Markers + reference

Phanera

13 species · Fabaceae · Fabales

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Species 13
Genome length 146–168 kb
Candidate markers 266
Primer pairs 65

Genome-wide nucleotide diversity

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

Candidate markers

6 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 266 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rbcL-accD LSC 1719 0.0498 0.89 78.1 yes View details
accD LSC 1077 0.0740 0.97 83.2 yes View details
clpP LSC 2012 0.0447 0.99 80.6 yes View details
clpP-psbB LSC 546 0.0691 1.00 81.8 yes View details
ycf1 SSC 5058 0.0663 0.98 77.8 yes View details
rpl2-trnH-GUG LSC 274 0.1340 1.00 77.8 no View details
trnG-UCC-trnR-UCU LSC 247 0.0548 1.00 81.5 yes View details
rps16-trnQ-UUG LSC 650 0.0294 0.98 80.5 yes View details
atpH-atpI LSC 716 0.0149 0.99 77.6 yes View details
rps3-rps19 LSC 948 0.0263 0.94 77.4 yes View details
psbZ-trnG-GCC LSC 592 0.0203 1.00 77.2 yes View details
trnS-GCU-trnG-UCC LSC 545 0.0364 0.99 77.1 yes View details
trnI-CAU-ycf2 IRb 335 0.0766 0.99 76.9 yes View details
ndhF-rpl32 SSC 1045 0.0296 0.99 76.7 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 65 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps16-trnQ-UUG_p1 rps16-trnQ-UUG TCACACGTTGCTTTCTACCC AAGGTTCGAATCCTTCCGTC 293–728 0.923 84.5
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCACACGTTGCTTTCTACCC GGTCCCGTTATTCGAAGGTT 307–742 0.923 84.3
rps16-trnQ-UUG_p3 rps16-trnQ-UUG ACACGTTGCTTTCTACCCAA AAGGTTCGAATCCTTCCGTC 291–726 0.923 82.8
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCACACGTTGCTTTCTACCC TTGGTCCCGTTATTCGAAGG 309–744 0.846 80.7
rps16-trnQ-UUG_p5 rps16-trnQ-UUG ACACGTTGCTTTCTACCCAA TTGGTCCCGTTATTCGAAGG 307–742 0.846 79.1
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC AGTCCACTCAGCCATCTCTC GGGGTCCATAGAACGAATCG 290–625 1.000 86.7
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AGTCCACTCAGCCATCTCTC GGTCCATAGAACGAATCGCA 288–623 1.000 86.1
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC TAGTCCACTCAGCCATCTCT GGGGTCCATAGAACGAATCG 291–626 1.000 84.1
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AGTCCACTCAGCCATCTCTC GGGTCCATAGAACGAATCGC 289–624 1.000 83.9
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC TAGTCCACTCAGCCATCTCT GGTCCATAGAACGAATCGCA 289–624 1.000 83.6
trnG-UCC-trnR-UCU_p1 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 280–346 1.000 75.3
trnG-UCC-trnR-UCU_p2 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 283–349 1.000 75.1
trnG-UCC-trnR-UCU_p3 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 286–352 1.000 74.7
trnG-UCC-trnR-UCU_p4 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 289–355 1.000 74.5
trnG-UCC-trnR-UCU_p5 trnG-UCC-trnR-UCU CCCTAGCCTTCCAAGCTAAC AGAAGACCTCTGTCCTATCCA 284–350 1.000 72.9
atpH-atpI_p1 atpH-atpI ATAACGGAAGCAGCGGAAAT TTTTGCAACTTTAGCTGCGG 757–851 1.000 87.9
atpH-atpI_p2 atpH-atpI ATAACGGAAGCAGCGGAAAT CCCGTCATGTTCCTTGGATT 804–898 1.000 87.8
atpH-atpI_p3 atpH-atpI TCCCAGGTCCAATAGAAGCA TTTTGCAACTTTAGCTGCGG 801–895 1.000 87.7
atpH-atpI_p4 atpH-atpI TCCCAGGTCCAATAGAAGCA CCCGTCATGTTCCTTGGATT 848–942 1.000 87.6
atpH-atpI_p5 atpH-atpI TACCTTGACCAATCCCAGGT CCCGTCATGTTCCTTGGATT 860–954 1.000 87.4
psbZ-trnG-GCC_p1 psbZ-trnG-GCC CTGTTGTATTTGCTTCGCCG CGTCTTCTCCTTGGCAAAGA 737–786 1.000 87.3
psbZ-trnG-GCC_p2 psbZ-trnG-GCC TTGTATTTGCTTCGCCGGAT CGTCTTCTCCTTGGCAAAGA 734–783 1.000 86.3
psbZ-trnG-GCC_p3 psbZ-trnG-GCC CTGTTGTATTTGCTTCGCCG AAAAAGACGGAGGCGGATAG 772–821 1.000 86.0
psbZ-trnG-GCC_p4 psbZ-trnG-GCC CGGATGGTTGGTCGAGTAAC CGTCTTCTCCTTGGCAAAGA 719–768 1.000 85.4
psbZ-trnG-GCC_p5 psbZ-trnG-GCC CCTGTTGTATTTGCTTCGCC CGTCTTCTCCTTGGCAAAGA 738–787 0.923 82.7
rbcL-accD_p1 rbcL-accD AGTCCTGAATTAGCTGCTGC CTCGATCAACCGGGTGATTT 1957–2957 1.000 91.5
rbcL-accD_p2 rbcL-accD AGTCCTGAATTAGCTGCTGC CGGAAGCACACACGAGAATA 2003–2787 0.923 88.6
rbcL-accD_p3 rbcL-accD AGATCTTTGGCGACGATTCC CGGAAGCACACACGAGAATA 2182–2966 0.923 88.4
rbcL-accD_p4 rbcL-accD AGTCCTGAATTAGCTGCTGC GATTCCTCCTCCTCCTCCTC 2285 0.077 42.7
rbcL-accD_p5 rbcL-accD AGATCTTTGGCGACGATTCC GATTCCTCCTCCTCCTCCTC 2464 0.077 42.5

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (13)

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

Species Accession Length (bp) Link
Phanera apertilobata PQ433124.1 156240 View on NCBI ↗
Phanera aureifolia PQ433128.1 159152 View on NCBI ↗
Phanera bidentata PQ433126.1 168155 View on NCBI ↗
Phanera carcinophylla OQ701677.1 158909 View on NCBI ↗
Phanera cardinalis OQ701678.1 145866 View on NCBI ↗
Phanera cercidifolia OQ701679.1 166617 View on NCBI ↗
Phanera erythropoda PQ433121.1 158488 View on NCBI ↗
Phanera japonica PQ433123.1 161243 View on NCBI ↗
Phanera macrostachya OQ701685.1 162422 View on NCBI ↗
Phanera ornata OQ701682.1 159488 View on NCBI ↗
Phanera saigonensis PQ433129.1 161329 View on NCBI ↗
Phanera vahlii PQ433127.1 159202 View on NCBI ↗
Phanera venustula OQ701684.1 157983 View on NCBI ↗