Markers + reference

Zollernia

2 species · Fabaceae · Fabales

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Species 2
Genome length 155–156 kb
Candidate markers 262
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 262 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnG-GCC-psbZ LSC 751 0.0013 0.99 48.7 yes View details
psbM-petN LSC 1176 0.0017 1.00 59.7 yes View details
atpI-atpH LSC 1355 0.0100 0.81 65.2 yes View details
atpF LSC 1293 0.0015 1.00 47.7 yes View details
psbK-trnQ-UUG LSC 801 0.0025 1.00 58.4 yes View details
accD-psaI LSC 726 0.0041 1.00 54.4 yes View details
rpl16 LSC 1503 0.0013 1.00 59.5 yes View details
trnR-ACG-trnN-GUU IRb 643 0.0063 0.99 63.1 yes View details
ndhG-ndhI SSC 401 0.0075 1.00 58.9 yes View details
trnN-GUU-trnR-ACG IRa 643 0.0063 0.99 63.1 yes View details
atpF-atpA LSC 73 0.0137 1.00 60.4 yes View details
petA-psbJ LSC 1206 0.0017 1.00 59.7 yes View details
rpl32-trnL-UAG SSC 713 0.0014 1.00 59.6 yes View details
trnT-GGU-trnE-UUC LSC 802 0.0012 1.00 59.5 yes View details
rps11-rpl36 LSC 590 0.0017 1.00 59.5 yes View details
trnC-GCA-rpoB LSC 1046 0.0010 1.00 59.4 yes View details
trnG-UCC-trnS-GCU LSC 900 0.0011 1.00 59.4 yes View details
petA LSC 963 0.0010 1.00 59.3 yes View details
ccsA SSC 972 0.0010 1.00 59.3 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
trnG-GCC-psbZ_p1 trnG-GCC-psbZ CGTCTTCTCCTTGGCAAAGA TGGATTAGTCTTTCTAGTGGGT 839–844 1.000 46.5
trnG-GCC-psbZ_p2 trnG-GCC-psbZ CGTCTTCTCCTTGGCAAAGA TTGGATTAGTCTTTCTAGTGGGT 840–845 1.000 44.3
trnG-GCC-psbZ_p3 trnG-GCC-psbZ CGTCTTCTCCTTGGCAAAGA TGGATTAGTCTTTCTAGTGGG 839–844 1.000 40.6
trnG-GCC-psbZ_p4 trnG-GCC-psbZ CGTCTTCTCCTTGGCAAAGA GGATTAGTCTTTCTAGTGGGT 838–843 1.000 40.6
trnG-GCC-psbZ_p5 trnG-GCC-psbZ CGTCTTCTCCTTGGCAAAGA TTGGATTAGTCTTTCTAGTGGG 840–845 1.000 40.6
trnT-GGU-trnE-UUC_p1 trnT-GGU-trnE-UUC GAACCGATGACTTACGCCTT TTTCGTAGTACCCTACCCCC 943 1.000 78.8
trnT-GGU-trnE-UUC_p2 trnT-GGU-trnE-UUC CCATGGCGTTACTCTACCAC TTTCGTAGTACCCTACCCCC 922 1.000 78.3
trnT-GGU-trnE-UUC_p3 trnT-GGU-trnE-UUC TGGCGTTACTCTACCACTGA TTTCGTAGTACCCTACCCCC 919 1.000 78.1
trnT-GGU-trnE-UUC_p4 trnT-GGU-trnE-UUC GAACCGATGACTTACGCCTT GCTGCCTCCTTGAAAGAGAG 905 1.000 77.9
trnT-GGU-trnE-UUC_p5 trnT-GGU-trnE-UUC GAACCGATGACTTACGCCTT TGTCCTGAACCACTAGACGA 884 1.000 77.8
psbM-petN_p1 psbM-petN TGCTACTGCACTGTTCATTCT TCTTGCTTGGGCTGCTTTAA 1331 1.000 68.8
psbM-petN_p2 psbM-petN TGCTACTGCACTGTTCATTCT AGTAAGTCTTGCTTGGGCTG 1337 1.000 67.3
psbM-petN_p3 psbM-petN TGCTACTGCACTGTTCATTCT ATGGGGAAGAAGTGGACTCT 1277 1.000 66.1
psbM-petN_p4 psbM-petN TGCTACTGCACTGTTCATTCT CCCTCGTAGTATGGGGAAGA 1287 1.000 65.9
psbM-petN_p5 psbM-petN TGCTACTGCACTGTTCATTCT TCCCTCGTAGTATGGGGAAG 1288 1.000 65.9
trnC-GCA-rpoB_p1 trnC-GCA-rpoB CCGGATTTGAACTGGGGAAA TAAGCCCCGATCAATGAACC 1201–1202 1.000 76.7
trnC-GCA-rpoB_p2 trnC-GCA-rpoB CTCTTGTTGATCAGGCGACA TAAGCCCCGATCAATGAACC 1222–1223 1.000 76.7
trnC-GCA-rpoB_p3 trnC-GCA-rpoB CCGGATTTGAACTGGGGAAA GCCCCGATCAATGAACCTAC 1198–1199 1.000 76.2
trnC-GCA-rpoB_p4 trnC-GCA-rpoB CTCTTGTTGATCAGGCGACA GCCCCGATCAATGAACCTAC 1219–1220 1.000 76.2
trnC-GCA-rpoB_p5 trnC-GCA-rpoB TCTTGTTGATCAGGCGACAC TAAGCCCCGATCAATGAACC 1221–1222 1.000 75.8
atpI-atpH_p1 atpI-atpH GCTGCGGCTTATATAGGTGA CGCAATCCCTTCTACAGCTT 1258–1517 1.000 78.4
atpI-atpH_p2 atpI-atpH GCTGCGGCTTATATAGGTGA ATAACGGAAGCGGCAGAAAT 1170–1429 1.000 78.4
atpI-atpH_p3 atpI-atpH ACAAGCGGTATTCAAGCTCT CGCAATCCCTTCTACAGCTT 1294–1553 1.000 78.2
atpI-atpH_p4 atpI-atpH ACAAGCGGTATTCAAGCTCT ATAACGGAAGCGGCAGAAAT 1206–1465 1.000 78.2
atpI-atpH_p5 atpI-atpH GCTGCGGCTTATATAGGTGA AATAACGGAAGCGGCAGAAA 1171–1430 1.000 77.3
atpF_p1 atpF TCCATAAGAGGAGATGAGATCA GCCTATACTCTATACTATAATAGAAGG 1344 1.000 40.1
atpF_p2 atpF ATCCATAAGAGGAGATGAGATCA GCCTATACTCTATACTATAATAGAAGG 1345 1.000 40.1
atpF_p3 atpF TCCATAAGAGGAGATGAGATCAT GCCTATACTCTATACTATAATAGAAGG 1344 1.000 40.1
atpF_p4 atpF AGTCTATCCATAAGAGGAGATGAGA GCCTATACTCTATACTATAATAGAAGG 1350 1.000 40.1
atpF_p5 atpF CCATAAGAGGAGATGAGATCA GCCTATACTCTATACTATAATAGAAGG 1343 1.000 40.1

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
Zollernia ilicifolia MW628959.1 155528 View on NCBI ↗
Zollernia splendens NC_047395.1 155371 View on NCBI ↗