Markers + reference

Nepenthes

2 species · Nepenthaceae · Caryophyllales

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Species 2
Genome length 156–157 kb
Candidate markers 273
Primer pairs 90

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 9 remaining regions by MarkerSeek score (out of 273 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps19 IRb 297 0.0102 0.33 35.6 yes View details
trnH-GUG-psbA LSC 294 0.0397 0.94 66.1 yes View details
trnS-GCU-trnS-CGA LSC 1107 0.0197 0.96 68.1 yes View details
trnR-UCU-atpA LSC 335 0.0403 0.89 67.3 yes View details
psbZ-trnG-GCC LSC 294 0.1707 0.98 80.6 yes View details
psbE-petL LSC 1271 0.0245 1.00 65.9 yes View details
rps19 IRa 279 0.0036 1.00 41.4 no View details
rpl32-trnL-UAG SSC 1099 0.0219 1.00 58.4 yes View details
ccsA-ndhD SSC 231 0.0649 1.00 68.6 yes View details
ycf1 SSC 5276 0.0140 1.00 51.7 yes View details
psbC-trnS-UGA LSC 191 0.0681 1.00 76.5 yes View details
rps3-rpl22 LSC 11 0.0909 1.00 72.7 yes View details
psbT-psbN LSC 66 0.0455 1.00 71.8 yes View details
trnK-rps16 LSC 709 0.0161 0.96 70.9 yes View details
rpl16-rps3 LSC 1117 0.0162 0.99 68.8 yes View details
rpl22-rps19 LSC 42 0.0476 1.00 66.2 yes View details
trnT-UGU-trnL-UAA LSC 1046 0.0154 1.00 65.2 yes View details
trnF-GAA-ndhJ LSC 515 0.0117 1.00 63.7 yes View details
petA-psbJ LSC 1046 0.0172 1.00 63.2 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps19_p1 rps19 TGGGTAGAGCCGGATCTAAG TCAGTGCTATGCATGGTTCC 1271 0.500 59.6
rps19_p2 rps19 TTATTCGTCGCCGTAGCAAA TCAGTGCTATGCATGGTTCC 1076 0.500 59.6
rps19_p3 rps19 TGGGTAGAGCCGGATCTAAG CAGTGCTATGCATGGTTCCT 1270 0.500 59.6
rps19_p4 rps19 TTATTCGTCGCCGTAGCAAA CAGTGCTATGCATGGTTCCT 1075 0.500 59.6
rps19_p5 rps19 TGGGTAGAGCCGGATCTAAG TTCCCTCTAGACCTAGCTGC 888 0.500 59.4
trnH-GUG-psbA_p1 trnH-GUG-psbA TGGGTAGAGCCGGATCTAAG CTGTTGCGTATTCAGCTCCT 1472 0.500 59.8
trnH-GUG-psbA_p2 trnH-GUG-psbA TTATTCGTCGCCGTAGCAAA CTGTTGCGTATTCAGCTCCT 1277 0.500 59.8
trnH-GUG-psbA_p3 trnH-GUG-psbA AAGCTTAACACAAAGGCGGA CTGTTGCGTATTCAGCTCCT 1139 0.500 59.7
trnH-GUG-psbA_p4 trnH-GUG-psbA AGCTTAACACAAAGGCGGAA CTGTTGCGTATTCAGCTCCT 1138 0.500 59.7
trnH-GUG-psbA_p5 trnH-GUG-psbA TGGGTAGAGCCGGATCTAAG TCAGTGCTATGCATGGTTCC 1271 0.500 59.6
trnK-rps16_p1 trnK-rps16 AAACTCTGCTGATGGTGTGG GGTGCTCAACCTACAGGAAC 893–902 1.000 81.0
trnK-rps16_p2 trnK-rps16 TGGTGTGGACGAATCCTTTG GGTGCTCAACCTACAGGAAC 881–890 1.000 80.9
trnK-rps16_p3 trnK-rps16 AAAGCCGAGTACTCTACCGT GGTGCTCAACCTACAGGAAC 824–833 1.000 80.7
trnK-rps16_p4 trnK-rps16 AAGCCGAGTACTCTACCGTT GGTGCTCAACCTACAGGAAC 823–832 1.000 80.7
trnK-rps16_p5 trnK-rps16 TGTGGACGAATCCTTTGCTT GGTGCTCAACCTACAGGAAC 878–887 1.000 79.7
trnS-GCU-trnS-CGA_p1 trnS-GCU-trnS-CGA ACGGAAAGAGAGGGATTCGA CGAAGGACCCCTTAACTCTT 1232–1264 1.000 71.4
trnS-GCU-trnS-CGA_p2 trnS-GCU-trnS-CGA ACGAAAACGGAAAGAGAGGG CGAAGGACCCCTTAACTCTT 1238–1270 1.000 71.3
trnS-GCU-trnS-CGA_p3 trnS-GCU-trnS-CGA CGAATGACTCGTACAACGGA CGAAGGACCCCTTAACTCTT 1202–1234 1.000 70.7
trnS-GCU-trnS-CGA_p4 trnS-GCU-trnS-CGA CGAAAACGGAAAGAGAGGGA CGAAGGACCCCTTAACTCTT 1237–1269 1.000 69.0
trnS-GCU-trnS-CGA_p5 trnS-GCU-trnS-CGA CTTTCGTCCACTCAGCCATC CGAAGGACCCCTTAACTCTT 1168–1200 1.000 67.7
trnR-UCU-atpA_p1 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC GAGGAAGCAGAAGCCCTTTT 430–432 1.000 72.0
trnR-UCU-atpA_p2 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC TTCACTGAGGAAGCAGAAGC 436–438 1.000 71.2
trnR-UCU-atpA_p3 trnR-UCU-atpA GTTCAAATCCTATTGGACGCA GAGGAAGCAGAAGCCCTTTT 429–431 1.000 66.4
trnR-UCU-atpA_p4 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC TCAAGAACAGATGGAACGCT 398–400 1.000 66.1
trnR-UCU-atpA_p5 trnR-UCU-atpA GTTCAAATCCTATTGGACGCA TTCACTGAGGAAGCAGAAGC 435–437 1.000 65.6
psbC-trnS-UGA_p1 psbC-trnS-UGA CCTGTTCTTTCGATGACCCC GAGAGATGGCTGAGTGGTTG 314–343 1.000 80.9
psbC-trnS-UGA_p2 psbC-trnS-UGA TCGTAGGTCATTTGTGGCAC GAGAGATGGCTGAGTGGTTG 394–423 1.000 80.8
psbC-trnS-UGA_p3 psbC-trnS-UGA TCGTAGGTCATTTGTGGCAC GCTGAGTGGTTGATAGCTCC 386–415 1.000 80.6
psbC-trnS-UGA_p4 psbC-trnS-UGA TCGTAGGTCATTTGTGGCAC GGCTGAGTGGTTGATAGCTC 387–416 1.000 80.6
psbC-trnS-UGA_p5 psbC-trnS-UGA TCGTAGGTCATTTGTGGCAC GGTTGATAGCTCCGGTCTTG 379–408 1.000 80.6

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
Nepenthes khasiana NC_051455.1 156914 View on NCBI ↗
Nepenthes mirabilis NC_041271.1 156381 View on NCBI ↗