Markers + reference

Glycine

11 species · Fabaceae · Fabales

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Species 11
Genome length 152–153 kb
Candidate markers 263
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 263 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rbcL LSC 1031 0.0279 0.99 72.7 yes View details
ndhJ-trnF-GAA LSC 692 0.0258 1.00 64.3 yes View details
trnT-GGU-trnE-UUC LSC 837 0.0264 0.99 73.8 yes View details
petN-trnC-GCA LSC 1072 0.0248 1.00 62.4 yes View details
trnQ-UUG-rps16 LSC 483 0.0307 1.00 67.2 yes View details
accD LSC 1527 0.0260 1.00 63.6 yes View details
rpl20 LSC 393 0.0161 1.00 40.5 yes View details
rps3-rps19 LSC 351 0.0358 1.00 67.5 yes View details
ycf1 SSC 5367 0.0215 1.00 52.5 yes View details
ycf1-rps15 SSC 416 0.0274 1.00 58.0 yes View details
ndhF SSC 2262 0.0157 1.00 52.5 yes View details
ycf1 IRa 471 0.0087 1.00 39.1 no View details
trnL-UAG-rpl32 SSC 285 0.0301 1.00 71.2 yes View details
atpI-atpH LSC 1090 0.0179 1.00 70.7 yes View details
petA-psbJ LSC 890 0.0236 1.00 70.6 yes View details
ndhD-ccsA SSC 258 0.0364 1.00 68.4 yes View details
trnG-GCC-psbZ LSC 709 0.0228 1.00 68.2 yes View details
rps18-rpl20 LSC 220 0.0459 1.00 67.3 yes View details
rps8-rpl14 LSC 277 0.0295 0.99 66.8 yes View details
psaC-ndhD SSC 135 0.0334 0.97 66.2 yes View details
trnL-UAA-trnT-UGU LSC 750 0.0212 0.99 66.1 yes View details
trnY-GUA-trnD-GUC LSC 455 0.0264 0.98 64.7 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rbcL_p1 trnK-UUU-rbcL AGAGTCGCTCTTAAAAGCCG TTGAAGCATGTGTGAAGGCT 1230–1261 1.000 89.8
trnK-UUU-rbcL_p2 trnK-UUU-rbcL AGTCGCTCTTAAAAGCCGAG TTGAAGCATGTGTGAAGGCT 1228–1259 1.000 89.8
trnK-UUU-rbcL_p3 trnK-UUU-rbcL GAGTCGCTCTTAAAAGCCGA TTGAAGCATGTGTGAAGGCT 1229–1260 1.000 89.8
trnK-UUU-rbcL_p4 trnK-UUU-rbcL AGAGTCGCTCTTAAAAGCCG AGTCCTGAATTAGCTGCTGC 1147–1178 1.000 89.8
trnK-UUU-rbcL_p5 trnK-UUU-rbcL AGTCGCTCTTAAAAGCCGAG AGTCCTGAATTAGCTGCTGC 1145–1176 1.000 89.8
ndhJ-trnF-GAA_p1 ndhJ-trnF-GAA TGAAATACAAGATGCTCACT CCTCGTGTCACCAGTTCAAA 742–750 1.000 47.1
ndhJ-trnF-GAA_p2 ndhJ-trnF-GAA TGAAATACAAGATGCTCACT AGAATGGTCGGGATAGCTCA 787–795 1.000 46.7
ndhJ-trnF-GAA_p3 ndhJ-trnF-GAA TGAAATACAAGATGCTCACT AATGGTCGGGATAGCTCAGT 785–793 1.000 46.7
ndhJ-trnF-GAA_p4 ndhJ-trnF-GAA TGAAATACAAGATGCTCACT ATGGTCGGGATAGCTCAGTT 784–792 1.000 46.7
ndhJ-trnF-GAA_p5 ndhJ-trnF-GAA TGAAATACAAGATGCTCACT TATGCGTCAAGAATGGTCGG 796–804 1.000 46.6
trnL-UAA-trnT-UGU_p1 trnL-UAA-trnT-UGU ACCAATTTCGCCATATCCCC GCGATGCTCTAACCTCTGAG 811–822 1.000 84.6
trnL-UAA-trnT-UGU_p2 trnL-UAA-trnT-UGU TAGCGTCTACCAATTTCGCC GCGATGCTCTAACCTCTGAG 819–830 1.000 84.0
trnL-UAA-trnT-UGU_p3 trnL-UAA-trnT-UGU ACCAATTTCGCCATATCCCC GGATTCGAACCGATGACCAT 843–854 1.000 83.5
trnL-UAA-trnT-UGU_p4 trnL-UAA-trnT-UGU TAGCGTCTACCAATTTCGCC GGATTCGAACCGATGACCAT 851–862 1.000 82.9
trnL-UAA-trnT-UGU_p5 trnL-UAA-trnT-UGU ACCAATTTCGCCATATCCCC TTGAGAAAAGCCGGCTATCG 862–873 1.000 82.5
trnG-GCC-psbZ_p1 trnG-GCC-psbZ CGTCTTCTCCTTGGCAAAGA CTTCTCCTGAAGGTTGGTCG 684–900 1.000 87.0
trnG-GCC-psbZ_p2 trnG-GCC-psbZ CGTCTTCTCCTTGGCAAAGA TCTCCTGAAGGTTGGTCGAA 682–898 1.000 85.4
trnG-GCC-psbZ_p3 trnG-GCC-psbZ CGTCTTCTCCTTGGCAAAGA TTCTCCTGAAGGTTGGTCGA 683–899 1.000 85.4
trnG-GCC-psbZ_p4 trnG-GCC-psbZ CGTCTTCTCCTTGGCAAAGA CTCCTGAAGGTTGGTCGAAT 681–897 1.000 81.5
trnG-GCC-psbZ_p5 trnG-GCC-psbZ CGGATAGCGGGAATCGAAC CTTCTCCTGAAGGTTGGTCG 706–922 1.000 78.7
trnT-GGU-trnE-UUC_p1 trnT-GGU-trnE-UUC GAACCGATGACTTACGCCTT GCTGCCTCCTTGAAAGAGAG 861–954 1.000 87.4
trnT-GGU-trnE-UUC_p2 trnT-GGU-trnE-UUC GAACCGATGACTTACGCCTT TGTCCTGAACCACTAGACGA 840–933 1.000 87.4
trnT-GGU-trnE-UUC_p3 trnT-GGU-trnE-UUC CCATGGCGTTACTCTACCAC GCTGCCTCCTTGAAAGAGAG 840–933 1.000 87.1
trnT-GGU-trnE-UUC_p4 trnT-GGU-trnE-UUC CCATGGCGTTACTCTACCAC TGTCCTGAACCACTAGACGA 819–912 1.000 87.1
trnT-GGU-trnE-UUC_p5 trnT-GGU-trnE-UUC TGGCGTTACTCTACCACTGA GCTGCCTCCTTGAAAGAGAG 837–930 1.000 86.9
trnY-GUA-trnD-GUC_p1 trnY-GUA-trnD-GUC TGGCAATATGTCTACGCTGG CGGTGCTCTGACCAATTGAA 514–527 1.000 82.6
trnY-GUA-trnD-GUC_p2 trnY-GUA-trnD-GUC GGCAATATGTCTACGCTGGT CGGTGCTCTGACCAATTGAA 513–526 1.000 82.6
trnY-GUA-trnD-GUC_p3 trnY-GUA-trnD-GUC GGGGACGGACTGTAAATTCG CGGTGCTCTGACCAATTGAA 535–548 1.000 81.3
trnY-GUA-trnD-GUC_p4 trnY-GUA-trnD-GUC GGGACGGACTGTAAATTCGT CGGTGCTCTGACCAATTGAA 534–547 1.000 81.2
trnY-GUA-trnD-GUC_p5 trnY-GUA-trnD-GUC CGGACTGTAAATTCGTTGGC CGGTGCTCTGACCAATTGAA 530–543 1.000 80.1

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (11)

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

Species Accession Length (bp) Link
Glycine canescens NC_021647.1 152518 View on NCBI ↗
Glycine cyrtoloba NC_021645.1 152381 View on NCBI ↗
Glycine dolichocarpa NC_021648.1 152804 View on NCBI ↗
Glycine falcata NC_021649.1 153023 View on NCBI ↗
Glycine max NC_007942.1 152218 View on NCBI ↗
Glycine soja NC_022868.1 152217 View on NCBI ↗
Glycine soja var. gracilis NC_030329.1 152218 View on NCBI ↗
Glycine stenophita NC_021646.1 152618 View on NCBI ↗
Glycine syndetika NC_021650.1 152783 View on NCBI ↗
Glycine tabacina PQ474255.1 152842 View on NCBI ↗
Glycine tomentella NC_021636.1 152728 View on NCBI ↗