Markers + reference

Boronia

2 species · Rutaceae · Sapindales

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Species 2
Genome length 157–157 kb
Candidate markers 273
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 273 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 564 0.0581 0.98 78.0 yes View details
rps16-trnQ-UUG LSC 466 0.0649 0.99 74.0 yes View details
trnS-GCU-trnG-UCC LSC 859 0.0564 0.76 73.2 yes View details
trnT-GGU-psbD LSC 1194 0.0441 0.99 77.4 yes View details
psbZ-trnG-GCC LSC 524 0.0686 0.97 81.1 yes View details
psbE-petL LSC 1392 0.0452 0.65 66.2 yes View details
trnN-GUU-rpl32 SSC 4486 0.0322 0.94 63.3 yes View details
ycf1 SSC 5490 0.0373 0.99 61.9 yes View details
rps8-rpl14 LSC 151 0.0728 1.00 76.8 yes View details
ndhD-psaC SSC 199 0.0535 0.94 76.5 yes View details
trnfM-CAU-rps14 LSC 163 0.0625 0.98 75.5 yes View details
trnH-GUG-psbA LSC 144 0.1071 0.97 75.4 yes View details
rpl14-rpl16 LSC 125 0.1068 0.82 75.2 yes View details
atpH-atpI LSC 1240 0.0394 0.98 75.1 yes View details
trnT-UGU-trnL-UAA LSC 960 0.0392 0.98 75.1 yes View details
psbK-psbI LSC 395 0.0522 0.97 74.9 yes View details
trnW-CCA-trnP-UGG LSC 181 0.0468 0.94 74.7 yes View details
petG-trnW-CCA LSC 144 0.0563 0.99 74.6 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT TCAGTGCTATGCATGGTTCC 604–861 1.000 81.6
trnH-GUG-psbA_p2 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT CAGTGCTATGCATGGTTCCT 603–860 1.000 81.6
trnH-GUG-psbA_p3 trnH-GUG-psbA ACTGCCTTAATCCACTTGGC TCAGTGCTATGCATGGTTCC 605–862 1.000 81.4
trnH-GUG-psbA_p4 trnH-GUG-psbA ACTGCCTTAATCCACTTGGC CAGTGCTATGCATGGTTCCT 604–861 1.000 81.4
trnH-GUG-psbA_p5 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT ATGCACCCATTCCACATGTT 656–913 1.000 81.3
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT ACAGAACTTAGTCTTAATCAAACGA 634–726 1.000 45.3
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT ACAGAACTTAGTCTTAATCAAACGA 633–725 1.000 45.3
trnK-UUU-rps16_p3 trnK-UUU-rps16 CTCCCGAAGATTTGGACGAA ACAGAACTTAGTCTTAATCAAACGA 698–790 1.000 44.8
trnK-UUU-rps16_p4 trnK-UUU-rps16 TTCTCCCGAAGATTTGGACG ACAGAACTTAGTCTTAATCAAACGA 700–792 1.000 44.8
trnK-UUU-rps16_p5 trnK-UUU-rps16 TCTCCCGAAGATTTGGACGA ACAGAACTTAGTCTTAATCAAACGA 699–791 1.000 44.8
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CAGCGGATCATGTCCTTCAA GGTTCGAATCCTTCCGTCC 555–558 1.000 76.2
rps16-trnQ-UUG_p2 rps16-trnQ-UUG CAGCGGATCATGTCCTTCAA GTTCGAATCCTTCCGTCCC 554–557 1.000 76.2
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GCGGATCATGTCCTTCAAGT GGTTCGAATCCTTCCGTCC 553–556 1.000 76.2
rps16-trnQ-UUG_p4 rps16-trnQ-UUG GCGGATCATGTCCTTCAAGT GTTCGAATCCTTCCGTCCC 552–555 1.000 76.2
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GTTCGAATCCTTCCGTCCC 536–539 1.000 75.5
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG AGACAGGAATCCGAAGATGA 490–500 1.000 66.0
psbK-psbI_p2 psbK-psbI GTTTGGCAAGCTGCTGTAAG GACAGGAATCCGAAGATGAAGA 489–499 1.000 65.6
psbK-psbI_p3 psbK-psbI GTTTGGCAAGCTGCTGTAAG ACAGGAATCCGAAGATGAAGAG 488–498 1.000 65.6
psbK-psbI_p4 psbK-psbI GTTTGGCAAGCTGCTGTAAG AGACAGGAATCCGAAGATGAAG 490–500 1.000 65.5
psbK-psbI_p5 psbK-psbI GTTTGGCAAGCTGCTGTAAG ACAGGAATCCGAAGATGAAGA 488–498 1.000 64.3
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CCGACGCTTTAATCCACTCA TACCACTAAACTATACCCGC 707–910 1.000 55.5
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC CCGACGCTTTAATCCACTCA TTACCACTAAACTATACCCGC 708–911 1.000 54.4
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA TACCACTAAACTATACCCGC 765–968 1.000 54.1
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC ACGCTTTAATCCACTCAGCC TACCACTAAACTATACCCGC 704–907 1.000 53.5
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC CGCTTTAATCCACTCAGCCA TACCACTAAACTATACCCGC 703–906 1.000 53.5
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT TACAAGCGGGATTCAAGCTC 1345–1351 1.000 83.6
atpH-atpI_p2 atpH-atpI GTCCAATAGAAGCAAGCCCA TACAAGCGGGATTCAAGCTC 1383–1389 1.000 82.8
atpH-atpI_p3 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTGCAACTTTAGCTGCGG 1321–1327 1.000 82.8
atpH-atpI_p4 atpH-atpI AATAACGGAAGCGGCAGAAA TACAAGCGGGATTCAAGCTC 1346–1352 1.000 82.4
atpH-atpI_p5 atpH-atpI GTCCAATAGAAGCAAGCCCA TTTTGCAACTTTAGCTGCGG 1359–1365 1.000 82.0

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
Boronia edwardsii NC_081866.1 156969 View on NCBI ↗
Boronia ternata NC_081867.1 157247 View on NCBI ↗