Markers + reference

Licania

6 species · Chrysobalanaceae · Malpighiales

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Species 6
Genome length 162–164 kb
Candidate markers 268
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 412 0.0169 1.00 55.5 yes View details
trnK-UUU-trnQ-UUG LSC 1433 0.0090 0.99 60.6 yes View details
trnR-UCU-atpA LSC 247 0.0408 0.92 74.2 yes View details
rpoB-trnC-GCA LSC 1300 0.0051 0.99 45.0 yes View details
trnF-GAA-ndhJ LSC 822 0.0076 1.00 53.4 yes View details
ndhC-trnV-UAC LSC 1143 0.0057 0.98 44.2 yes View details
psbE-petL LSC 1432 0.0053 1.00 55.0 yes View details
psaJ-rpl33 LSC 511 0.0138 1.00 48.7 yes View details
rrn4.5-rrn5 IRb 227 0.0206 1.00 45.6 yes View details
ndhF-rpl32 SSC 1065 0.0076 1.00 56.4 yes View details
trnR-ACG-rrn5 IRa 274 0.0066 0.92 34.9 yes View details
rps19-trnH-GUG LSC 46 0.0681 0.89 65.9 no View details
rpl32-trnL-UAG SSC 1286 0.0038 1.00 63.4 yes View details
trnT-GGU-psbD LSC 1594 0.0032 0.99 62.3 yes View details
psbT-psbN LSC 79 0.0540 1.00 60.0 yes View details
rpl16 LSC 1505 0.0059 0.97 59.7 yes View details
psbI-trnS-GCU LSC 116 0.0149 1.00 57.3 yes View details
atpF-atpH LSC 491 0.0067 1.00 56.6 yes View details
trnG-UCC-trnfM-CAU LSC 201 0.0124 0.99 56.2 yes View details
trnE-UUC-trnT-GGU LSC 640 0.0049 1.00 55.9 yes View details
accD-psaI LSC 823 0.0040 1.00 55.6 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 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 ACTGCCTTAATCCACTTGGC CCGTGCTAACCTTGGTATGG 474–546 1.000 83.0
trnH-GUG-psbA_p2 trnH-GUG-psbA CCTTAATCCACTTGGCCACA CCGTGCTAACCTTGGTATGG 470–542 1.000 82.6
trnH-GUG-psbA_p3 trnH-GUG-psbA ACTGCCTTAATCCACTTGGC ACCGTGCTAACCTTGGTATG 475–547 1.000 82.6
trnH-GUG-psbA_p4 trnH-GUG-psbA CCTTAATCCACTTGGCCACA ACCGTGCTAACCTTGGTATG 471–543 1.000 82.1
trnH-GUG-psbA_p5 trnH-GUG-psbA TAATCCACTTGGCCACATCC CCGTGCTAACCTTGGTATGG 467–539 1.000 80.9
trnK-UUU-trnQ-UUG_p1 trnK-UUU-trnQ-UUG AAAGCCGAGTACTCTACCGT TGAATAGAAATGGGGCGTGG 1514–1554 1.000 81.4
trnK-UUU-trnQ-UUG_p2 trnK-UUU-trnQ-UUG AAGCCGAGTACTCTACCGTT TGAATAGAAATGGGGCGTGG 1513–1553 1.000 81.4
trnK-UUU-trnQ-UUG_p3 trnK-UUU-trnQ-UUG AAAGCCGAGTACTCTACCGT GAGGTTCGAATCCTTCCGTC 1456–1496 1.000 81.3
trnK-UUU-trnQ-UUG_p4 trnK-UUU-trnQ-UUG AAGCCGAGTACTCTACCGTT GAGGTTCGAATCCTTCCGTC 1455–1495 1.000 81.3
trnK-UUU-trnQ-UUG_p5 trnK-UUU-trnQ-UUG TACCGTTGAGTTAGCAACCC TGAATAGAAATGGGGCGTGG 1500–1540 1.000 79.1
psbI-trnS-GCU_p1 psbI-trnS-GCU TTTATCTAATGACCCGGGGC TGGACTAAAGCGTCGGATTG 232–265 1.000 73.8
psbI-trnS-GCU_p2 psbI-trnS-GCU TTTATCTAATGACCCGGGGC GTGGACTAAAGCGTCGGATT 233–266 1.000 73.7
psbI-trnS-GCU_p3 psbI-trnS-GCU TTTATCTAATGACCCGGGGC ATTGGGAGAGATGGCTGAGT 251–284 1.000 72.8
psbI-trnS-GCU_p4 psbI-trnS-GCU TTTATCTAATGACCCGGGGC CATTGGGAGAGATGGCTGAG 252–285 1.000 71.6
psbI-trnS-GCU_p5 psbI-trnS-GCU TTTTATCTAATGACCCGGGGC TGGACTAAAGCGTCGGATTG 233–266 1.000 71.6
trnR-UCU-atpA_p1 trnR-UCU-atpA TGGAAAAGCGTCCATTGTCT ATTCGGGAACAGATGGAACG 361–411 1.000 84.9
trnR-UCU-atpA_p2 trnR-UCU-atpA TGGAAAAGCGTCCATTGTCT CGGGAACAGATGGAACGTTT 358–408 1.000 81.3
trnR-UCU-atpA_p3 trnR-UCU-atpA TTTGGAATGGAAAAGCGTCC ATTCGGGAACAGATGGAACG 368–418 1.000 78.3
trnR-UCU-atpA_p4 trnR-UCU-atpA TGGAAAAGCGTCCATTGTCT AAACATTCACCGAAGAGGCG 402–452 1.000 77.8
trnR-UCU-atpA_p5 trnR-UCU-atpA TGGAAAAGCGTCCATTGTCT GCTATTCGGGAACAGATGGA 364–414 1.000 77.8
atpF-atpH_p1 atpF-atpH GATGGCCAGTGACCAAAAGA CGGAGGGAAAAATACGAGGT 637–651 1.000 76.5
atpF-atpH_p2 atpF-atpH GATGGCCAGTGACCAAAAGA CGAGGCGGAGGGAAAAATAC 642–656 1.000 76.4
atpF-atpH_p3 atpF-atpH GATGGCCAGTGACCAAAAGA GAGGCGGAGGGAAAAATACG 641–655 1.000 76.4
atpF-atpH_p4 atpF-atpH GATGGCCAGTGACCAAAAGA GCGGAGGGAAAAATACGAGG 638–652 1.000 76.4
atpF-atpH_p5 atpF-atpH GATGGCCAGTGACCAAAAGA GGCGGAGGGAAAAATACGAG 639–653 1.000 76.4
rpoB-trnC-GCA_p1 rpoB-trnC-GCA ATTCCCTCATTTGCAGTCCC CTTACCGCTCGGCCATGT 1339–1348 1.000 49.8
rpoB-trnC-GCA_p2 rpoB-trnC-GCA ATTCCCTCATTTGCAGTCCC TTACCGCTCGGCCATGTC 1338–1347 1.000 49.8
rpoB-trnC-GCA_p3 rpoB-trnC-GCA ATTCCCTCATTTGCAGTCCC ATTTGCAGTCCCCCGCCTTA 1355–1364 1.000 49.5
rpoB-trnC-GCA_p4 rpoB-trnC-GCA ATTCCCTCATTTGCAGTCCC CTTACCGCTCGGCCATGTC 1339–1348 1.000 49.3
rpoB-trnC-GCA_p5 rpoB-trnC-GCA GCCCTGACCAATGAACCTAC CTTACCGCTCGGCCATGT 1403–1412 1.000 49.0

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (6)

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

Species Accession Length (bp) Link
Licania alba NC_024064.1 162467 View on NCBI ↗
Licania canescens NC_030566.1 164238 View on NCBI ↗
Licania majuscula NC_030569.1 162445 View on NCBI ↗
Licania membranacea NC_030570.1 162201 View on NCBI ↗
Licania micrantha NC_030572.1 162313 View on NCBI ↗
Licania ovalifolia NC_030574.1 162227 View on NCBI ↗