Markers + reference

Neolamarckia

2 species · Rubiaceae · Gentianales

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Species 2
Genome length 155–155 kb
Candidate markers 266
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 266 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 299 0.0558 0.90 75.8 yes View details
rps16 LSC 1086 0.0111 1.00 60.1 yes View details
rps16-trnQ-UUG LSC 1459 0.0118 0.99 53.6 yes View details
rps2-rpoC2 LSC 242 0.0124 1.00 45.4 yes View details
trnC-GCA-petN LSC 851 0.0153 1.00 65.9 yes View details
trnE-UUC-trnT-GGU LSC 740 0.0136 0.99 61.2 yes View details
ycf3-trnS-GGA LSC 402 0.0100 1.00 54.0 yes View details
petA-psbJ LSC 992 0.0133 0.99 64.7 yes View details
ycf1 IRb 1136 0.0000 1.00 26.5 no View details
rpl32-trnL-UAG SSC 857 0.0187 1.00 59.2 yes View details
ycf1 SSC 5631 0.0053 1.00 42.4 yes View details
ycf4-cemA LSC 620 0.0148 0.98 68.8 yes View details
ndhI-ndhA SSC 87 0.0465 0.99 68.5 yes View details
ndhC-trnV-UAC LSC 1189 0.0085 0.99 64.7 yes View details
rpl2-trnH-GUG IRa 109 0.0286 0.96 64.1 no View details
psbM-trnD-GUC LSC 900 0.0078 1.00 63.7 yes View details
accD LSC 1620 0.0032 0.97 63.6 yes View details
trnR-ACG-trnN-GUU IRb 564 0.0089 1.00 63.1 yes View details
trnN-GUU-trnR-ACG IRa 564 0.0089 1.00 63.1 yes View details
matK LSC 1518 0.0072 1.00 62.9 yes View details
petG-trnW-CCA LSC 141 0.0146 0.97 62.9 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT TTCCCTCTAGACCTAGCTGC 361–376 1.000 85.6
trnH-GUG-psbA_p2 trnH-GUG-psbA ACTGCCTTAATCCACTTGGC TTCCCTCTAGACCTAGCTGC 362–377 1.000 85.4
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 354–369 1.000 84.1
trnH-GUG-psbA_p4 trnH-GUG-psbA CGCATGGTGGATTCACAATC TTCCCTCTAGACCTAGCTGC 383–398 1.000 82.6
trnH-GUG-psbA_p5 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT TCCCTCTAGACCTAGCTGCT 360–375 1.000 80.0
matK_p1 matK ACATGCTACATCAACATTTCAGA TCGTCTACCTTTGCTTTGGT 1655–1658 1.000 40.5
matK_p2 matK ACATGCTACATCAACATTTCAGA TCGTCTACCTTTGCTTTGGTT 1655–1658 1.000 40.5
matK_p3 matK ACATGCTACATCAACATTTCAGAA TCGTCTACCTTTGCTTTGGT 1655–1658 1.000 40.5
matK_p4 matK ACATGCTACATCAACATTTCAG TCGTCTACCTTTGCTTTGGT 1655–1658 1.000 40.5
matK_p5 matK ACATGCTACATCAACATTTCAGA ATCGTCTACCTTTGCTTTGGT 1656–1659 1.000 40.5
rps16_p1 rps16 AGATAAATAGATAGGGGAGGGGG TCAATTCCATACCGGTTCCA 1219–1225 1.000 43.1
rps16_p2 rps16 AGATAAATAGATAGGGGAGGGGG TCAATTCCATACCGGTTCCAA 1219–1225 1.000 41.1
rps16_p3 rps16 TAAATAGATAGGGGAGGGGG TCAATTCCATACCGGTTCCA 1216–1222 1.000 40.9
rps16_p4 rps16 AGATAAATAGATAGGGGAGGGGG ACCGGTTCCAAATTAGAGGA 1209–1215 1.000 40.9
rps16_p5 rps16 GATAAATAGATAGGGGAGGGGG TCAATTCCATACCGGTTCCA 1218–1224 1.000 40.9
rps16-trnQ-UUG_p1 rps16-trnQ-UUG GATTCCCGCGTGATACACTT CTTTTGACCCCACCCAATCA 2110–2120 1.000 81.0
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GATTCCCGCGTGATACACTT GAGGTTCGAATCCTTCCGTC 1824–1834 1.000 80.6
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GATTCCCGCGTGATACACTT AGCAGCTTGCCAAACAAAAG 2379–2389 1.000 80.4
rps16-trnQ-UUG_p4 rps16-trnQ-UUG GATTCCCGCGTGATACACTT CTTACAGCAGCTTGCCAAAC 2384–2394 1.000 80.4
rps16-trnQ-UUG_p5 rps16-trnQ-UUG GAACAATTGATTCCCGCGTG CTTTTGACCCCACCCAATCA 2128 0.500 59.1
trnG-GCC_p1 trnG-GCC ATTAGCAATCCGCCGCTTTA AGGAGCAAATGGACCGTTTT 1778–1862 1.000 84.5
trnG-GCC_p2 trnG-GCC ATTAGCAATCCGCCGCTTTA TTGCCCAATTTGCCTCTGAT 2075–2159 1.000 84.0
trnG-GCC_p3 trnG-GCC ACTCAGCCATCTCTCCCAAT AGGAGCAAATGGACCGTTTT 1754–1838 1.000 84.0
trnG-GCC_p4 trnG-GCC ATTAGCAATCCGCCGCTTTA CTTTGCCCAATTTGCCTCTG 2077–2161 1.000 83.7
trnG-GCC_p5 trnG-GCC GCAAGGAAGGGCTATTTCCA AGGAGCAAATGGACCGTTTT 1310–1312 1.000 79.8
rps2-rpoC2_p1 rps2-rpoC2 CCCTCACAAATTGCGAACAC AGGTGCGTTCGATTGATTCA 1632–1644 1.000 79.9
rps2-rpoC2_p2 rps2-rpoC2 CCCTTACGCTTTGCAGAGAT AGGTGCGTTCGATTGATTCA 1071–1092 1.000 79.8
rps2-rpoC2_p3 rps2-rpoC2 CTGCTAAATCGGGGTCACAA AGGTGCGTTCGATTGATTCA 1550–1562 1.000 79.5
rps2-rpoC2_p4 rps2-rpoC2 CCCTTACGCTTTGCAGAGAT ATTGGATTGTTGCGAGCAGA 787–808 1.000 79.4
rps2-rpoC2_p5 rps2-rpoC2 CCCTTACGCTTTGCAGAGAT TCTGTTACCGAGCCGTCTTA 738–759 1.000 79.4

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
Neolamarckia cadamba NC_041149.1 154999 View on NCBI ↗
Neolamarckia macrophylla MN877388.1 155406 View on NCBI ↗