Markers + reference

Pternandra

2 species · Melastomataceae · Myrtales

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Species 2
Genome length 157–157 kb
Candidate markers 263
Primer pairs 110

Genome-wide nucleotide diversity

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

Candidate markers

15 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 263 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 388 0.0525 0.98 75.6 yes View details
rps16-trnQ-UUG LSC 1240 0.0259 1.00 66.2 yes View details
trnR-UCU-atpA LSC 403 0.0649 0.96 83.2 yes View details
trnD-GUC-trnY-GUA LSC 429 0.0260 0.99 62.2 yes View details
trnE-UUC-trnT-GGU LSC 924 0.0231 0.94 61.7 yes View details
trnC-GCA-ndhJ LSC 870 0.0260 0.97 67.1 yes View details
ndhC-trnV-UAC LSC 458 0.0306 1.00 63.8 yes View details
ycf1 IRb 1827 0.0016 1.00 44.6 no View details
ndhF-rpl32 SSC 1028 0.0358 0.95 73.3 yes View details
rpl32-trnL-UAG SSC 296 0.0441 1.00 72.2 yes View details
ccsA SSC 963 0.0114 1.00 51.0 yes View details
ccsA-ndhD SSC 286 0.0524 1.00 72.2 yes View details
ndhG-ndhI SSC 458 0.0316 0.97 63.9 yes View details
rps15-ycf1 SSC 485 0.0250 0.99 57.2 yes View details
ycf1 SSC 5637 0.0142 1.00 46.6 yes View details
psbT-psbN LSC 75 0.1333 1.00 87.5 yes View details
rpl2-trnH-GUG IRa 54 0.1111 0.99 86.0 no View details
psbL-psbF LSC 22 0.0455 1.00 78.6 yes View details
rpl2-rpl23 IRb 22 0.0455 1.00 78.6 yes View details
rpl23-rpl2 IRa 22 0.0455 1.00 78.6 yes View details
ndhD-psaC SSC 151 0.0662 1.00 76.4 yes View details
petA-psbJ LSC 881 0.0178 0.83 70.1 yes View details
ndhK-ndhC LSC 64 0.0469 1.00 69.6 yes View details
psaA-ycf3 LSC 589 0.0172 0.99 69.5 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 453–455 1.000 83.2
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 456–458 1.000 83.1
trnH-GUG-psbA_p3 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCTCTAGACCTAGCTGCTGT 467–469 1.000 83.0
trnH-GUG-psbA_p4 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCTCTAGACCTAGCTGCTGT 466–468 1.000 83.0
trnH-GUG-psbA_p5 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCTCTAGACCTAGCTGCTGT 468–470 1.000 83.0
rps16-trnQ-UUG_p1 rps16-trnQ-UUG TCATGTCCGTCAAGTCACAC GAGGTTCGAATCCTTCCGTC 1324–1339 1.000 80.5
rps16-trnQ-UUG_p2 rps16-trnQ-UUG ACACGTTGCTTTCTACCACA GAGGTTCGAATCCTTCCGTC 1308–1323 1.000 79.1
rps16-trnQ-UUG_p3 rps16-trnQ-UUG TCACACGTTGCTTTCTACCA GAGGTTCGAATCCTTCCGTC 1310–1325 1.000 76.9
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CCACAGATGATCATGTCCGT GAGGTTCGAATCCTTCCGTC 1334–1349 1.000 76.8
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CACACGTTGCTTTCTACCAC GAGGTTCGAATCCTTCCGTC 1309–1324 1.000 76.4
trnR-UCU-atpA_p1 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC CACCGAGGAAGCAGAATCTC 494–495 1.000 72.9
trnR-UCU-atpA_p2 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC CATTCACCGAGGAAGCAGAA 498–499 1.000 72.6
trnR-UCU-atpA_p3 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC AAGACATTCACCGAGGAAGC 502–503 1.000 72.5
trnR-UCU-atpA_p4 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC ACCGAGGAAGCAGAATCTCT 493–494 1.000 72.3
trnR-UCU-atpA_p5 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC TTCACCGAGGAAGCAGAATC 496–497 1.000 70.3
trnD-GUC-trnY-GUA_p1 trnD-GUC-trnY-GUA GCGGTGCTCTAACCAATTGA ATGGATTCTTCCTGGGTCGA 551–557 1.000 77.1
trnD-GUC-trnY-GUA_p2 trnD-GUC-trnY-GUA GCGGTGCTCTAACCAATTGA TGGATTCTTCCTGGGTCGAT 550–556 1.000 77.1
trnD-GUC-trnY-GUA_p3 trnD-GUC-trnY-GUA GCGGTGCTCTAACCAATTGA TGGCAATATGTCTACGCTGG 494–500 1.000 76.4
trnD-GUC-trnY-GUA_p4 trnD-GUC-trnY-GUA GCGGTGCTCTAACCAATTGA GGCAATATGTCTACGCTGGT 493–499 1.000 76.4
trnD-GUC-trnY-GUA_p5 trnD-GUC-trnY-GUA GCGGTGCTCTAACCAATTGA GGATTCTTCCTGGGTCGATG 549–555 1.000 76.1
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU TGGATCAGCGAATTCTTGGG GAACCGATGACTTACGCCTT 1159–1211 1.000 84.9
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU TGGATCAGCGAATTCTTGGG GACAGATTCGTGTGGAGTCC 1562–1618 1.000 84.3
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU TGGATCAGCGAATTCTTGGG CAAGACTACGGAATCGGCAA 1586–1642 1.000 84.2
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU TGGATCAGCGAATTCTTGGG AACAAGACTACGGAATCGGC 1588–1644 1.000 84.2
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU TTGATTTCGTCGGGACTGAC GACAGATTCGTGTGGAGTCC 2053–2115 1.000 83.6
psaA-ycf3_p1 psaA-ycf3 TGAGAAATGACCCGGTTTGG AAGATCACAAGGCGTTTCGA 705–712 1.000 79.8
psaA-ycf3_p2 psaA-ycf3 TGAGAAATGACCCGGTTTGG AGATCACAAGGCGTTTCGAA 704–711 1.000 79.8
psaA-ycf3_p3 psaA-ycf3 GCCCATTCCTCGAAAGAAGT AAGATCACAAGGCGTTTCGA 686–693 1.000 79.7
psaA-ycf3_p4 psaA-ycf3 GCCCATTCCTCGAAAGAAGT AGATCACAAGGCGTTTCGAA 685–692 1.000 79.7
psaA-ycf3_p5 psaA-ycf3 TGAGAAATGACCCGGTTTGG TAGCGCTTACTCCCGGTAAT 749–756 1.000 78.6

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
Pternandra korthalsiana MK994877.1 157496 View on NCBI ↗
Pternandra tessellata MK994896.1 156994 View on NCBI ↗