Markers + reference

Pleurophora

3 species · Lythraceae · Myrtales

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Species 3
Genome length 160–161 kb
Candidate markers 266
Primer pairs 110

Genome-wide nucleotide diversity

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

Candidate markers

12 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 430 0.0501 0.90 80.5 yes View details
trnK-UUU-rps16 LSC 901 0.0157 0.99 63.1 yes View details
rps16-trnQ-UUG LSC 1444 0.0159 0.99 64.7 yes View details
trnR-UCU-atpA LSC 359 0.0288 1.00 74.0 yes View details
rpoC2 LSC 4170 0.0042 1.00 44.9 yes View details
trnE-UUC-trnT-GGU LSC 949 0.0119 1.00 59.4 yes View details
psbZ-trnG-GCC LSC 350 0.0057 1.00 56.3 yes View details
trnT-UGU-trnL-UAA LSC 1201 0.0128 1.00 70.0 yes View details
psbE-petL LSC 1417 0.0106 1.00 65.9 yes View details
rpl33-rps18 LSC 347 0.0215 0.98 59.0 yes View details
ndhF-rpl32 SSC 1007 0.0146 1.00 70.7 yes View details
rps15-ycf1 SSC 446 0.0254 1.00 57.9 yes View details
psbT-pbf1 LSC 59 0.0678 1.00 87.5 yes View details
rps2-rpoC2 LSC 225 0.0341 1.00 69.4 yes View details
rpoB-trnC-GCA LSC 1220 0.0109 1.00 66.7 yes View details
trnG-GCC-trnfM-CAU LSC 200 0.0300 1.00 66.0 yes View details
psaJ-rpl33 LSC 566 0.0083 1.00 65.3 yes View details
psaA-pafI LSC 703 0.0095 1.00 65.1 yes View details
trnL-UAG-ccsA SSC 107 0.0187 1.00 63.9 yes View details
petA-psbJ LSC 969 0.0089 1.00 63.0 yes View details
ndhG-ndhI SSC 438 0.0107 1.00 62.6 yes View details
psbK-psbI LSC 420 0.0103 1.00 62.3 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 110 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 CCTCTAGACCTAGCTGCTGT 453–497 1.000 87.4
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 456–500 1.000 87.3
trnH-GUG-psbA_p3 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCTCTAGACCTAGCTGCTGT 467–511 1.000 87.2
trnH-GUG-psbA_p4 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCTCTAGACCTAGCTGCTGT 466–510 1.000 87.2
trnH-GUG-psbA_p5 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCTCTAGACCTAGCTGCTGT 468–512 1.000 87.2
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT AAAAGGCGGGGGTTTTTACA 956–990 1.000 82.4
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AAAAGGCGGGGGTTTTTACA 955–989 1.000 82.4
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCAGTCGTGGTCTTCCAAAC AAAAGGCGGGGGTTTTTACA 1041–1075 1.000 81.4
trnK-UUU-rps16_p4 trnK-UUU-rps16 CAGTCGTGGTCTTCCAAACT AAAAGGCGGGGGTTTTTACA 1040–1074 1.000 81.4
trnK-UUU-rps16_p5 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA AAAAGGCGGGGGTTTTTACA 965–999 1.000 81.4
rps16-trnQ-UUG_p1 rps16-trnQ-UUG GCACGTTGCTTTTTACCACA GAGGTTCGAATCCTTCCGTC 1490–1512 1.000 81.6
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCTGTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1506–1528 1.000 81.4
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AGTCGCACGTTGCTTTTTAC GAGGTTCGAATCCTTCCGTC 1494–1516 1.000 80.1
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CAAGTCGCACGTTGCTTTTT GAGGTTCGAATCCTTCCGTC 1496–1518 1.000 79.5
rps16-trnQ-UUG_p5 rps16-trnQ-UUG GTCGCACGTTGCTTTTTACC GAGGTTCGAATCCTTCCGTC 1493–1515 1.000 78.3
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG TTCTTCACGCCCAGGATTAC 554–558 1.000 79.0
psbK-psbI_p2 psbK-psbI TGGCAAGCTGCTGTAAGTTT TTCTTCACGCCCAGGATTAC 551–555 1.000 77.0
psbK-psbI_p3 psbK-psbI TTGGCAAGCTGCTGTAAGTT TTCTTCACGCCCAGGATTAC 552–556 1.000 77.0
psbK-psbI_p4 psbK-psbI TTTGGCAAGCTGCTGTAAGT TTCTTCACGCCCAGGATTAC 553–557 1.000 76.9
psbK-psbI_p5 psbK-psbI TGTTTGGCAAGCTGCTGTAA TTCTTCACGCCCAGGATTAC 555–559 1.000 74.6
trnR-UCU-atpA_p1 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC CAGGAACAGAAGGAACGCTT 420–427 1.000 70.1
trnR-UCU-atpA_p2 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC TTCAGGAACAGAAGGAACGC 422–429 1.000 70.0
trnR-UCU-atpA_p3 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC CATTTACCCCGGAAGCAGAA 461–468 1.000 69.6
trnR-UCU-atpA_p4 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC AACATTTACCCCGGAAGCAG 463–470 1.000 69.2
trnR-UCU-atpA_p5 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC AAACATTTACCCCGGAAGCA 464–471 1.000 68.2
rps2-rpoC2_p1 rps2-rpoC2 AGGTGCCATCCTAGGATTCC CGCGGGCGAAATCATAGATA 437–446 1.000 77.8
rps2-rpoC2_p2 rps2-rpoC2 TGCCGAAATATAAGGTGCCA CGCGGGCGAAATCATAGATA 449–458 1.000 76.5
rps2-rpoC2_p3 rps2-rpoC2 GGTGCCATCCTAGGATTCCA CGCGGGCGAAATCATAGATA 436–445 1.000 75.4
rps2-rpoC2_p4 rps2-rpoC2 TTGCCGAAATATAAGGTGCCA CGCGGGCGAAATCATAGATA 450–459 1.000 74.2
rps2-rpoC2_p5 rps2-rpoC2 TGCCGAAATATAAGGTGCCAT CGCGGGCGAAATCATAGATA 449–458 1.000 72.4

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
Pleurophora anomala NC_082010.1 159726 View on NCBI ↗
Pleurophora pulchra NC_082009.1 159999 View on NCBI ↗
Pleurophora saccocarpa NC_082007.1 160595 View on NCBI ↗