Markers + reference

Symplocarpus

2 species · Araceae · Alismatales

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Species 2
Genome length 158–159 kb
Candidate markers 266
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 266 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0000 1.00 35.8 yes View details
rps16 LSC 1326 0.0031 0.98 62.1 yes View details
trnC-GCA-petN LSC 1088 0.0046 1.00 61.5 yes View details
trnT-UGU-trnL-UAA LSC 635 0.0080 0.99 64.5 yes View details
ycf4 LSC 555 0.0000 1.00 39.1 yes View details
ycf4-cemA LSC 1185 0.0034 1.00 60.9 yes View details
petA-psbJ LSC 1045 0.0048 0.99 62.1 yes View details
rpl22 LSC 390 0.0077 1.00 48.9 yes View details
ndhF SSC 2217 0.0014 1.00 58.0 yes View details
rpoA-rps11 LSC 68 0.0147 1.00 61.0 yes View details
rbcL-accD LSC 800 0.0000 0.98 60.6 yes View details
atpB-rbcL LSC 795 0.0025 1.00 60.4 yes View details
rpl22-rps19 LSC 77 0.0130 1.00 60.0 yes View details
psbM-trnD-GUC LSC 1001 0.0020 1.00 59.9 yes View details
GFC13_pgt029-ndhF IRb 1201 0.0008 1.00 59.7 yes View details
psaA-ycf3 LSC 673 0.0015 1.00 59.6 yes View details
ndhK LSC 747 0.0013 1.00 59.5 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbA_p1 psbA GGCTTGGTATTGCTCCTTCA TAGCTAATACGTGCGCTTGG 1165 1.000 77.8
psbA_p2 psbA GGCTTGGTATTGCTCCTTCA CGCTTGGGAGTCCTTGAAAA 1152 1.000 75.8
psbA_p3 psbA AGAGGCTTGGTATTGCTCCT TAGCTAATACGTGCGCTTGG 1168 1.000 75.5
psbA_p4 psbA AGGCTTGGTATTGCTCCTTC TAGCTAATACGTGCGCTTGG 1166 1.000 75.4
psbA_p5 psbA GAGGCTTGGTATTGCTCCTT TAGCTAATACGTGCGCTTGG 1167 1.000 75.4
trnK-UUU_p1 trnK-UUU TGAAGTGAGTTAAAATGGAAAA ATTTCGAGCGTATCTACATAT 2695–2696 1.000 40.1
trnK-UUU_p2 trnK-UUU TGAAGTGAGTTAAAATGGAAAAA ATTTCGAGCGTATCTACATAT 2695–2696 1.000 40.1
trnK-UUU_p3 trnK-UUU TGAAGTGAGTTAAAATGGAAAA TCGAGCGTATCTACATATATACA 2692–2693 1.000 40.1
trnK-UUU_p4 trnK-UUU TGAAGTGAGTTAAAATGGAAAAA TCGAGCGTATCTACATATATACA 2692–2693 1.000 40.1
trnK-UUU_p5 trnK-UUU ATGAAGTGAGTTAAAATGGAAAA ATTTCGAGCGTATCTACATAT 2696–2697 1.000 40.1
rps16_p1 rps16 GCAAGATTAACCCCACTTTTGT TGTACCGATTGAGCCAATGA 1503–1519 1.000 52.0
rps16_p2 rps16 GCAAGATTAACCCCACTTTTGT GTACCGATTGAGCCAATGACT 1502–1518 1.000 51.8
rps16_p3 rps16 AGGCAAATGTTGAGGAAAGA TGTACCGATTGAGCCAATGA 1425–1441 1.000 50.0
rps16_p4 rps16 AGCAAGATTAACCCCACTTTTG TGTACCGATTGAGCCAATGA 1504–1520 1.000 49.8
rps16_p5 rps16 AGGCAAATGTTGAGGAAAGA GTACCGATTGAGCCAATGACT 1424–1440 1.000 49.8
trnG_p1 trnG TGTTCGACAAAAGGTTCATTGA GGATTGCATGGGGAAGGTTT 933–934 1.000 50.8
trnG_p2 trnG TGTTCGACAAAAGGTTCATTGA TTTGGATTGCATGGGGAAGG 936–937 1.000 50.8
trnG_p3 trnG TTGTTCGACAAAAGGTTCATTGA GGATTGCATGGGGAAGGTTT 934–935 1.000 48.1
trnG_p4 trnG TTGTTCGACAAAAGGTTCATTGA TTTGGATTGCATGGGGAAGG 937–938 1.000 48.1
trnG_p5 trnG TGTTCGACAAAAGGTTCATTGA AGATTTGGATTGCATGGGGA 939–940 1.000 47.4
trnC-GCA-petN_p1 trnC-GCA-petN TTGATTGTTTTGGCGGCATG AGCCCAAGCGAGACTTACTA 1196–1197 1.000 77.5
trnC-GCA-petN_p2 trnC-GCA-petN TTGATTGTTTTGGCGGCATG AGAGTCCACTTCTTCCCCAT 1257–1258 1.000 75.9
trnC-GCA-petN_p3 trnC-GCA-petN GGGGGACTGCAAATCCTTTA AGCCCAAGCGAGACTTACTA 1161–1162 1.000 75.0
trnC-GCA-petN_p4 trnC-GCA-petN GGGGGACTGCAAATCCTTTA AGAGTCCACTTCTTCCCCAT 1222–1223 1.000 73.4
trnC-GCA-petN_p5 trnC-GCA-petN ATTGATTGTTTTGGCGGCAT AGCCCAAGCGAGACTTACTA 1197–1198 1.000 73.1
psbM-trnD-GUC_p1 psbM-trnD-GUC AGAATGAACAGTGCAGTAGC AGTTCAATCGGTCAGAGCAC 1115–1233 1.000 61.6
psbM-trnD-GUC_p2 psbM-trnD-GUC AGGAACTAGAATGAACAGTGCA AGTTCAATCGGTCAGAGCAC 1122–1240 1.000 58.5
psbM-trnD-GUC_p3 psbM-trnD-GUC GGAACTAGAATGAACAGTGCAG AGTTCAATCGGTCAGAGCAC 1121–1239 1.000 56.0
psbM-trnD-GUC_p4 psbM-trnD-GUC AGAATGAACAGTGCAGTAGC GTTCAATCGGTCAGAGCACC 1114–1232 1.000 54.9
psbM-trnD-GUC_p5 psbM-trnD-GUC GGAACTAGAATGAACAGTGCA AGTTCAATCGGTCAGAGCAC 1121–1239 1.000 54.7

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
Symplocarpus nipponicus NC_045121.1 158322 View on NCBI ↗
Symplocarpus renifolius NC_033970.1 158521 View on NCBI ↗