Markers + reference

Pinellia

5 species · Araceae · Alismatales

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Species 5
Genome length 164–166 kb
Candidate markers 267
Primer pairs 85

Genome-wide nucleotide diversity

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

Candidate markers

7 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-psbA LSC 649 0.1075 0.95 84.3 yes View details
trnS(GCU)-trnG(UCC) LSC 1576 0.1423 0.93 85.8 yes View details
trnT(UGU)-trnL(UAA) LSC 1220 0.0836 0.96 95.4 yes View details
trnN(GUU)-ndhF SSC 1933 0.1562 0.89 76.6 yes View details
ndhG-ndhI SSC 817 0.1414 0.95 78.9 yes View details
rps15-ycf1 SSC 1386 0.1925 0.94 78.0 yes View details
ycf1-trnR(ACG) SSC 1674 0.0552 0.91 81.6 yes View details
trnR(ACG)-trnN(GUU) SSC 597 0.0525 0.94 97.6 yes View details
rpoB-trnC(GCA) LSC 1515 0.0474 1.00 88.6 yes View details
ndhF-rpl32 SSC 1181 0.0586 0.94 86.0 yes View details
ycf3-trnS(GGA) LSC 916 0.0480 0.96 85.8 yes View details
petA-psbJ LSC 953 0.0642 0.98 83.8 yes View details
rps4-trnT(UGU) LSC 467 0.0401 0.99 80.8 yes View details
ndhE-ndhG SSC 373 0.1283 1.00 80.6 yes View details
psaC-ndhE SSC 939 0.0709 0.87 80.3 yes View details
psbE-petL LSC 1242 0.0400 0.99 80.0 yes View details
ndhB-trnL(CAA) IRa 754 0.0262 1.00 77.9 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 85 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-psbA_p1 trnH-psbA GATCCACTTGGCTACATCCG AGCTGCTGTTGAAGTTCCAT 696–714 0.800 80.7
trnH-psbA_p2 trnH-psbA CAATCCACTGCCTTGATCCA AGCTGCTGTTGAAGTTCCAT 710–728 0.800 80.7
trnH-psbA_p3 trnH-psbA AATCCACTGCCTTGATCCAC AGCTGCTGTTGAAGTTCCAT 709–727 0.800 80.7
trnH-psbA_p4 trnH-psbA ACAATCCACTGCCTTGATCC AGCTGCTGTTGAAGTTCCAT 711–729 0.800 80.7
trnH-psbA_p5 trnH-psbA GATCCACTTGGCTACATCCG GCTGCTGTTGAAGTTCCATC 695–713 0.800 78.0
trnS(GCU)-trnG(UCC)_p1 trnS(GCU)-trnG(UCC) GAGAAAGCGGAGAAAGAGGG AGGACGAATCACACTTTTACCA 1617–1743 1.000 73.1
trnS(GCU)-trnG(UCC)_p2 trnS(GCU)-trnG(UCC) ATTAGCAATCCGCCGCTTTA AGGACGAATCACACTTTTACCA 1562–1688 1.000 72.9
trnS(GCU)-trnG(UCC)_p3 trnS(GCU)-trnG(UCC) GAGAAAGCGGAGAAAGAGGG GGACGAATCACACTTTTACCAC 1616–1742 1.000 72.7
trnS(GCU)-trnG(UCC)_p4 trnS(GCU)-trnG(UCC) ATTAGCAATCCGCCGCTTTA GGACGAATCACACTTTTACCAC 1561–1687 1.000 72.5
trnS(GCU)-trnG(UCC)_p5 trnS(GCU)-trnG(UCC) AGAAAGCGGAGAAAGAGGGA AGGACGAATCACACTTTTACCA 1616–1742 1.000 70.4
rpoB-trnC(GCA)_p1 rpoB-trnC(GCA) CCCTCATTTTCATCCCGGAG TGGGGTTTAGATCAGCAGGA 1612–1830 1.000 91.0
rpoB-trnC(GCA)_p2 rpoB-trnC(GCA) CTCATTTTCATCCCGGAGCA TGGGGTTTAGATCAGCAGGA 1610–1828 1.000 90.9
rpoB-trnC(GCA)_p3 rpoB-trnC(GCA) CCCTCATTTTCATCCCGGAG GCGACACCCAGATTTGAACT 1566–1784 1.000 87.7
rpoB-trnC(GCA)_p4 rpoB-trnC(GCA) CTCATTTTCATCCCGGAGCA GCGACACCCAGATTTGAACT 1564–1782 1.000 87.5
rpoB-trnC(GCA)_p5 rpoB-trnC(GCA) CCCTCATTTTCATCCCGGAG TAAAGGATTTGCAGTCCCCC 1541–1759 1.000 87.4
ycf3-trnS(GGA)_p1 ycf3-trnS(GGA) TGGCTACAATCGAAGAGGTC CCCTCGGTAAACAAAAGCCT 1013–1103 1.000 83.6
ycf3-trnS(GGA)_p2 ycf3-trnS(GGA) TGGCTACAATCGAAGAGGTC ACGGAAAGAGAGGGATTCGA 1034–1124 1.000 83.0
ycf3-trnS(GGA)_p3 ycf3-trnS(GGA) TGGCTACAATCGAAGAGGTC TTCCAATGCTACGCCTTGAA 984–1074 1.000 82.8
ycf3-trnS(GGA)_p4 ycf3-trnS(GGA) TTGGCTACAATCGAAGAGGTC CCCTCGGTAAACAAAAGCCT 1014–1104 1.000 81.3
ycf3-trnS(GGA)_p5 ycf3-trnS(GGA) TGGCTACAATCGAAGAGGTC ACCCTCGGTAAACAAAAGCC 1014–1104 1.000 81.2
rps4-trnT(UGU)_p1 rps4-trnT(UGU) CTCCCAGACGGCGTATTTTT GATGGTCATCGGTTCGACTC 542–938 1.000 85.1
rps4-trnT(UGU)_p2 rps4-trnT(UGU) CTCCCAGACGGCGTATTTTT CTCAGAGGTTAGAGCATCGC 573–969 1.000 85.0
rps4-trnT(UGU)_p3 rps4-trnT(UGU) CTAGTCAGTCCTGGCAAAGC GATGGTCATCGGTTCGACTC 561–957 1.000 84.9
rps4-trnT(UGU)_p4 rps4-trnT(UGU) CTAGTCAGTCCTGGCAAAGC CTCAGAGGTTAGAGCATCGC 592–988 1.000 84.7
rps4-trnT(UGU)_p5 rps4-trnT(UGU) CTCCCAGACGGCGTATTTTT CCGCTTAGCTCAGAGGTTAG 581–977 1.000 81.9
trnT(UGU)-trnL(UAA)_p1 trnT(UGU)-trnL(UAA) GGAAAAAGCCAGCTATCGGA TCCATACCAAGGCTCAATGC 1267–1548 1.000 91.2
trnT(UGU)-trnL(UAA)_p2 trnT(UGU)-trnL(UAA) AGGGAAAAAGCCAGCTATCG TCCATACCAAGGCTCAATGC 1269–1550 1.000 91.2
trnT(UGU)-trnL(UAA)_p3 trnT(UGU)-trnL(UAA) GGAAAAAGCCAGCTATCGGA ACCAAGGCTCAATGCAATCA 1262–1543 1.000 91.1
trnT(UGU)-trnL(UAA)_p4 trnT(UGU)-trnL(UAA) AGGGAAAAAGCCAGCTATCG ACCAAGGCTCAATGCAATCA 1264–1545 1.000 91.1
trnT(UGU)-trnL(UAA)_p5 trnT(UGU)-trnL(UAA) GGAAAAAGCCAGCTATCGGA GCGTCTACCTATTTCGCCAT 1234–1515 1.000 90.5

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
Pinellia cordata MT863558.1 164850 View on NCBI ↗
Pinellia discolor OP991877.1 165519 View on NCBI ↗
Pinellia pedatisecta NC_058756.1 164682 View on NCBI ↗
Pinellia peltata NC_052862.1 164923 View on NCBI ↗
Pinellia ternata NC_027681.1 164013 View on NCBI ↗