Markers + reference

Pandanus

3 species · Pandanaceae · Pandanales

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Species 3
Genome length 158–159 kb
Candidate markers 272
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 9 remaining regions by MarkerSeek score (out of 272 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 948 0.0121 0.99 52.2 yes View details
petN-psbM LSC 1215 0.0079 0.98 59.6 yes View details
trnT-UGU-trnL-UAA LSC 803 0.0159 1.00 62.0 yes View details
accD-psaI LSC 737 0.0612 0.97 89.9 yes View details
pafII-cemA LSC 813 0.0121 0.98 65.8 yes View details
petA-psbJ LSC 1102 0.0176 1.00 67.9 yes View details
clpP1 LSC 2055 0.0116 1.00 53.9 yes View details
psbB-psbT LSC 175 0.0229 1.00 56.2 yes View details
ndhE SSC 303 0.0066 1.00 41.8 yes View details
ndhE-psaC SSC 369 0.0247 0.95 60.9 yes View details
trnL-UAG-rpl32 SSC 784 0.0494 1.00 90.5 yes View details
atpH-atpI LSC 746 0.0063 0.99 63.9 yes View details
psbM-trnD-GUC LSC 1040 0.0058 0.99 62.9 yes View details
trnK-UUU-rps16 LSC 563 0.0084 0.99 62.8 yes View details
psaA-pafI LSC 625 0.0054 0.99 62.8 yes View details
trnW-CCA-trnP-UGG LSC 181 0.0147 1.00 62.8 yes View details
trnR-ACG-trnN-GUU IRb 591 0.0046 0.99 62.7 yes View details
trnN-GUU-trnR-ACG IRa 591 0.0046 0.99 62.7 yes View details
rps18-rpl20 LSC 254 0.0079 1.00 62.3 yes View details
psbK-psbI LSC 343 0.0117 1.00 61.1 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
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT AAAAGGGCGCTCAACCTAC 672–677 1.000 71.7
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AAAAGGGCGCTCAACCTAC 671–676 1.000 71.7
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT GAAAAGGGCGCTCAACCTAC 673–678 1.000 70.6
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GAAAAGGGCGCTCAACCTAC 672–677 1.000 70.6
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GAAAAGGGCGCTCAACCTA 672–677 1.000 70.3
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CAGCCGATCATGTCCTTCAA GAAATTGAAATGGGGCGTGG 1097–1188 1.000 81.5
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GCCGATCATGTCCTTCAAGT GAAATTGAAATGGGGCGTGG 1095–1186 1.000 81.5
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AATCCACAGCCGATCATGTC GAAATTGAAATGGGGCGTGG 1103–1194 1.000 81.4
rps16-trnQ-UUG_p4 rps16-trnQ-UUG GAATCCACAGCCGATCATGT GAAATTGAAATGGGGCGTGG 1104–1195 1.000 81.4
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CAGCCGATCATGTCCTTCAA GAGGTTCGAATCCTTCCGTC 1039–1130 1.000 81.1
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG TCTTCACGTCCAGGATTACG 480–489 1.000 73.2
psbK-psbI_p2 psbK-psbI AATCGTAGACGTTATGCCCG TCTTCACGTCCAGGATTACG 532–541 1.000 72.5
psbK-psbI_p3 psbK-psbI ATGCCCGTCATACCTGTACT TCTTCACGTCCAGGATTACG 519–528 1.000 71.9
psbK-psbI_p4 psbK-psbI TGGCAAGCTGCTGTAAGTTT TCTTCACGTCCAGGATTACG 477–486 1.000 71.2
psbK-psbI_p5 psbK-psbI TTGGCAAGCTGCTGTAAGTT TCTTCACGTCCAGGATTACG 478–487 1.000 71.2
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTGCAACTTTAGCTGCGG 828–833 1.000 80.2
atpH-atpI_p2 atpH-atpI TACCTTGACCAACTCCAGGT TTTTGCAACTTTAGCTGCGG 884–889 1.000 79.5
atpH-atpI_p3 atpH-atpI AATAACGGAAGCGGCAGAAA TTTTGCAACTTTAGCTGCGG 829–834 1.000 79.0
atpH-atpI_p4 atpH-atpI GCAGTACCTTGACCAACTCC TTTTGCAACTTTAGCTGCGG 888–893 1.000 78.9
atpH-atpI_p5 atpH-atpI GCCAATCCAGCAGCAATAAC TTTTGCAACTTTAGCTGCGG 843–848 1.000 78.7
petN-psbM_p1 petN-psbM AGTATGGGGAAGGAGTGGAC TGCTACTGCACTGTTCATTCT 1309–1356 1.000 71.3
petN-psbM_p2 petN-psbM GTATGGGGAAGGAGTGGACT TGCTACTGCACTGTTCATTCT 1308–1355 1.000 71.3
petN-psbM_p3 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCACTGTTCATTCT 1367–1414 1.000 70.9
petN-psbM_p4 petN-psbM TATGGGGAAGGAGTGGACTC TGCTACTGCACTGTTCATTCT 1307–1354 1.000 70.9
petN-psbM_p5 petN-psbM GGGGAAGGAGTGGACTCTAG TGCTACTGCACTGTTCATTCT 1304–1351 1.000 70.6
psbM-trnD-GUC_p1 psbM-trnD-GUC AGAATGAACAGTGCAGTAGC TATGCCTCACCGGGATTGTA 1165–1200 1.000 61.8
psbM-trnD-GUC_p2 psbM-trnD-GUC AGAATGAACAGTGCAGTAGC CCTCACCGGGATTGTAGTTC 1161–1196 1.000 61.0
psbM-trnD-GUC_p3 psbM-trnD-GUC AGAATGAACAGTGCAGTAGC CATATGCCTCACCGGGATTG 1167–1202 1.000 59.7
psbM-trnD-GUC_p4 psbM-trnD-GUC AGAATGAACAGTGCAGTAGC TTCAATTGGTCAGAGCACCG 1144–1179 1.000 59.7
psbM-trnD-GUC_p5 psbM-trnD-GUC AGGAACTAGAATGAACAGTGCA TATGCCTCACCGGGATTGTA 1172–1207 1.000 58.7

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

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

Species Accession Length (bp) Link
Pandanus amaryllifolius NC_070105.1 157839 View on NCBI ↗
Pandanus odorifer NC_070192.1 157885 View on NCBI ↗
Pandanus tectorius NC_042747.1 159362 View on NCBI ↗