Markers + reference

Millettia

2 species · Fabaceae · Fabales

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Species 2
Genome length 154–154 kb
Candidate markers 258
Primer pairs 105

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 9 remaining regions by MarkerSeek score (out of 258 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnT-rps4 LSC 316 0.0164 0.97 50.9 yes View details
psbM-petN LSC 874 0.0127 0.99 60.6 yes View details
atpI-atpH LSC 1196 0.0156 0.97 57.2 yes View details
atpH-atpF LSC 566 0.0196 0.99 58.5 yes View details
trnQ-psbK LSC 471 0.0065 0.98 60.9 yes View details
trnP-psaJ LSC 373 0.0215 1.00 56.3 yes View details
rpl33 LSC 201 0.0100 1.00 47.3 yes View details
rps8-rpl14 LSC 485 0.0236 0.96 63.6 yes View details
ycf1 IRb 447 0.0000 1.00 21.8 no View details
ndhF SSC 2247 0.0093 1.00 47.6 yes View details
ccsA SSC 975 0.0082 1.00 52.2 yes View details
rps15-ycf1 SSC 394 0.0385 0.99 65.4 yes View details
ycf1 SSC 5376 0.0069 1.00 43.1 yes View details
ycf1-ndhF IRb 9 0.2222 1.00 76.3 yes View details
trnL-ccsA SSC 94 0.0638 1.00 72.5 yes View details
rpl33-rps18 LSC 175 0.0571 1.00 72.4 yes View details
atpF-atpA LSC 110 0.0463 0.98 71.7 yes View details
trnK-rbcL LSC 647 0.0130 0.95 71.0 yes View details
trnH-psbA LSC 258 0.0310 1.00 67.0 yes View details
rps16 LSC 1151 0.0096 0.99 64.9 yes View details
psbE-petL LSC 1346 0.0082 0.99 64.2 yes View details
rpl2-trnH LSC 115 0.0182 0.96 63.8 no 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
trnH-psbA_p1 trnH-psbA GATCCACTTGGCTACATCCG CCCTCTAGATCTAGCTGCGA 325–336 1.000 79.4
trnH-psbA_p2 trnH-psbA GATCCACTTGGCTACATCCG TCCCTCTAGATCTAGCTGCG 326–337 1.000 79.4
trnH-psbA_p3 trnH-psbA CAATCCACTGCCTTGATCCA CCCTCTAGATCTAGCTGCGA 339–350 1.000 79.3
trnH-psbA_p4 trnH-psbA CAATCCACTGCCTTGATCCA TCCCTCTAGATCTAGCTGCG 340–351 1.000 79.2
trnH-psbA_p5 trnH-psbA AATCCACTGCCTTGATCCAC CCCTCTAGATCTAGCTGCGA 338–349 1.000 79.2
trnK-rbcL_p1 trnK-rbcL AGTCGCTCTTAAAAGCCGAG AGTCCTGAATTAGCTGCTGC 739–766 1.000 84.1
trnK-rbcL_p2 trnK-rbcL GAGTCGCTCTTAAAAGCCGA AGTCCTGAATTAGCTGCTGC 740–767 1.000 84.0
trnK-rbcL_p3 trnK-rbcL AGTCGCTCTTAAAAGCCGAG GAGGCTAGCAAATGGAGTCC 754–781 1.000 83.9
trnK-rbcL_p4 trnK-rbcL GAGTCGCTCTTAAAAGCCGA GAGGCTAGCAAATGGAGTCC 755–782 1.000 83.9
trnK-rbcL_p5 trnK-rbcL TGGAGTCGCTCTTAAAAGCC AGTCCTGAATTAGCTGCTGC 742–769 1.000 83.3
trnV_p1 trnV ATCCACAAGAAGCACAGCAA TCTAATGCCCCCTTTCTCCA 1895–1896 1.000 80.5
trnV_p2 trnV AACAAGTTGGTTCGTCCGAA TCTAATGCCCCCTTTCTCCA 1757–1758 1.000 80.4
trnV_p3 trnV CTCTCAGACGAGCTAGGACA TCTAATGCCCCCTTTCTCCA 1805–1806 1.000 80.4
trnV_p4 trnV CGAGCTAGGACACGAGTAGA TCTAATGCCCCCTTTCTCCA 1797–1798 1.000 80.1
trnV_p5 trnV ATCCACAAGAAGCACAGCAA AGACCATTCTAATGCCCCCT 1902–1903 1.000 80.0
trnT-rps4_p1 trnT-rps4 GTTATTGAGCCCGCTTAGCT AGGTCCTCTGTAACGTGACA 412–418 1.000 83.0
trnT-rps4_p2 trnT-rps4 GTTATTGAGCCCGCTTAGCT AGCGCGATTGGTTTCTAAGT 503–509 1.000 81.9
trnT-rps4_p3 trnT-rps4 GTTATTGAGCCCGCTTAGCT CGGGCTTGAGGAATAGTCAC 714–720 1.000 81.4
trnT-rps4_p4 trnT-rps4 GTTATTGAGCCCGCTTAGCT AACTTTTCCGGCGATACGAA 616–622 1.000 81.4
trnT-rps4_p5 trnT-rps4 GTTATTGAGCCCGCTTAGCT TCACAGCCATACCCAACCTA 704 0.500 59.3
psbM-petN_p1 psbM-petN ACGGTAAGTCAAAGTGGTGAC TCTTGCTTGGGCTGCTTTAA 973–974 1.000 72.1
psbM-petN_p2 psbM-petN ACGGTAAGTCAAAGTGGTGA TCTTGCTTGGGCTGCTTTAA 973–974 1.000 71.2
psbM-petN_p3 psbM-petN ACGGTAAGTCAAAGTGGTGAC AGTAAGTCTTGCTTGGGCTG 979–980 1.000 70.6
psbM-petN_p4 psbM-petN ACGGTAAGTCAAAGTGGTGA AGTAAGTCTTGCTTGGGCTG 979–980 1.000 69.7
psbM-petN_p5 psbM-petN AACGGTAAGTCAAAGTGGTGA TCTTGCTTGGGCTGCTTTAA 974–975 1.000 69.1
atpI-atpH_p1 atpI-atpH GAATATGGTCCGTGGGTTCC ATAACGGAAGCGGCAGAAAT 1670–1705 1.000 82.3
atpI-atpH_p2 atpI-atpH TCTGCTGTGGAAGTAGGTCA ATAACGGAAGCGGCAGAAAT 1886–1921 1.000 82.2
atpI-atpH_p3 atpI-atpH GAATATGGTCCGTGGGTTCC CAAGAGCAGCAAAGCAAGTC 1950–1989 1.000 82.2
atpI-atpH_p4 atpI-atpH TCTGCTGTGGAAGTAGGTCA CAAGAGCAGCAAAGCAAGTC 2166–2205 1.000 82.1
atpI-atpH_p5 atpI-atpH GGCAAATAGGGGGTTTCCAA ATAACGGAAGCGGCAGAAAT 1855–1890 1.000 81.9

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
Millettia laurentii MZ274110.1 154202 View on NCBI ↗
Millettia stuhlmannii MZ274111.1 154288 View on NCBI ↗