATTCGA ATGAATCAAACCGAGGGACC 790–973 1.000 82.4
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC TCGCACAACGGATTAGCAAT ATGAATCAAACCGAGGGACC 752–935 1.000 81.6
trnG-GCC_p1 trnG-GCC CCAATTCCCCTGTTCGACAA TCAAATAGATAGAATTCGAATATCG 881–902 1.000 42.6
trnG-GCC_p2 trnG-GCC ATTCCCCTGTTCGACAAAGG TCAAATAGATAGAATTCGAATATCG 878–899 1.000 42.6
trnG-GCC_p3 trnG-GCC TTGATTACGCCCAATTCCCC TCAAATAGATAGAATTCGAATATCG 891–912 1.000 42.6
trnG-GCC_p4 trnG-GCC CCAATTCCCCTGTTCGACAA TTCAAATAGATAGAATTCGAATATCG 882–903 1.000 42.6
trnG-GCC_p5 trnG-GCC ATTCCCCTGTTCGACAAAGG TTCAAATAGATAGAATTCGAATATCG 879–900 1.000 42.6
trnG-GCC-trnR-UCU_p1 trnG-GCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 264–270 1.000 66.7
trnG-GCC-trnR-UCU_p2 trnG-GCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 267–273 1.000 66.4
trnG-GCC-trnR-UCU_p3 trnG-GCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 270–276 1.000 65.9
trnG-GCC-trnR-UCU_p4 trnG-GCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 273–279 1.000 65.7
trnG-GCC-trnR-UCU_p5 trnG-GCC-trnR-UCU CCCTAGCCTTCCAAGCTAAC AGAAGACCTCTGTCCTATCCA 268–274 1.000 64.2
atpH-atpI_p1 atpH-atpI AATAGAAGCAAGCCCGACAG TTTTGCAACTTTAGCTGCGG 1320–1332 1.000 79.9
atpH-atpI_p2 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTGCAACTTTAGCTGCGG 1286–1298 1.000 79.9
atpH-atpI_p3 atpH-atpI AATAGAAGCAAGCCCGACAG CGAATCCATGGAGGGTCATC 1290–1302 1.000 79.6
atpH-atpI_p4 atpH-atpI ATAACGGAAGCGGCAGAAAT CGAATCCATGGAGGGTCATC 1256–1268 1.000 79.6
atpH-atpI_p5 atpH-atpI TACCTTGACCAACTCCAGGT TTTTGCAACTTTAGCTGCGG 1342–1354 1.000 79.2
psbZ-trnG-UCC_p1 psbZ-trnG-UCC TTGCTTCTCCTGATGGTTGG CGTCTTCTCCTTGGCAAAGA 827–1004 1.000 83.6
psbZ-trnG-UCC_p2 psbZ-trnG-UCC GCTTCTCCTGATGGTTGGTT CGTCTTCTCCTTGGCAAAGA 825–1002 1.000 83.6
psbZ-trnG-UCC_p3 psbZ-trnG-UCC TTGCTTCTCCTGATGGTTGG TACATTGTCCTGGGCGGATA 863–1040 1.000 83.2
psbZ-trnG-UCC_p4 psbZ-trnG-UCC GCTTCTCCTGATGGTTGGTT TACATTGTCCTGGGCGGATA 861–1038 1.000 83.2
psbZ-trnG-UCC_p5 psbZ-trnG-UCC TTGCTTCTCCTGATGGTTGG AAATACATTGTCCTGGGCGG 866–1043 1.000 83.0

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
Adansonia digitata MT052998.1 160068 View on NCBI ↗
Adansonia grandidieri MT052999.1 160094 View on NCBI ↗
Adansonia gregorii MT053000.1 159891 View on NCBI ↗
Adansonia kilima MT053001.1 160072 View on NCBI ↗
Adansonia madagascariensis MT053002.1 160230 View on NCBI ↗
Adansonia perrieri MT053003.1 159710 View on NCBI ↗
Adansonia rubrostipa MT053004.1 160322 View on NCBI ↗
Adansonia suarezensis MT053005.1 160621 View on NCBI ↗
Adansonia za MT053006.1 160449 View on NCBI ↗