Markers + reference

Fagaropsis

2 species · Rutaceae · Sapindales

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Species 2
Genome length 158–158 kb
Candidate markers 266
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 266 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 400 0.0200 1.00 66.1 yes View details
rps16 LSC 1170 0.0043 1.00 47.0 yes View details
psbK-psbI LSC 385 0.0078 1.00 49.8 yes View details
trnS-GCU-trnS-CGA LSC 976 0.0062 1.00 58.1 yes View details
petN-psbM LSC 1304 0.0054 1.00 61.8 yes View details
ndhC-trnV-UAC LSC 423 0.0118 1.00 52.4 yes View details
ycf4-cemA LSC 477 0.0191 0.99 68.6 yes View details
ndhF-trnL-UAG SSC 1909 0.0037 1.00 54.1 yes View details
ndhG SSC 537 0.0019 1.00 44.7 yes View details
ndhA SSC 2231 0.0027 0.99 53.2 yes View details
psbT-psbN LSC 75 0.0267 1.00 67.8 yes View details
rps16-trnQ-UUG LSC 822 0.0051 0.96 65.6 yes View details
accD-psaI LSC 716 0.0056 1.00 62.0 yes View details
rpoB-trnC-GCA LSC 1224 0.0041 1.00 61.2 yes View details
psbE-petL LSC 1345 0.0023 0.99 61.1 yes View details
ycf2-trnL-CAA IRb 1012 0.0040 1.00 61.0 yes View details
trnL-CAA-ycf2 IRa 1012 0.0040 1.00 61.0 yes View details
trnE-UUC-trnT-GGU LSC 837 0.0024 0.99 60.9 yes View details
petA-psbJ LSC 1083 0.0028 1.00 60.3 yes View details
rpl14-rpl16 LSC 127 0.0081 0.97 60.2 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 100 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 469 1.000 79.7
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TTCCCTCTAGACCTAGCTGC 483 1.000 79.7
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TTCCCTCTAGACCTAGCTGC 482 1.000 79.7
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TTCCCTCTAGACCTAGCTGC 484 1.000 79.6
trnH-GUG-psbA_p5 trnH-GUG-psbA CGCATGGTGGATTCACAATC TTCCCTCTAGACCTAGCTGC 498 1.000 76.8
rps16_p1 rps16 AGCCGTACTTAAAAGCCGAG CGTGTCGGTCCAAATCTCAT 2356–2387 1.000 81.5
rps16_p2 rps16 AGCCGTACTTAAAAGCCGAG TGTGGTGAGCCCTTACCTTA 2044–2075 1.000 81.5
rps16_p3 rps16 CCTTTCAGGATCAGTCGTGG CGTGTCGGTCCAAATCTCAT 2440–2471 1.000 81.3
rps16_p4 rps16 AGCCGTACTTAAAAGCCGAG CATCATCCCCGCAGAAAGAA 2433–2464 1.000 81.1
rps16_p5 rps16 AGCCGTACTTAAAAGCCGAG TTCATCATCCCCGCAGAAAG 2435–2466 1.000 81.1
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CGAAAACGGTGGATGCAAAA GAGGTTCGAATCCTTCCGTC 908–942 1.000 81.7
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 861–895 1.000 81.7
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAAATTGAAATGGGGCGTCG 919–953 1.000 81.4
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CGAAAACGGTGGATGCAAAA GAAATTGAAATGGGGCGTCG 966–1000 1.000 81.3
rps16-trnQ-UUG_p5 rps16-trnQ-UUG GGATCGTGTCCTTCAAGTCG GAGGTTCGAATCCTTCCGTC 875–909 1.000 79.8
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG CGCCCTGGATCATTAGACAG 504–505 1.000 78.7
psbK-psbI_p2 psbK-psbI TGGCAAGCTGCTGTAAGTTT CGCCCTGGATCATTAGACAG 501–502 1.000 76.7
psbK-psbI_p3 psbK-psbI TTGGCAAGCTGCTGTAAGTT CGCCCTGGATCATTAGACAG 502–503 1.000 76.7
psbK-psbI_p4 psbK-psbI TTTGGCAAGCTGCTGTAAGT CGCCCTGGATCATTAGACAG 503–504 1.000 76.7
psbK-psbI_p5 psbK-psbI GTTTGGCAAGCTGCTGTAAG ACGCCCTGGATCATTAGACA 505–506 1.000 76.0
trnS-GCU-trnS-CGA_p1 trnS-GCU-trnS-CGA CCGACGCTTTAATCCACTCA AACTGAAGGACCCCTTAACT 1079–1106 1.000 61.8
trnS-GCU-trnS-CGA_p2 trnS-GCU-trnS-CGA ACGGAAAGAGAGGGATTCGA AACTGAAGGACCCCTTAACT 1137–1164 1.000 60.6
trnS-GCU-trnS-CGA_p3 trnS-GCU-trnS-CGA CCGACGCTTTAATCCACTCA AAACTGAAGGACCCCTTAACT 1080–1107 1.000 60.3
trnS-GCU-trnS-CGA_p4 trnS-GCU-trnS-CGA ACGCTTTAATCCACTCAGCC AACTGAAGGACCCCTTAACT 1076–1103 1.000 59.7
trnS-GCU-trnS-CGA_p5 trnS-GCU-trnS-CGA CGCTTTAATCCACTCAGCCA AACTGAAGGACCCCTTAACT 1075–1102 1.000 59.7
rpoB-trnC-GCA_p1 rpoB-trnC-GCA ATTCCCGCATTTCCATCTCC ATCGTTTGTTGATCAGGCGA 1335–1345 1.000 79.5
rpoB-trnC-GCA_p2 rpoB-trnC-GCA ATTCCCGCATTTCCATCTCC ACCAGCCAAGCAGAATAAGG 1368–1378 1.000 79.2
rpoB-trnC-GCA_p3 rpoB-trnC-GCA ATTCCCGCATTTCCATCTCC GTTTGTTGATCAGGCGACAC 1332–1342 1.000 77.7
rpoB-trnC-GCA_p4 rpoB-trnC-GCA ATTCCCGCATTTCCATCTCC AAAAGGATTTGCAGTCCCCC 1294–1304 1.000 77.4
rpoB-trnC-GCA_p5 rpoB-trnC-GCA ATTCCCGCATTTCCATCTCC CAGCCAAGCAGAATAAGGGA 1366–1376 1.000 76.8

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
Fagaropsis angolensis PQ310232.1 158196 View on NCBI ↗
Fagaropsis hildebrandtii PQ310233.1 157937 View on NCBI ↗