Markers + reference

Philotheca

4 species · Rutaceae · Sapindales

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Species 4
Genome length 156–157 kb
Candidate markers 270
Primer pairs 110

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 7 remaining regions by MarkerSeek score (out of 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 586 0.0348 0.97 71.9 yes View details
rps16-trnQ-UUG LSC 790 0.0295 1.00 72.4 yes View details
psbK-psbI LSC 381 0.0359 1.00 66.5 yes View details
trnS-GCU-trnG-UCC LSC 944 0.0291 0.99 71.2 yes View details
trnG-UCC-trnR-UCU LSC 187 0.0579 1.00 77.9 yes View details
trnR-UCU-atpA LSC 211 0.0498 0.99 77.6 yes View details
atpH-atpI LSC 1113 0.0274 0.97 68.0 yes View details
rpoB-trnC-GCA LSC 1218 0.0317 1.00 72.8 yes View details
psbZ-trnG-GCC LSC 531 0.0370 0.97 78.9 yes View details
trnT-UGU-trnL-UAA LSC 1000 0.0355 1.00 72.0 yes View details
trnN-GUU-rpl32 SSC 4238 0.0151 1.00 53.0 yes View details
rpl32-trnL-UAG SSC 667 0.0330 0.98 69.3 yes View details
ndhA SSC 2227 0.0168 1.00 55.7 yes View details
ycf1 SSC 5445 0.0188 1.00 55.2 yes View details
trnS-GGA-rps4 LSC 220 0.0462 1.00 77.4 yes View details
petG-trnW-CCA LSC 151 0.0530 0.96 76.8 yes View details
psbI-trnS-GCU LSC 125 0.0440 1.00 75.8 yes View details
rps3-rpl22 LSC 239 0.0558 1.00 75.5 yes View details
trnH-GUG-psbA LSC 367 0.0460 0.99 74.6 yes View details
psbA-trnK-UUU LSC 267 0.0362 1.00 73.5 yes View details
ndhE-ndhG SSC 258 0.0460 0.99 71.7 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 110 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG TGAAGCTCCATCTACAAATGG 411–429 1.000 59.3
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TGAAGCTCCATCTACAAATGG 425–443 1.000 59.0
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TGAAGCTCCATCTACAAATGG 424–442 1.000 59.0
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TGAAGCTCCATCTACAAATGG 426–444 1.000 59.0
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG TTGAAGCTCCATCTACAAATGG 412–430 1.000 57.3
psbA-trnK-UUU_p1 psbA-trnK-UUU ATGTAAAGGCGGTTTTCGGT ACTCCATCCGACTAGTTCCG 393–404 1.000 80.0
psbA-trnK-UUU_p2 psbA-trnK-UUU ACCATCCAATGTAAAGGCGG ACTCCATCCGACTAGTTCCG 401–412 1.000 78.8
psbA-trnK-UUU_p3 psbA-trnK-UUU CCATCCAATGTAAAGGCGGT ACTCCATCCGACTAGTTCCG 400–411 1.000 78.8
psbA-trnK-UUU_p4 psbA-trnK-UUU ATGTAAAGGCGGTTTTCGGT ACTAGTTCCGGGTTCGAGTC 383–394 1.000 78.4
psbA-trnK-UUU_p5 psbA-trnK-UUU ATGTAAAGGCGGTTTTCGGT GACTAGTTCCGGGTTCGAGT 384–395 1.000 78.3
trnK-UUU-rps16_p1 trnK-UUU-rps16 AGCCGTACTTAAAAGCCGAG ATTTCAAAGAAAGCGGGGGT 668–691 1.000 88.6
trnK-UUU-rps16_p2 trnK-UUU-rps16 AATTGGAACCCTAGGGCTCT ATTTCAAAGAAAGCGGGGGT 911–939 1.000 87.6
trnK-UUU-rps16_p3 trnK-UUU-rps16 AGCCGTACTTAAAAGCCGAG CCCAATGAGCCGTTTATCGA 841–864 1.000 86.9
trnK-UUU-rps16_p4 trnK-UUU-rps16 AGCCGTACTTAAAAGCCGAG TCCCAATGAGCCGTTTATCG 842–865 1.000 86.9
trnK-UUU-rps16_p5 trnK-UUU-rps16 GGTAAGGAAGTTAGTGGGCG ATTTCAAAGAAAGCGGGGGT 1352–1380 1.000 85.9
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CCACAACGGATCATGTCCTT GAGGTTCGAATCCTTCCGTC 882–907 1.000 82.8
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 861–886 1.000 82.7
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CCACAACGGATCATGTCCTT GAAATTGAAATGGGGCGTCG 940–965 1.000 82.4
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAAATTGAAATGGGGCGTCG 919–944 1.000 82.3
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 872–897 1.000 82.1
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG ACAAAGAGTTTGAGAGTAAGCA 433–435 1.000 49.8
psbK-psbI_p2 psbK-psbI TGGCAAGCTGCTGTAAGTTT ACAAAGAGTTTGAGAGTAAGCA 430–432 1.000 47.8
psbK-psbI_p3 psbK-psbI TTGGCAAGCTGCTGTAAGTT ACAAAGAGTTTGAGAGTAAGCA 431–433 1.000 47.8
psbK-psbI_p4 psbK-psbI TTTGGCAAGCTGCTGTAAGT ACAAAGAGTTTGAGAGTAAGCA 432–434 1.000 47.8
psbK-psbI_p5 psbK-psbI GTTTGGCAAGCTGCTGTAAG ACAAAGAGTTTGAGAGTAAGCAT 433–435 1.000 45.9
psbI-trnS-GCU_p1 psbI-trnS-GCU CTGTCTAATGATCCAGGGCG TGAGTGGATTAAAGCGTCGG 243–246 1.000 82.6
psbI-trnS-GCU_p2 psbI-trnS-GCU CTGTCTAATGATCCAGGGCG TAGGAGAGATGGCTGAGTGG 256–259 1.000 81.8
psbI-trnS-GCU_p3 psbI-trnS-GCU CTGTCTAATGATCCAGGGCG GGCTGAGTGGATTAAAGCGT 246–249 1.000 80.5
psbI-trnS-GCU_p4 psbI-trnS-GCU CTGTCTAATGATCCAGGGCG TGGCTGAGTGGATTAAAGCG 247–250 1.000 80.5
psbI-trnS-GCU_p5 psbI-trnS-GCU CTGTCTAATGATCCAGGGCG GAGTGGATTAAAGCGTCGGA 242–245 1.000 80.3

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (4)

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

Species Accession Length (bp) Link
Philotheca difformis subsp. smithiana OL591210.1 156403 View on NCBI ↗
Philotheca gardneri NC_081896.1 157239 View on NCBI ↗
Philotheca tomentella NC_081898.1 156643 View on NCBI ↗
Philotheca trachyphylla NC_081899.1 156805 View on NCBI ↗