Markers + reference

Wisteriopsis

2 species · Fabaceae · Fabales

Back to catalogue

Species 2
Genome length 133–133 kb
Candidate markers 226
Primer pairs 80

Genome-wide nucleotide diversity

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

Candidate markers

7 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 226 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnG-GCC-psbZ Genome 814 0.0025 1.00 57.8 yes View details
atpI-atpH Genome 1418 0.0014 1.00 59.6 yes View details
ycf4 Genome 639 0.0016 1.00 46.7 yes View details
ycf4-cemA Genome 334 0.0269 1.00 68.7 yes View details
petA Genome 963 0.0010 1.00 47.4 yes View details
psbE-petL Genome 1522 0.0013 1.00 59.5 yes View details
ndhF Genome 2235 0.0009 1.00 49.6 yes View details
ndhF-trnH-GUG Genome 233 0.0043 1.00 70.4 no View details
ycf1-rps15 Genome 491 0.0000 0.96 60.4 yes View details
rbcL-atpB Genome 782 0.0013 1.00 59.6 yes View details
rps3 Genome 654 0.0015 1.00 59.6 yes View details
matK Genome 1521 0.0013 1.00 59.5 yes View details
matK-trnK-UUU Genome 729 0.0014 1.00 59.5 yes View details
trnT-GGU-trnE-UUC Genome 820 0.0012 1.00 59.5 yes View details
psbK-trnQ-UUG Genome 719 0.0014 1.00 59.5 yes View details
rpl32-ndhF Genome 769 0.0013 1.00 59.5 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 80 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU_p1 trnK-UUU AGAAATGACTTCGCTATGAT TGCGATTGGATATACACATCCT 2731 1.000 40.1
trnK-UUU_p2 trnK-UUU ACCTCATTTCATCATTCATTCA TGCGATTGGATATACACATCCT 2780–2781 1.000 40.1
trnK-UUU_p3 trnK-UUU AGAAATGACTTCGCTATGAT TTGCGATTGGATATACACATCCT 2732 1.000 40.1
trnK-UUU_p4 trnK-UUU AGAAATGACTTCGCTATGAT TGCGATTGGATATACACATCC 2731 1.000 40.1
trnK-UUU_p5 trnK-UUU ACCTCATTTCATCATTCATTCAA TGCGATTGGATATACACATCCT 2780–2781 1.000 40.1
matK_p1 matK ACAAAGTCTCATAACATAACCA CCTTGTTTTGACTGTATCGCA 1625 1.000 40.1
matK_p2 matK ACAAAGTCTCATAACATAACCA ACCTTGTTTTGACTGTATCGC 1626 1.000 40.1
matK_p3 matK ACAAAGTCTCATAACATAACCA CCTTGTTTTGACTGTATCGCAC 1625 1.000 40.1
matK_p4 matK ACAAAGTCTCATAACATAACCAA CCTTGTTTTGACTGTATCGCA 1625 1.000 40.1
matK_p5 matK ACAAAGTCTCATAACATAACCAA ACCTTGTTTTGACTGTATCGC 1626 1.000 40.1
matK-trnK-UUU_p1 matK-trnK-UUU AGTCCTGTTGGCGAGATCTA TCAATGGTAGAGTACTCGGCT 807 1.000 70.8
matK-trnK-UUU_p2 matK-trnK-UUU GAAGTCCTGTTGGCGAGATC TCAATGGTAGAGTACTCGGCT 809 1.000 69.2
matK-trnK-UUU_p3 matK-trnK-UUU AGTCCTGTTGGCGAGATCTA AGGGTTGCTAACTCAATGGT 819 1.000 68.7
matK-trnK-UUU_p4 matK-trnK-UUU AGTCCTGTTGGCGAGATCTA CTCAATGGTAGAGTACTCGGC 808 1.000 68.1
matK-trnK-UUU_p5 matK-trnK-UUU GAAGTCCTGTTGGCGAGATC AGGGTTGCTAACTCAATGGT 821 1.000 67.1
rbcL-atpB_p1 rbcL-atpB AACACCAGCTTTGAACCCAA GGCGATACGTCCCAGATTTT 904–905 1.000 78.6
rbcL-atpB_p2 rbcL-atpB AACACCAGCTTTGAACCCAA CCTGGGGGAAAAGCTACATC 945–946 1.000 78.6
rbcL-atpB_p3 rbcL-atpB AACACCAGCTTTGAACCCAA GGACCGATTATTTGGGCGAT 918–919 1.000 78.2
rbcL-atpB_p4 rbcL-atpB GCTTTGAACCCAACACTTGC GGCGATACGTCCCAGATTTT 897–898 1.000 76.3
rbcL-atpB_p5 rbcL-atpB GCTTTGAACCCAACACTTGC CCTGGGGGAAAAGCTACATC 938–939 1.000 76.3
trnG-GCC-psbZ_p1 trnG-GCC-psbZ CGTCTTCTCCTTGGCAAAGA CTTCTCCTGATGGTTGGTCG 968 1.000 78.7
trnG-GCC-psbZ_p2 trnG-GCC-psbZ TACATAAAAAGGCAGGGGCG CTTCTCCTGATGGTTGGTCG 1008 1.000 78.1
trnG-GCC-psbZ_p3 trnG-GCC-psbZ CGTCTTCTCCTTGGCAAAGA TTGCTTCTCCTGATGGTTGG 971 1.000 77.2
trnG-GCC-psbZ_p4 trnG-GCC-psbZ CGTCTTCTCCTTGGCAAAGA TCCTGATGGTTGGTCGAGTA 964 1.000 77.0
trnG-GCC-psbZ_p5 trnG-GCC-psbZ CGTCTTCTCCTTGGCAAAGA GCTTCTCCTGATGGTTGGTC 969 1.000 76.8
trnT-GGU-trnE-UUC_p1 trnT-GGU-trnE-UUC GAACCGATGACTTACGCCTT TTTCGTAGTACCCTACCCCC 961–962 1.000 78.8
trnT-GGU-trnE-UUC_p2 trnT-GGU-trnE-UUC GGCGTTACTCTACCACACTG TTTCGTAGTACCCTACCCCC 936–937 1.000 78.7
trnT-GGU-trnE-UUC_p3 trnT-GGU-trnE-UUC GAACCGATGACTTACGCCTT CGTTGCCTCCTTGAAAGAGA 924–925 1.000 78.7
trnT-GGU-trnE-UUC_p4 trnT-GGU-trnE-UUC GGCGTTACTCTACCACACTG CGTTGCCTCCTTGAAAGAGA 899–900 1.000 78.7
trnT-GGU-trnE-UUC_p5 trnT-GGU-trnE-UUC CCATGGCGTTACTCTACCAC TTTCGTAGTACCCTACCCCC 940–941 1.000 78.3

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
Wisteriopsis japonica NC_061959.1 132547 View on NCBI ↗
Wisteriopsis reticulata NC_062691.1 132546 View on NCBI ↗