Markers + reference

Gardneria

2 species · Loganiaceae · Gentianales

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Species 2
Genome length 145–145 kb
Candidate markers 257
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 10 remaining regions by MarkerSeek score (out of 257 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA Genome 444 0.0180 1.00 58.0 yes View details
rps16-trnQ-UUG Genome 1721 0.0089 0.98 56.9 yes View details
ndhC-trnV-UAC Genome 1218 0.0091 0.99 55.6 yes View details
ndhB Genome 2218 0.0032 1.00 59.1 yes View details
ycf1 Genome 939 0.0021 1.00 60.0 no View details
ndhF-rpl32 Genome 784 0.0128 1.00 60.7 yes View details
rpl32-trnL-UAG Genome 892 0.0114 0.99 54.2 yes View details
ndhG-ndhI Genome 477 0.0200 0.94 68.9 yes View details
ycf1 Genome 5616 0.0041 1.00 54.9 yes View details
rps19-rpl2 Genome 66 0.0312 0.97 73.3 yes View details
rps2-rpoC2 Genome 250 0.0127 0.95 64.5 yes View details
trnK-UUU-rps16 Genome 900 0.0056 0.99 63.2 yes View details
psbE-petL Genome 1167 0.0069 1.00 62.7 yes View details
trnT-UGU-trnL-UAA Genome 768 0.0013 0.97 62.3 yes View details
atpH-atpI Genome 1115 0.0027 0.98 62.1 yes View details
rpoB-trnC-GCA Genome 1191 0.0050 1.00 61.6 yes View details
trnE-UUC-trnT-GGU Genome 796 0.0050 1.00 61.6 yes View details
pafII-cemA Genome 880 0.0046 1.00 61.6 yes View details
clpP1-psbB Genome 465 0.0022 0.96 61.4 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
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG GCGCTAACCTTGGTATGGAA 561–597 1.000 79.8
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA GCGCTAACCTTGGTATGGAA 575–611 1.000 79.8
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC GCGCTAACCTTGGTATGGAA 574–610 1.000 79.7
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC GCGCTAACCTTGGTATGGAA 576–612 1.000 79.7
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCCTCTGGATCTAGCTGCTA 512–548 1.000 77.8
trnK-UUU_p1 trnK-UUU TGCTCGTGTCAACCAATACC AGCTCAACGGTTTAATTGCT 2785–2786 1.000 62.3
trnK-UUU_p2 trnK-UUU TGCTCGTGTCAACCAATACC TCAACGGTTTAATTGCTTCGTC 2782–2783 1.000 61.6
trnK-UUU_p3 trnK-UUU TGCTCGTGTCAACCAATACC CAACGGTTTAATTGCTTCGTCT 2781–2782 1.000 61.6
trnK-UUU_p4 trnK-UUU TGCTCGTGTCAACCAATACC CTCAACGGTTTAATTGCTTCGT 2783–2784 1.000 61.6
trnK-UUU_p5 trnK-UUU TGCTCGTGTCAACCAATACC AGCTCAACGGTTTAATTGCTTC 2785–2786 1.000 61.4
trnK-UUU-rps16_p1 trnK-UUU-rps16 CGAATCCCTTGCTTCATCCA GGTGCTCAACCTACAGGAAC 1072–1082 1.000 79.3
trnK-UUU-rps16_p2 trnK-UUU-rps16 ACGAATCCCTTGCTTCATCC GGTGCTCAACCTACAGGAAC 1073–1083 1.000 79.3
trnK-UUU-rps16_p3 trnK-UUU-rps16 ATGGACGAATCCCTTGCTTC GGTGCTCAACCTACAGGAAC 1077–1087 1.000 79.3
trnK-UUU-rps16_p4 trnK-UUU-rps16 GGACGAATCCCTTGCTTCAT GGTGCTCAACCTACAGGAAC 1075–1085 1.000 79.3
trnK-UUU-rps16_p5 trnK-UUU-rps16 CGATGGTATGGACGAATCCC GGTGCTCAACCTACAGGAAC 1084–1094 1.000 79.0
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1793–1794 1.000 80.2
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GGATCGTGTCCTTCAAGTCG GAGGTTCGAATCCTTCCGTC 1807–1808 1.000 78.3
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 1797–1798 1.000 75.4
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TAAGGCAACGGGTTTTGGTC 1823–1824 1.000 75.3
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG GAGGTTCGAATCCTTCCGTC 1785–1786 1.000 75.0
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTGCAACTTTAGCTGCAGC 1191–1201 1.000 80.2
atpH-atpI_p2 atpH-atpI TACCCTCTACAGCTTGACCC TTTGCAACTTTAGCTGCAGC 1274–1284 1.000 79.3
atpH-atpI_p3 atpH-atpI GCGATACCCTCTACAGCTTG TTTGCAACTTTAGCTGCAGC 1278–1288 1.000 79.3
atpH-atpI_p4 atpH-atpI AATAACGGAAGCGGCAGAAA TTTGCAACTTTAGCTGCAGC 1192–1202 1.000 79.0
atpH-atpI_p5 atpH-atpI CCGGGTCCAATAGAAGCAAG TTTGCAACTTTAGCTGCAGC 1233–1243 1.000 77.8
rps2-rpoC2_p1 rps2-rpoC2 CCTGCCTCCATCATCTCTTC TTCGAGGGGGAAATGAGAGA 404–417 1.000 76.8
rps2-rpoC2_p2 rps2-rpoC2 ATGGCCAAAATGAACCCCTG TTCGAGGGGGAAATGAGAGA 420–433 1.000 75.2
rps2-rpoC2_p3 rps2-rpoC2 CATGGCCAAAATGAACCCCT TTCGAGGGGGAAATGAGAGA 421–434 1.000 75.2
rps2-rpoC2_p4 rps2-rpoC2 CCTGCCTCCATCATCTCTTC TCGAGGGGGAAATGAGAGAT 403–416 1.000 74.9
rps2-rpoC2_p5 rps2-rpoC2 CCCTGCCTCCATCATCTCTT TTCGAGGGGGAAATGAGAGA 405–418 1.000 74.2

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
Gardneria multiflora NC_079965.1 144920 View on NCBI ↗
Gardneria ovata NC_065470.1 144750 View on NCBI ↗