Markers + reference

Helicia

2 species · Proteaceae · Proteales

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Species 2
Genome length 157–157 kb
Candidate markers 269
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 269 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0009 1.00 59.3 yes View details
tRNA-Lys(TTT)-rps16 LSC 1032 0.0019 1.00 60.0 yes View details
rps16 LSC 1110 0.0000 1.00 37.8 yes View details
tRNA-Ser(GCT)-tRNA-Arg(TCT) LSC 1683 0.0006 0.99 59.7 yes View details
rps2 LSC 711 0.0014 1.00 46.8 yes View details
atpB-rbcL LSC 793 0.0013 0.98 61.2 yes View details
rbcL LSC 1428 0.0000 1.00 29.4 yes View details
rbcL-accD LSC 739 0.0068 1.00 62.6 yes View details
rpoA LSC 987 0.0081 1.00 63.4 yes View details
rpl16-rps3 LSC 1123 0.0009 1.00 59.3 yes View details
cemA LSC 690 0.0014 1.00 59.6 yes View details
psaA-ycf3 LSC 740 0.0000 0.99 59.5 yes View details
psbE-petL LSC 807 0.0012 1.00 59.5 yes View details
tRNA-Glu(TTC)-tRNA-Thr(GGT) LSC 1072 0.0009 1.00 59.4 yes View details
atpF LSC 1353 0.0007 1.00 59.2 yes View details
ndhC-tRNA-Lys(TTT) LSC 520 0.0000 0.99 58.4 yes View details
clpP LSC 2065 0.0005 1.00 57.9 yes View details
ycf3 LSC 1995 0.0000 1.00 57.8 yes View details
ndhF SSC 2196 0.0009 1.00 57.8 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 TGCGGTATTGCTACTTCAACA AATTCGTGTGCTTGGGAGTC 1158 1.000 67.9
psbA_p2 psbA TGCGGTATTGCTACTTCAACA TAATTCGTGTGCTTGGGAGT 1159 1.000 64.9
psbA_p3 psbA TGCGGTATTGCTACTTCAACA GCTTGGGAGTCCCTGATGAT 1149 1.000 62.4
psbA_p4 psbA TGAAGGAGCAATACCAACACT AATTCGTGTGCTTGGGAGTC 1196 1.000 62.0
psbA_p5 psbA TGCGGTATTGCTACTTCAACA ATTCGTGTGCTTGGGAGTC 1157 1.000 61.8
tRNA-Lys(TTT)-rps16_p1 tRNA-Lys(TTT)-rps16 CGAATCCCTTGCTTCATCCA GGTGCTCAACCTACAGGAAC 1206–1207 1.000 78.3
tRNA-Lys(TTT)-rps16_p2 tRNA-Lys(TTT)-rps16 ACGAATCCCTTGCTTCATCC GGTGCTCAACCTACAGGAAC 1207–1208 1.000 78.3
tRNA-Lys(TTT)-rps16_p3 tRNA-Lys(TTT)-rps16 ATGGACGAATCCCTTGCTTC GGTGCTCAACCTACAGGAAC 1211–1212 1.000 78.3
tRNA-Lys(TTT)-rps16_p4 tRNA-Lys(TTT)-rps16 GGACGAATCCCTTGCTTCAT GGTGCTCAACCTACAGGAAC 1209–1210 1.000 78.3
tRNA-Lys(TTT)-rps16_p5 tRNA-Lys(TTT)-rps16 AAGCCGAGTACTCTACCGTT GGTGCTCAACCTACAGGAAC 1157–1158 1.000 77.3
rps16_p1 rps16 AGCTAGATCTAAGGGTGACTCC TGCTGGTTCCAAATTAGAGGA 1191 1.000 46.0
rps16_p2 rps16 GCTAGATCTAAGGGTGACTCC TGCTGGTTCCAAATTAGAGGA 1190 1.000 44.9
rps16_p3 rps16 AGCTAGATCTAAGGGTGACTCC TGCTGGTTCCAAATTAGAGGAA 1191 1.000 43.7
rps16_p4 rps16 AGCTAGATCTAAGGGTGACTCC TCAATTTCATGCTGGTTCCA 1200 1.000 42.9
rps16_p5 rps16 GCTAGATCTAAGGGTGACTCC TGCTGGTTCCAAATTAGAGGAA 1190 1.000 42.6
tRNA-Ser(GCT)-tRNA-Arg(TCT)_p1 tRNA-Ser(GCT)-tRNA-Arg(TCT) CAACGGATTAGCAATTCGCC AGAAGACCTCTGTCCTATCCA 1748–1765 1.000 63.6
tRNA-Ser(GCT)-tRNA-Arg(TCT)_p2 tRNA-Ser(GCT)-tRNA-Arg(TCT) ACGGAAAGAGAGGGATTCGA AGAAGACCTCTGTCCTATCCA 1791–1808 1.000 63.2
tRNA-Ser(GCT)-tRNA-Arg(TCT)_p3 tRNA-Ser(GCT)-tRNA-Arg(TCT) CAACGGATTAGCAATTCGCC AGGTTTAGAAGACCTCTGTCCT 1754–1771 1.000 62.9
tRNA-Ser(GCT)-tRNA-Arg(TCT)_p4 tRNA-Ser(GCT)-tRNA-Arg(TCT) ACGGAAAGAGAGGGATTCGA AGGTTTAGAAGACCTCTGTCCT 1797–1814 1.000 62.5
tRNA-Ser(GCT)-tRNA-Arg(TCT)_p5 tRNA-Ser(GCT)-tRNA-Arg(TCT) ATTAGCAATTCGCCGCTTTC AGAAGACCTCTGTCCTATCCA 1742–1759 1.000 60.6
atpF_p1 atpF TTTCATCGGCTCGAATGGTT AAAAGGGGCGAAGTGATACA 1504 1.000 72.2
atpF_p2 atpF TTTCATCGGCTCGAATGGTT AAAGGGGCGAAGTGATACAA 1503 1.000 72.2
atpF_p3 atpF TTTCATCGGCTCGAATGGTT AAGGGGCGAAGTGATACAAA 1502 1.000 72.2
atpF_p4 atpF TTTCATCGGCTCGAATGGTT AGGGGCGAAGTGATACAAAA 1501 1.000 72.2
atpF_p5 atpF TCATCGGCTCGAATGGTTAC AGGGGCGAAGTGATACAAAA 1499 1.000 71.3
rps2_p1 rps2 TGGAGTTCCCGAAGTAATTGA AAAGAGGAAGTGTGGAGAGA 769 1.000 40.6
rps2_p2 rps2 TGGAGTTCCCGAAGTAATTGA AAGAGGAAGTGTGGAGAGAA 768 1.000 40.6
rps2_p3 rps2 TGGAGTTCCCGAAGTAATTGA AAAAGAGGAAGTGTGGAGAGA 770 1.000 40.1
rps2_p4 rps2 TGGAGTTCCCGAAGTAATTGA AAAGAGGAAGTGTGGAGAGAA 769 1.000 40.1
rps2_p5 rps2 TCCCCAGTGATTTTGATCTCT AAGAGGAAGTGTGGAGAGAA 829 1.000 40.1

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
Helicia nilagirica NC_057271.1 157217 View on NCBI ↗
Helicia shweliensis NC_045942.1 157151 View on NCBI ↗