Markers + reference

Phellodendron

2 species · Rutaceae · Sapindales

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Species 2
Genome length 158–159 kb
Candidate markers 275
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 11 remaining regions by MarkerSeek score (out of 275 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 417 0.0096 1.00 60.5 yes View details
rps16 LSC 1166 0.0017 1.00 59.7 yes View details
trnR-UCU-atpA LSC 213 0.0769 0.98 86.7 yes View details
psbZ-trnG-GCC LSC 551 0.0449 0.97 86.4 yes View details
psaJ-rpl33 LSC 498 0.0000 1.00 37.9 yes View details
ycf15-trnL-CAA IRb 739 0.0054 1.00 61.9 yes View details
ndhF-rpl32 SSC 903 0.0000 1.00 35.1 yes View details
ndhB-trnL-CAA IRa 586 0.0000 1.00 35.4 yes View details
trnL-CAA-ycf15 IRa 739 0.0054 1.00 61.9 yes View details
rpl33-rps18 LSC 192 0.0469 1.00 79.5 yes View details
trnT-UGU-trnL-UAA LSC 842 0.0000 0.99 59.6 yes View details
rpl22 IRa 222 0.0000 0.93 56.7 yes View details
rpl32 SSC 174 0.0057 1.00 55.8 yes View details
atpF-atpH LSC 398 0.0000 1.00 54.8 yes View details
ycf1 SSC 5469 0.0002 1.00 52.6 yes View details
matK LSC 1521 0.0000 1.00 40.0 yes View details
matK-trnK-UUU LSC 725 0.0000 1.00 40.0 yes View details
rps16-trnQ-UUG LSC 1258 0.0000 1.00 40.0 yes View details
ycf1 IRb 1095 0.0000 1.00 40.0 no View details
rpl22 LSC 501 0.0000 1.00 37.9 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 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 GATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 487 1.000 79.0
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TTCCCTCTAGACCTAGCTGC 501 1.000 79.0
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TTCCCTCTAGACCTAGCTGC 500 1.000 79.0
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TTCCCTCTAGACCTAGCTGC 502 1.000 79.0
trnH-GUG-psbA_p5 trnH-GUG-psbA CGCATGGTGGATTCACAATC TTCCCTCTAGACCTAGCTGC 516 1.000 76.2
matK_p1 matK AATTACATGGTCTCGTAACC CGCCCACTAAATCCCTTACC 1593 1.000 40.0
matK_p2 matK AATTACATGGTCTCGTAACC GTATCGTTTGATCGCCCACT 1605 1.000 40.0
matK_p3 matK AAATTACATGGTCTCGTAACC CGCCCACTAAATCCCTTACC 1594 1.000 40.0
matK_p4 matK AAATTACATGGTCTCGTAACC GTATCGTTTGATCGCCCACT 1606 1.000 40.0
matK_p5 matK AATTACATGGTCTCGTAACC TGTTTTCACCGTATCGCACT 1627 1.000 40.0
matK-trnK-UUU_p1 matK-trnK-UUU ACTCCCGAAAAAGAAGTGGG AACGGTAGAGTACTCGGCTT 828 1.000 76.5
matK-trnK-UUU_p2 matK-trnK-UUU ACTCCCGAAAAAGAAGTGGG ACGGTAGAGTACTCGGCTTT 827 1.000 76.5
matK-trnK-UUU_p3 matK-trnK-UUU CTCCCGAAAAAGAAGTGGGT AACGGTAGAGTACTCGGCTT 827 1.000 76.5
matK-trnK-UUU_p4 matK-trnK-UUU CTCCCGAAAAAGAAGTGGGT ACGGTAGAGTACTCGGCTTT 826 1.000 76.5
matK-trnK-UUU_p5 matK-trnK-UUU CTCCCGAAAAAGAAGTGGGT TTGGGTTGCTAACTCAACGG 842 1.000 74.6
rps16_p1 rps16 TATAAGACTCCTCCCCACCC AGACTGTGTATAGACTGAAGCA 1289 1.000 44.4
rps16_p2 rps16 CTCCTCCCCACCCTCTTTTT AGACTGTGTATAGACTGAAGCA 1282 1.000 43.3
rps16_p3 rps16 ATAAGACTCCTCCCCACCCT AGACTGTGTATAGACTGAAGCA 1288 1.000 42.9
rps16_p4 rps16 TATAAGACTCCTCCCCACCC AAGACTGTGTATAGACTGAAGCA 1290 1.000 41.9
rps16_p5 rps16 TATAAGACTCCTCCCCACCC AGACTGTGTATAGACTGAAGCAA 1289 1.000 41.9
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1331 1.000 78.3
rps16-trnQ-UUG_p2 rps16-trnQ-UUG CGGATCGTGTCCTTCAAGTC GAGGTTCGAATCCTTCCGTC 1346 1.000 76.4
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GGATCGTGTCCTTCAAGTCG GAGGTTCGAATCCTTCCGTC 1345 1.000 76.4
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GGGTTTTGGTCCCGGTATTC 1352 1.000 74.6
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 1335 1.000 73.5
trnR-UCU-atpA_p1 trnR-UCU-atpA CTGAAAGGCGTCCATTGTCT GAGGAAGCAGAAGCCCTTTT 366–367 1.000 82.4
trnR-UCU-atpA_p2 trnR-UCU-atpA CTGAAAGGCGTCCATTGTCT GAAGCCCTTTTGCAAGAAGC 357–358 1.000 81.5
trnR-UCU-atpA_p3 trnR-UCU-atpA CTGAAAGGCGTCCATTGTCT TCAGGAACAAATGGAACGCT 334–335 1.000 81.4
trnR-UCU-atpA_p4 trnR-UCU-atpA CTGAAAGGCGTCCATTGTCT AGCCCTTTTGCAAGAAGCTA 355–356 1.000 80.9
trnR-UCU-atpA_p5 trnR-UCU-atpA ACTGAAAGGCGTCCATTGTC GAGGAAGCAGAAGCCCTTTT 367–368 1.000 80.1

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
Phellodendron amurense NC_035551.1 158442 View on NCBI ↗
Phellodendron chinense NC_050949.1 158537 View on NCBI ↗