Markers + reference

Canavalia

4 species · Fabaceae · Fabales

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Species 4
Genome length 158–159 kb
Candidate markers 281
Primer pairs 95

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 281 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rbcL LSC 1010 0.0055 0.97 64.8 yes View details
trnL-UAA-trnT-UGU LSC 1577 0.0020 0.97 63.3 yes View details
trnG-GCC-psbZ LSC 620 0.0056 0.98 61.8 yes View details
trnQ-UUG-psbK LSC 540 0.0107 0.97 69.5 yes View details
atpF-atpH LSC 469 0.0114 0.94 67.9 yes View details
rpoB-trnC-GCA LSC 1131 0.0032 1.00 61.2 yes View details
trnP-UGG-psaJ LSC 468 0.0058 0.93 63.8 yes View details
psaJ-rpl33 LSC 493 0.0078 1.00 52.2 yes View details
rpl32-trnL-UAG SSC 465 0.0068 1.00 61.3 yes View details
ndhD SSC 1497 0.0000 1.00 28.8 yes View details
psbD-trnT-GGU LSC 1433 0.0009 1.00 64.1 yes View details
psbM-trnQ-UUG LSC 980 0.0024 0.99 61.8 yes View details
petA-psbJ LSC 407 0.0029 0.98 61.8 yes View details
ycf3-psaA LSC 737 0.0023 0.99 60.0 yes View details
trnG-UCC-trnR-UCU LSC 270 0.0000 0.95 56.8 yes View details
trnS-GCU-trnG-UCC LSC 349 0.0033 1.00 56.4 yes View details
ndhG-ndhI SSC 297 0.0017 0.99 55.7 yes View details
ndhA SSC 2360 0.0004 1.00 54.7 yes View details
trnC-GCA-petN LSC 830 0.0032 1.00 51.7 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
trnK-UUU-rbcL_p1 trnK-UUU-rbcL AGTCGCTCTTAAAAGCCGAG AGTCCTGAATTAGCTGCTGC 1107–1188 1.000 82.2
trnK-UUU-rbcL_p2 trnK-UUU-rbcL AGTCGCTCTTAAAAGCCGAG GAGGCTAGCAAATGGAGTCC 1122–1203 1.000 82.1
trnK-UUU-rbcL_p3 trnK-UUU-rbcL GAGTCGCTCTTAAAAGCCGA AGTCCTGAATTAGCTGCTGC 1108–1189 1.000 82.1
trnK-UUU-rbcL_p4 trnK-UUU-rbcL GAGTCGCTCTTAAAAGCCGA GAGGCTAGCAAATGGAGTCC 1123–1204 1.000 82.1
trnK-UUU-rbcL_p5 trnK-UUU-rbcL TGGAGTCGCTCTTAAAAGCC AGTCCTGAATTAGCTGCTGC 1110–1191 1.000 81.4
trnL-UAA-trnT-UGU_p1 trnL-UAA-trnT-UGU ACCAATTTCGCCATATCCCC GCGATGCTCTAACCTCTGAG 1588–1677 1.000 81.8
trnL-UAA-trnT-UGU_p2 trnL-UAA-trnT-UGU TAGCGTCTACCAATTTCGCC GCGATGCTCTAACCTCTGAG 1596–1685 1.000 81.3
trnL-UAA-trnT-UGU_p3 trnL-UAA-trnT-UGU ACCAATTTCGCCATATCCCC GGAATCGAACCGATGACCAT 1620–1709 1.000 80.9
trnL-UAA-trnT-UGU_p4 trnL-UAA-trnT-UGU ACCAATTTCGCCATATCCCC AGAAAATCGAGGAAAGCCGG 1645–1734 1.000 80.7
trnL-UAA-trnT-UGU_p5 trnL-UAA-trnT-UGU TAGCGTCTACCAATTTCGCC GGAATCGAACCGATGACCAT 1628–1717 1.000 80.3
ycf3-psaA_p1 ycf3-psaA AGCCCTTACCCCTGGTAATT GAGAAATGACCGGGTTTTGC 890–902 1.000 79.0
ycf3-psaA_p2 ycf3-psaA AGCTATAGCCCTTACCCCTG GAGAAATGACCGGGTTTTGC 896–908 1.000 78.7
ycf3-psaA_p3 ycf3-psaA TTGGTTGAAGATCACAGGGC GAGAAATGACCGGGTTTTGC 854–866 1.000 78.4
ycf3-psaA_p4 ycf3-psaA TGGTTTAATCAAGCCGCTGA GAGAAATGACCGGGTTTTGC 928–940 1.000 77.4
ycf3-psaA_p5 ycf3-psaA AGATCACAGGGCGTTTTGAA GAGAAATGACCGGGTTTTGC 846–858 1.000 76.9
trnG-GCC-psbZ_p1 trnG-GCC-psbZ CGTCTTCTCCTTGGCAAAGA CTTCTCCTGATGGTTGGTCG 727–774 1.000 82.9
trnG-GCC-psbZ_p2 trnG-GCC-psbZ CGTCTTCTCCTTGGCAAAGA TTGCTTCTCCTGATGGTTGG 730–777 1.000 81.4
trnG-GCC-psbZ_p3 trnG-GCC-psbZ CGTCTTCTCCTTGGCAAAGA TCCTGATGGTTGGTCGAGTA 723–770 1.000 81.3
trnG-GCC-psbZ_p4 trnG-GCC-psbZ CGTCTTCTCCTTGGCAAAGA GCTTCTCCTGATGGTTGGTC 728–775 1.000 81.0
trnG-GCC-psbZ_p5 trnG-GCC-psbZ CGTCTTCTCCTTGGCAAAGA TTCTCCTGATGGTTGGTCGA 726–773 1.000 80.2
psbD-trnT-GGU_p1 psbD-trnT-GGU CACAAAAACGAAACGGTCCC GTGGTAGAGTAACGCCATGG 1335–1587 1.000 82.2
psbD-trnT-GGU_p2 psbD-trnT-GGU CCACAAAAACGAAACGGTCC GTGGTAGAGTAACGCCATGG 1336–1588 1.000 82.2
psbD-trnT-GGU_p3 psbD-trnT-GGU CCCACAAAAACGAAACGGTC GTGGTAGAGTAACGCCATGG 1337–1589 1.000 82.2
psbD-trnT-GGU_p4 psbD-trnT-GGU CACAAAAACGAAACGGTCCC TCAGTGGTAGAGTAACGCCA 1338–1590 1.000 82.1
psbD-trnT-GGU_p5 psbD-trnT-GGU CCACAAAAACGAAACGGTCC TCAGTGGTAGAGTAACGCCA 1339–1591 1.000 82.1
psbM-trnQ-UUG_p1 psbM-trnQ-UUG TCATTCTAGTTCCGACTGCC TAAGGCAACGGGTTTTGGTC 1088–1099 1.000 68.2
psbM-trnQ-UUG_p2 psbM-trnQ-UUG CATTCTAGTTCCGACTGCCT TAAGGCAACGGGTTTTGGTC 1087–1098 1.000 68.1
psbM-trnQ-UUG_p3 psbM-trnQ-UUG TCATTCTAGTTCCGACTGCC TGTCAAGTCGAAATTGGGGC 1120–1131 1.000 67.5
psbM-trnQ-UUG_p4 psbM-trnQ-UUG CATTCTAGTTCCGACTGCCT TGTCAAGTCGAAATTGGGGC 1119–1130 1.000 67.5
psbM-trnQ-UUG_p5 psbM-trnQ-UUG TCATTCTAGTTCCGACTGCC GGGTTTTGGTCCCGCTATTC 1079–1090 1.000 66.4

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (4)

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

Species Accession Length (bp) Link
Canavalia cathartica NC_047311.1 158223 View on NCBI ↗
Canavalia gladiata NC_050951.1 157923 View on NCBI ↗
Canavalia rosea LC554221.1 158059 View on NCBI ↗
Canavalia villosa MW628947.1 158532 View on NCBI ↗