Markers + reference

Simarouba

2 species · Simaroubaceae · Sapindales

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Species 2
Genome length 160–160 kb
Candidate markers 268
Primer pairs 85

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 9 remaining regions by MarkerSeek score (out of 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ycf1 SSC 5688 0.3166 0.83 74.2 yes View details
ndhH SSC 1182 0.4896 0.81 80.4 yes View details
ndhA SSC 2239 0.4847 0.86 79.5 yes View details
ndhG SSC 537 0.4820 0.88 80.3 yes View details
ndhD SSC 1530 0.4901 0.86 81.0 yes View details
ndhD-ccsA SSC 297 0.5255 0.92 76.6 yes View details
ccsA SSC 960 0.4764 0.93 82.9 yes View details
ndhF SSC 2220 0.4590 0.86 79.6 yes View details
trnL-UAG-rpl32 SSC 619 0.4364 0.98 80.9 yes View details
ndhI SSC 513 0.4652 0.90 80.4 yes View details
ndhI-ndhG SSC 374 0.4602 0.91 77.8 yes View details
ycf1-rps15 SSC 389 0.4841 0.89 77.5 yes View details
rpl32-ndhF SSC 296 0.4191 0.92 76.5 yes View details
trnL-UAG SSC 80 0.4935 0.96 76.1 yes View details
ndhG-ndhE SSC 268 0.4936 0.88 75.4 yes View details
atpA-atpF LSC 59 0.0678 1.00 74.6 yes View details
ndhE SSC 306 0.4462 0.82 73.8 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 85 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
atpA-atpF_p1 atpA-atpF TACTTGAAGGACGGTACCGA TGTTTGGGGCGATGAAAGAA 196–200 1.000 79.9
atpA-atpF_p2 atpA-atpF GCCTACTTGAAGGACGGTAC TGTTTGGGGCGATGAAAGAA 199–203 1.000 79.2
atpA-atpF_p3 atpA-atpF TACTTGAAGGACGGTACCGA ATGTTTGGGGCGATGAAAGA 197–201 1.000 78.3
atpA-atpF_p4 atpA-atpF ACTTGAAGGACGGTACCGAT TGTTTGGGGCGATGAAAGAA 195–199 1.000 78.0
atpA-atpF_p5 atpA-atpF TACTTGAAGGACGGTACCGA CATGTTTGGGGCGATGAAAG 198–202 1.000 77.7
ycf1_p1 ycf1 GGATCAGTTCGCTCAAACCA TTTTCTCCAAAGGGTGTCCG 709 0.500 58.3
ycf1_p2 ycf1 TGGATCAGTTCGCTCAAACC TTTTCTCCAAAGGGTGTCCG 710 0.500 58.3
ycf1_p3 ycf1 GGATCAGTTCGCTCAAACCA AAAGGGTGTCCGCTCTTTTT 701 0.500 57.9
ycf1_p4 ycf1 TGGATCAGTTCGCTCAAACC AAAGGGTGTCCGCTCTTTTT 702 0.500 57.9
ycf1_p5 ycf1 ACCTGGAGCTTTGGTTCTTC TTTTCTCCAAAGGGTGTCCG 963 0.500 57.6
ycf1-rps15_p1 ycf1-rps15 CGAGAAGCGGGTTATGTTGA ACGATTAGGCGAAGAACACC 1281 0.500 59.9
ycf1-rps15_p2 ycf1-rps15 CGAGAAGCGGGTTATGTTGA GATTAGGCGAAGAACACCGT 1279 0.500 59.9
ycf1-rps15_p3 ycf1-rps15 CGGACACCCTTTGGAGAAAA ACGATTAGGCGAAGAACACC 1060 0.500 59.8
ycf1-rps15_p4 ycf1-rps15 CGGACACCCTTTGGAGAAAA GATTAGGCGAAGAACACCGT 1058 0.500 59.8
ycf1-rps15_p5 ycf1-rps15 CGAGAAGCGGGTTATGTTGA ATAAGCTAGCAGACGTTGGC 1013 0.500 59.5
ndhH_p1 ndhH GCCAACGTCTGCTAGCTTAT AGCCTCAATCCACCCTTACT 2128 0.500 59.3
ndhH_p2 ndhH GCCAACGTCTGCTAGCTTAT TGAGCCTCAATCCACCCTTA 2130 0.500 59.3
ndhH_p3 ndhH GCCAACGTCTGCTAGCTTAT CCTCAATCCACCCTTACTGC 2126 0.500 59.2
ndhH_p4 ndhH GCCAACGTCTGCTAGCTTAT GCCTCAATCCACCCTTACTG 2127 0.500 59.2
ndhH_p5 ndhH TGCGGATCGGTTGAATTTCA AGCCTCAATCCACCCTTACT 2252 0.500 58.3
ndhA_p1 ndhA AGAGTTGAAGCCCCAAAAGG TGCGCGTATTGTTTGTTGAC 2579 0.500 59.8
ndhA_p2 ndhA AGTTGAAGCCCCAAAAGGAG TGCGCGTATTGTTTGTTGAC 2577 0.500 59.8
ndhA_p3 ndhA GAGTTGAAGCCCCAAAAGGA TGCGCGTATTGTTTGTTGAC 2578 0.500 59.8
ndhA_p4 ndhA GTTGAAGCCCCAAAAGGAGA TGCGCGTATTGTTTGTTGAC 2576 0.500 59.8
ndhA_p5 ndhA TCCCACTTTTGAATTGCCGA TGCGCGTATTGTTTGTTGAC 2616 0.500 59.7
ndhI_p1 ndhI GTTGATATAGTTGGGGCGCA TGAACCGACCGGGAATTTTT 1444 0.500 59.6
ndhI_p2 ndhI GTTGATATAGTTGGGGCGCA TTGAACCGACCGGGAATTTT 1445 0.500 59.6
ndhI_p3 ndhI GTTGATATAGTTGGGGCGCA ACCCCATCACCAATAGTCCA 1795 0.500 59.5
ndhI_p4 ndhI GTTGATATAGTTGGGGCGCA TAATCCCGTACCACGACGTA 1869 0.500 59.4
ndhI_p5 ndhI GTTGATATAGTTGGGGCGCA ACGGAACCCTAGGAATTGGA 1141 0.500 59.4

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
Simarouba amara NC_085162.1 159838 View on NCBI ↗
Simarouba versicolor NC_088060.1 159693 View on NCBI ↗