Markers + reference

Phrynium

5 species · Marantaceae · Zingiberales

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Species 5
Genome length 167–172 kb
Candidate markers 274
Primer pairs 95

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 274 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-GCU-trnG-UCC LSC 2537 0.0126 0.98 64.8 yes View details
atpH-atpI LSC 1664 0.0133 1.00 63.2 yes View details
trnE-UUC-trnT-GGU LSC 1026 0.0105 0.99 71.1 yes View details
petA-psbJ LSC 1006 0.0093 1.00 62.6 yes View details
clpP LSC 2108 0.0080 1.00 50.8 yes View details
rpl16 LSC 1705 0.0073 1.00 67.9 yes View details
rpl22-rps19 IRb 271 0.0284 1.00 64.9 yes View details
ycf1 IRb 1098 0.0273 1.00 68.2 yes View details
ndhF-rpl32 SSC 1260 0.0117 0.99 68.6 yes View details
psaC-ndhE SSC 1705 0.0084 0.98 50.0 yes View details
ycf1 SSC 5649 0.0056 1.00 46.9 no View details
ycf1-ndhF SSC 102 0.0624 1.00 77.7 yes View details
trnI-CAU-ycf2 IRb 66 0.0439 1.00 65.5 yes View details
ycf2-trnI-CAU IRa 66 0.0439 1.00 65.5 yes View details
petN-psbM LSC 975 0.0040 0.99 64.8 yes View details
rps15-ycf1 SSC 621 0.0089 1.00 63.7 yes View details
rpl36-infA LSC 108 0.0389 1.00 62.9 yes View details
trnK-UUU-rps16 LSC 886 0.0077 1.00 62.6 yes View details
trnG-GCC-trnfM-CAU LSC 202 0.0119 1.00 62.1 yes View details
rps19-psbA IRa 465 0.0077 1.00 62.0 no View details
rps16-trnQ-UUG LSC 1171 0.0067 1.00 61.9 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 AGTCGCACTTAAAAGCCGAG TCAACCAACAGGAACCGTTT 999–1006 1.000 79.6
trnK-UUU-rps16_p2 trnK-UUU-rps16 TAGTCGCACTTAAAAGCCGA TCAACCAACAGGAACCGTTT 1000–1007 1.000 78.3
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCGCACTTAAAAGCCGAGTA TCAACCAACAGGAACCGTTT 997–1004 1.000 78.3
trnK-UUU-rps16_p4 trnK-UUU-rps16 AGTCGCACTTAAAAGCCGAG CTCAACCAACAGGAACCGTT 1000–1007 1.000 78.0
trnK-UUU-rps16_p5 trnK-UUU-rps16 CGCACTTAAAAGCCGAGTAC TCAACCAACAGGAACCGTTT 996–1003 1.000 77.9
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CAGCCGATCATGTCCTTCAA GAGGTTCGAATCCTTCCGTC 755–1262 1.000 84.2
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GCCGATCATGTCCTTCAAGT GAGGTTCGAATCCTTCCGTC 753–1260 1.000 84.2
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AATCCACAGCCGATCATGTC GAGGTTCGAATCCTTCCGTC 761–1268 1.000 84.1
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 737–1244 1.000 83.3
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CAGCCGATCATGTCCTTCAA CCAAACAGAAAAATGGGGCG 816–1323 1.000 83.1
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA AACGGAGAGACCCCTTAACT 1928–2801 1.000 83.5
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC AACGGAGAGACCCCTTAACT 1927–2800 1.000 83.5
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC TCAAGTAATCAGAGCGAGCG AACGGAGAGACCCCTTAACT 1999–2872 1.000 81.9
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CGGAGAGAGAGGGATTCGAA AACGGAGAGACCCCTTAACT 1981–2854 1.000 81.0
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AGCAATCCGACGCTTTAGTC AACGGAGAGACCCCTTAACT 1930–2803 1.000 80.7
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT GCGAATCCATGGAAGGTCAT 1614–1747 1.000 85.8
atpH-atpI_p2 atpH-atpI AGCCAATCCAGCAGCAATAA GCGAATCCATGGAAGGTCAT 1630–1763 1.000 84.9
atpH-atpI_p3 atpH-atpI AATAACGGAAGCGGCAGAAA GCGAATCCATGGAAGGTCAT 1615–1748 1.000 84.7
atpH-atpI_p4 atpH-atpI GCCAATCCAGCAGCAATAAC GCGAATCCATGGAAGGTCAT 1629–1762 1.000 84.4
atpH-atpI_p5 atpH-atpI TCCAGCAGCAATAACGGAAG GCGAATCCATGGAAGGTCAT 1624–1757 1.000 84.0
petN-psbM_p1 petN-psbM AGTATGGGGAAGGAGTGGAC TGCTACTGCACTTTTCATTCT 1018–1079 1.000 58.1
petN-psbM_p2 petN-psbM GTATGGGGAAGGAGTGGACT TGCTACTGCACTTTTCATTCT 1017–1078 1.000 58.1
petN-psbM_p3 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCACTTTTCATTCT 1076–1137 1.000 57.8
petN-psbM_p4 petN-psbM TATGGGGAAGGAGTGGACTC TGCTACTGCACTTTTCATTCT 1016–1077 1.000 57.7
petN-psbM_p5 petN-psbM GGGGAAGGAGTGGACTCTAG TGCTACTGCACTTTTCATTCT 1013–1074 1.000 57.3
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU AGAGATGTCCTGAACCGCTA GAACCGATGACTTACGCCTT 947–1135 1.000 84.5
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU AGATGTCCTGAACCGCTAGA GAACCGATGACTTACGCCTT 945–1133 1.000 84.5
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU TCCTTTCGTAGTACCCCCAG GAACCGATGACTTACGCCTT 999–1187 1.000 84.4
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU AGATGTCCTGAACCGCTAGA CCATGGCGTTACTCTACCAC 924–1112 1.000 84.1
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU TCCTTTCGTAGTACCCCCAG CCATGGCGTTACTCTACCAC 978–1166 1.000 84.0

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (5)

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

Species Accession Length (bp) Link
Phrynium hainanense PQ835414.1 166773 View on NCBI ↗
Phrynium imbricatum PQ835416.1 166570 View on NCBI ↗
Phrynium pedunculiferum PQ835420.1 171625 View on NCBI ↗
Phrynium tonkinense PQ835437.1 166803 View on NCBI ↗
Phrynium yunnanense PQ835442.1 166694 View on NCBI ↗