Markers + reference

Aeschynomene

2 species · Fabaceae · Fabales

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Species 2
Genome length 156–161 kb
Candidate markers 266
Primer pairs 110

Genome-wide nucleotide diversity

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

Candidate markers

13 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 266 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnL-UAA-trnT-UGU LSC 1369 0.2013 0.98 81.0 yes View details
trnC-GCA-rpoB LSC 1010 0.1299 0.75 80.7 yes View details
trnR-UCU-trnG-UCC LSC 409 0.2118 0.83 81.9 yes View details
trnG-UCC-trnS-GCU LSC 544 0.1984 0.90 83.8 yes View details
trnQ-UUG-rps16 LSC 541 0.1957 0.94 82.7 yes View details
rps16-accD LSC 756 0.1865 0.74 78.0 yes View details
ycf4-cemA LSC 492 0.1470 0.84 78.6 yes View details
petA-psbJ LSC 823 0.1701 0.94 87.2 yes View details
trnP-UGG-psaJ LSC 706 0.2045 0.37 70.9 yes View details
ycf1 IRb 460 0.0326 1.00 59.6 no View details
rpl32-trnL-UAG SSC 925 0.2577 0.95 83.7 yes View details
ndhG-ndhI SSC 671 0.2332 0.80 79.4 yes View details
ycf1 SSC 5379 0.1111 0.98 74.5 yes View details
psbD-trnT-GGU LSC 1286 0.0983 0.94 89.5 yes View details
ndhJ-trnF-GAA LSC 476 0.1490 0.97 85.6 yes View details
psbM-petN LSC 1158 0.1421 0.93 85.3 yes View details
rpl20-rps12 LSC 854 0.0998 0.94 84.8 yes View details
ycf3-psaA LSC 874 0.1209 0.95 84.0 yes View details
trnG-GCC-psbZ LSC 519 0.1339 0.95 83.9 yes View details
atpI-atpH LSC 923 0.1200 0.93 83.8 yes View details
trnT-GGU-trnE-UUC LSC 751 0.1271 0.87 83.4 yes View details
ycf4 LSC 570 0.1688 0.97 82.9 yes View details
psaJ-rpl33 LSC 487 0.1333 0.95 82.9 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 110 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
ndhJ-trnF-GAA_p1 ndhJ-trnF-GAA TTGGATAGGATGGCCTTTGC GGGATAGCTCAGCTGGTAGA 616–1049 1.000 87.3
ndhJ-trnF-GAA_p2 ndhJ-trnF-GAA TTGGATAGGATGGCCTTTGC CCTCGTGTCACCAGTTCAAA 580–1013 1.000 87.2
ndhJ-trnF-GAA_p3 ndhJ-trnF-GAA TTGGATAGGATGGCCTTTGC AGAATGGTCGGGATAGCTCA 625–1058 1.000 86.5
ndhJ-trnF-GAA_p4 ndhJ-trnF-GAA TTGGATAGGATGGCCTTTGC CTGGTAGAGCAGAGGACTGA 604–1037 1.000 86.3
ndhJ-trnF-GAA_p5 ndhJ-trnF-GAA ATGCCCGAAAGTTGGATAGG GGGATAGCTCAGCTGGTAGA 627–1060 1.000 85.0
trnL-UAA-trnT-UGU_p1 trnL-UAA-trnT-UGU TAGCGTCTACCAATTTCGCC CGGAGCGTGATTGGTTTCTA 1893–2698 1.000 90.9
trnL-UAA-trnT-UGU_p2 trnL-UAA-trnT-UGU TGTCGTCAACCCCATTTGTT CGGAGCGTGATTGGTTTCTA 2094 0.500 59.5
trnL-UAA-trnT-UGU_p3 trnL-UAA-trnT-UGU GTCTACGCGGATCCATTTGT CGGAGCGTGATTGGTTTCTA 2567 0.500 59.5
trnL-UAA-trnT-UGU_p4 trnL-UAA-trnT-UGU CTACGCGGATCCATTTGTGA CGGAGCGTGATTGGTTTCTA 2565 0.500 59.4
trnL-UAA-trnT-UGU_p5 trnL-UAA-trnT-UGU TCTACGCGGATCCATTTGTG CGGAGCGTGATTGGTTTCTA 2566 0.500 59.4
ycf3-psaA_p1 ycf3-psaA AGCCCTTACCCCAGGTAATT ATGCCACTCAGCCAAAGAAA 1204 0.500 60.0
ycf3-psaA_p2 ycf3-psaA CTATTCCTATTCCGACCGCG ATGCCACTCAGCCAAAGAAA 1306 0.500 59.8
ycf3-psaA_p3 ycf3-psaA AGCTATAGCCCTTACCCCAG ATGCCACTCAGCCAAAGAAA 1210 0.500 59.7
ycf3-psaA_p4 ycf3-psaA AGCCCTTACCCCAGGTAATT AACCCTGCCAAATGGTGATT 1546 0.500 59.7
ycf3-psaA_p5 ycf3-psaA AGCCCTTACCCCAGGTAATT GGCACTAGGTCCAATGTGAG 1277 0.500 59.7
trnG-GCC-psbZ_p1 trnG-GCC-psbZ CGTCTTCTCCTTGGCAAAGA ATTCTTAATTCTCTCATTTCTTGA 590–871 1.000 50.1
trnG-GCC-psbZ_p2 trnG-GCC-psbZ CGTCTTCTCCTTGGCAAAGA GGTATTCTTAATTCTCTCATTTCTTGA 593–874 1.000 50.0
trnG-GCC-psbZ_p3 trnG-GCC-psbZ CGTCTTCTCCTTGGCAAAGA GGTATTCTTAATTCTCTCATTTCTTG 593–874 1.000 50.0
trnG-GCC-psbZ_p4 trnG-GCC-psbZ CGTCTTCTCCTTGGCAAAGA GGTATTCTTAATTCTCTCATTTCT 593–874 1.000 50.0
trnG-GCC-psbZ_p5 trnG-GCC-psbZ CGTCTTCTCCTTGGCAAAGA GGTATTCTTAATTCTCTCATTTCTT 593–874 1.000 50.0
psbD-trnT-GGU_p1 psbD-trnT-GGU CACAAAAACGAAACGGTCCC GTGGTAGAGTAACGCCATGG 1437–1480 1.000 88.7
psbD-trnT-GGU_p2 psbD-trnT-GGU CCACAAAAACGAAACGGTCC GTGGTAGAGTAACGCCATGG 1438–1481 1.000 88.7
psbD-trnT-GGU_p3 psbD-trnT-GGU CCCACAAAAACGAAACGGTC GTGGTAGAGTAACGCCATGG 1439–1482 1.000 88.6
psbD-trnT-GGU_p4 psbD-trnT-GGU CACAAAAACGAAACGGTCCC TCAGTGGTAGAGTAACGCCA 1440–1483 1.000 88.5
psbD-trnT-GGU_p5 psbD-trnT-GGU CCACAAAAACGAAACGGTCC TCAGTGGTAGAGTAACGCCA 1441–1484 1.000 88.5
trnT-GGU-trnE-UUC_p1 trnT-GGU-trnE-UUC GAACCGATGACTTACGCCTT GTCCTGGACCACTAGACGAT 832–842 1.000 90.0
trnT-GGU-trnE-UUC_p2 trnT-GGU-trnE-UUC GAACCGATGACTTACGCCTT TCCTGGACCACTAGACGATG 831–841 1.000 90.0
trnT-GGU-trnE-UUC_p3 trnT-GGU-trnE-UUC CCATGGCGTTACTCTACCAC GTCCTGGACCACTAGACGAT 811–821 1.000 89.6
trnT-GGU-trnE-UUC_p4 trnT-GGU-trnE-UUC CCATGGCGTTACTCTACCAC TCCTGGACCACTAGACGATG 810–820 1.000 89.6
trnT-GGU-trnE-UUC_p5 trnT-GGU-trnE-UUC TGGCGTTACTCTACCACTGA GTCCTGGACCACTAGACGAT 808–818 1.000 89.4

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
Aeschynomene brevifolia PV870793.1 155771 View on NCBI ↗
Aeschynomene indica PP566030.1 160502 View on NCBI ↗