Markers + reference

Gymnotheca

2 species · Saururaceae · Piperales

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Species 2
Genome length 162–162 kb
Candidate markers 273
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 273 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 926 0.0033 1.00 61.0 yes View details
rps16-trnQ-UUG LSC 1482 0.0020 1.00 59.9 yes View details
trnS-GCU-trnG-UCC LSC 967 0.0031 1.00 60.6 yes View details
rps2 LSC 711 0.0000 1.00 27.2 yes View details
rpoB LSC 3213 0.0016 1.00 42.2 yes View details
rpoB-trnC-GCA LSC 1279 0.0039 1.00 61.2 yes View details
petA-psbJ LSC 1321 0.0031 0.99 61.9 yes View details
petD LSC 893 0.0034 1.00 60.8 yes View details
ndhF SSC 2220 0.0027 1.00 58.8 yes View details
ndhF-rpl32 SSC 1213 0.0058 1.00 52.3 yes View details
ccsA SSC 972 0.0041 1.00 52.6 yes View details
ndhA SSC 2209 0.0023 1.00 58.6 yes View details
psbT-psbN LSC 63 0.0159 1.00 61.6 yes View details
petN-psbM LSC 1173 0.0043 1.00 61.2 yes View details
accD-psaI LSC 713 0.0014 0.98 61.2 yes View details
trnE-UUC-trnT-GGU LSC 688 0.0029 1.00 60.4 yes View details
trnT-UGU-trnL-UAA LSC 858 0.0023 1.00 60.1 yes View details
ccsA-ndhD SSC 245 0.0204 1.00 60.1 yes View details
rps2-rpoC2 LSC 232 0.0129 1.00 59.9 yes View details
ndhH SSC 1182 0.0017 1.00 59.7 yes View details
psbC LSC 1422 0.0014 1.00 59.6 yes View details
trnF-GAA-ndhJ LSC 699 0.0014 1.00 59.6 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
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT GGTGCTCAACCTACAGGAAC 1043–1044 1.000 77.7
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GGTGCTCAACCTACAGGAAC 1042–1043 1.000 77.7
trnK-UUU-rps16_p3 trnK-UUU-rps16 TACCGTTGAGTTAGCAACCC GGTGCTCAACCTACAGGAAC 1029–1030 1.000 75.3
trnK-UUU-rps16_p4 trnK-UUU-rps16 AGTCGCACTTAAAAGCCGAG GGTGCTCAACCTACAGGAAC 1054–1055 1.000 74.4
trnK-UUU-rps16_p5 trnK-UUU-rps16 TCGCACTTAAAAGCCGAGTA GGTGCTCAACCTACAGGAAC 1052–1053 1.000 73.2
rps16-trnQ-UUG_p1 rps16-trnQ-UUG TATGTCCTTCAAGTCGCACG TGGTCCTGTTATTCGGAGGT 1581–1582 1.000 79.7
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TATGTCCTTCAAGTCGCACG GAGGTTCGAATCCTTCCGTC 1566–1567 1.000 79.5
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TGGTCCTGTTATTCGGAGGT 1571–1572 1.000 78.6
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1556–1557 1.000 78.4
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TATGTCCTTCAAGTCGCACG CCGGGTTTTGGTCCTGTTAT 1589–1590 1.000 78.4
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC AGAAACCTCAAGGGATCCGA ACGAATCACACTTTTACCACT 1113–1114 1.000 51.6
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AGAAACCTCAAGGGATCCGA AGAACGAATCACACTTTTACCAC 1116–1117 1.000 50.6
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC AGAAACCTCAAGGGATCCGA GAACGAATCACACTTTTACCACT 1115–1116 1.000 50.6
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC GGAACGGAGAGAGAGGGATT ACGAATCACACTTTTACCACT 1092–1093 1.000 50.3
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AATCTGCCGCTTTAGTCCAC ACGAATCACACTTTTACCACT 1034–1035 1.000 49.9
rps2_p1 rps2 CAATCTGCGTTTTGCTCAGG CGGGGTCGTATTGATTGGTT 1651 1.000 79.8
rps2_p2 rps2 CCAATCTGCGTTTTGCTCAG CGGGGTCGTATTGATTGGTT 1652 1.000 79.8
rps2_p3 rps2 CAATCTGCGTTTTGCTCAGG TCTCCGGGAGAAAGTTCCTT 1269 1.000 79.7
rps2_p4 rps2 CCAATCTGCGTTTTGCTCAG TCTCCGGGAGAAAGTTCCTT 1270 1.000 79.7
rps2_p5 rps2 CAATCTGCGTTTTGCTCAGG CGCCCGAGTTTTAGCAAAAG 1679 1.000 79.7
rps2-rpoC2_p1 rps2-rpoC2 ATGACCGAAATGAACTCCCG ATTCGAGGGGGAAATAAGCG 380 1.000 78.4
rps2-rpoC2_p2 rps2-rpoC2 AATGAACTCCCGCTTCCATC ATTCGAGGGGGAAATAAGCG 372 1.000 78.2
rps2-rpoC2_p3 rps2-rpoC2 TGCAGAGATGTAAGGTCCCA ATTCGAGGGGGAAATAAGCG 425 1.000 78.1
rps2-rpoC2_p4 rps2-rpoC2 CCCGCTTCCATCATCTCTTC ATTCGAGGGGGAAATAAGCG 364 1.000 77.6
rps2-rpoC2_p5 rps2-rpoC2 GAAATGAACTCCCGCTTCCA ATTCGAGGGGGAAATAAGCG 374 1.000 77.2
rpoB_p1 rpoB AACTCGATTTTCGCCCATGA TCAATTCGGATTGGCTCTGG 215 1.000 79.5
rpoB_p2 rpoB ACTCGATTTTCGCCCATGAA TCAATTCGGATTGGCTCTGG 214 1.000 79.5
rpoB_p3 rpoB TCGATTTTCGCCCATGAACT TCAATTCGGATTGGCTCTGG 212 1.000 79.5
rpoB_p4 rpoB ACTCGATTTTCGCCCATGAA ATTCGGATTGGCTCTGGTTC 211 1.000 79.5
rpoB_p5 rpoB TCGATTTTCGCCCATGAACT ATTCGGATTGGCTCTGGTTC 209 1.000 79.5

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
Gymnotheca chinensis NC_056145.1 161621 View on NCBI ↗
Gymnotheca involucrata PV608437.1 161556 View on NCBI ↗