Markers + reference

Erythrina

3 species · Fabaceae · Fabales

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Species 3
Genome length 152–152 kb
Candidate markers 268
Primer pairs 115

Genome-wide nucleotide diversity

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

Candidate markers

14 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rbcL LSC 934 0.0222 1.00 59.8 yes View details
trnG-GCC-psbZ LSC 503 0.0497 1.00 84.7 yes View details
psbD-trnT-GGU LSC 1250 0.0191 0.98 60.4 yes View details
trnC-GCA-rpoB LSC 1117 0.0167 1.00 60.8 yes View details
rpoC1 LSC 2864 0.0083 1.00 62.4 yes View details
rpoC2 LSC 4104 0.0102 1.00 46.4 yes View details
trnR-UCU-trnG-UCC LSC 274 0.0243 1.00 65.6 yes View details
psbK-trnQ-UUG LSC 437 0.0277 0.99 71.9 yes View details
rpl36-rps8 LSC 488 0.0219 1.00 57.2 yes View details
rpl16 LSC 1567 0.0141 1.00 58.3 yes View details
rps3-rps19 LSC 512 0.0268 1.00 70.9 yes View details
ycf1 IRb 1249 0.0037 1.00 46.4 no View details
ndhA SSC 2258 0.0107 1.00 51.5 yes View details
ycf1 SSC 5283 0.0131 0.99 48.4 yes View details
psbB-psbT LSC 179 0.0409 0.96 81.8 yes View details
ndhK-ndhJ LSC 114 0.0760 1.00 81.7 yes View details
atpA-trnR-UCU LSC 208 0.0353 1.00 72.5 yes View details
ycf3-psaA LSC 739 0.0126 1.00 68.8 yes View details
petA-psbJ LSC 680 0.0098 1.00 67.2 yes View details
atpI-atpH LSC 877 0.0125 1.00 66.7 yes View details
trnS-UGA-psbC LSC 207 0.0322 1.00 66.3 yes View details
psaJ-rpl33 LSC 540 0.0154 0.96 66.3 yes View details
psbM-petN LSC 721 0.0134 1.00 66.0 yes View details
ndhI-ndhA SSC 75 0.0267 1.00 65.3 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 115 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 AGTCCTGAATTAGCTGCTGC 1056–1114 1.000 82.7
trnK-UUU-rbcL_p2 trnK-UUU-rbcL AGTCGCTCTTAAAAGCCGAG AGTCCTGAATTAGCTGCTGC 1054–1112 1.000 82.7
trnK-UUU-rbcL_p3 trnK-UUU-rbcL AGAGTCGCTCTTAAAAGCCG GAGGCTAGCAAATGGAGTCC 1071–1129 1.000 82.6
trnK-UUU-rbcL_p4 trnK-UUU-rbcL AGTCGCTCTTAAAAGCCGAG GAGGCTAGCAAATGGAGTCC 1069–1127 1.000 82.6
trnK-UUU-rbcL_p5 trnK-UUU-rbcL GAGTCGCTCTTAAAAGCCGA AGTCCTGAATTAGCTGCTGC 1055–1113 1.000 82.6
ndhK-ndhJ_p1 ndhK-ndhJ ACCGCCATCTACTTCAGAGA AGAAGACAAACGACCTTGCA 178–198 1.000 81.9
ndhK-ndhJ_p2 ndhK-ndhJ ACCGCCATCTACTTCAGAGA AGCCAAGAAGACAAACGACC 183–203 1.000 81.1
ndhK-ndhJ_p3 ndhK-ndhJ ACCGCCATCTACTTCAGAGA GCCAAGAAGACAAACGACCT 182–202 1.000 81.1
ndhK-ndhJ_p4 ndhK-ndhJ GATGCAGTACTCATACCGGC AGAAGACAAACGACCTTGCA 224–244 1.000 80.2
ndhK-ndhJ_p5 ndhK-ndhJ GCAGTACTCATACCGGCAAT AGAAGACAAACGACCTTGCA 221–241 1.000 80.0
ycf3-psaA_p1 ycf3-psaA AGCCCTTACCCCTGGTAATT ATGACCAGGTTTTGCCCATT 888–899 1.000 82.2
ycf3-psaA_p2 ycf3-psaA AGCCCTTACCCCTGGTAATT AATGACCAGGTTTTGCCCAT 889–900 1.000 82.1
ycf3-psaA_p3 ycf3-psaA AGCTATAGCCCTTACCCCTG AATGACCAGGTTTTGCCCAT 895–906 1.000 81.9
ycf3-psaA_p4 ycf3-psaA AGCTATAGCCCTTACCCCTG ATGACCAGGTTTTGCCCATT 894–905 1.000 81.9
ycf3-psaA_p5 ycf3-psaA AGCCCTTACCCCTGGTAATT TGCCCATTCCTCGAAAGAAG 876–887 1.000 81.5
trnG-GCC-psbZ_p1 trnG-GCC-psbZ CGTCTTCTCCTTGGCAAAGA CTCTTGAAGGTTGGTCGAGT 654–939 1.000 79.5
trnG-GCC-psbZ_p2 trnG-GCC-psbZ CGTCTTCTCCTTGGCAAAGA TCTCTTGAAGGTTGGTCGAG 655–940 1.000 77.2
trnG-GCC-psbZ_p3 trnG-GCC-psbZ CGTCTTCTCCTTGGCAAAGA CTTCTCTTGAAGGTTGGTCGA 657–942 1.000 75.0
trnG-GCC-psbZ_p4 trnG-GCC-psbZ CGTCTTCTCCTTGGCAAAGA TTCTCTTGAAGGTTGGTCGAG 656–941 1.000 75.0
trnG-GCC-psbZ_p5 trnG-GCC-psbZ CGTCTTCTCCTTGGCAAAGA TGAAGGTTGGTCGAGTAACA 650–935 1.000 73.5
trnS-UGA-psbC_p1 trnS-UGA-psbC GAGAGATGGCTGAGTGGTTG CGCCGGATTTGAAAAAGGAA 366–370 1.000 76.5
trnS-UGA-psbC_p2 trnS-UGA-psbC ATAGCCCCGGTCTTGAAAAC CGCCGGATTTGAAAAAGGAA 346–350 1.000 75.8
trnS-UGA-psbC_p3 trnS-UGA-psbC GCTTTTGGAGAGATGGCTGA CGCCGGATTTGAAAAAGGAA 373–377 1.000 75.7
trnS-UGA-psbC_p4 trnS-UGA-psbC AGCTTTTGGAGAGATGGCTG CGCCGGATTTGAAAAAGGAA 374–378 1.000 75.6
trnS-UGA-psbC_p5 trnS-UGA-psbC GGGTTCGAATCCCTCTCTCT CGCCGGATTTGAAAAAGGAA 297–301 1.000 75.5
psbD-trnT-GGU_p1 psbD-trnT-GGU AATTTACCAAGAGCTATAGTCA GTAACGCCATGGTAAGACGT 943–1325 1.000 46.1
psbD-trnT-GGU_p2 psbD-trnT-GGU AATTTACCAAGAGCTATAGTCA GTGGTAGAGTAACGCCATGG 951–1333 1.000 46.1
psbD-trnT-GGU_p3 psbD-trnT-GGU AATTTACCAAGAGCTATAGTCA TCAGTGGTAGAGTAACGCCA 954–1336 1.000 46.1
psbD-trnT-GGU_p4 psbD-trnT-GGU AAATTTACCAAGAGCTATAGTCA GTAACGCCATGGTAAGACGT 944–1326 1.000 46.1
psbD-trnT-GGU_p5 psbD-trnT-GGU AAATTTACCAAGAGCTATAGTCA GTGGTAGAGTAACGCCATGG 952–1334 1.000 46.1

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

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

Species Accession Length (bp) Link
Erythrina crista-galli NC_057450.1 151751 View on NCBI ↗
Erythrina herbacea NC_067539.1 151821 View on NCBI ↗
Erythrina variegata PQ469842.1 152351 View on NCBI ↗