Markers + reference

Lasianthus

3 species · Rubiaceae · Gentianales

Back to catalogue

Species 3
Genome length 160–160 kb
Candidate markers 269
Primer pairs 105

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 10 remaining regions by MarkerSeek score (out of 269 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbK-psbI LSC 724 0.0086 0.97 54.2 yes View details
atpI-rps2 LSC 331 0.0234 0.99 72.3 yes View details
trnT-GGU-psbD LSC 1340 0.0075 0.99 58.6 yes View details
rps4-trnT-UGU LSC 569 0.0234 0.93 75.6 yes View details
ndhC-trnV-UAC LSC 512 0.0163 1.00 71.6 yes View details
psaI-ycf4 LSC 538 0.0305 0.98 77.2 yes View details
ycf4-cemA LSC 876 0.0247 1.00 75.6 yes View details
petA-psbJ LSC 1246 0.0065 1.00 68.3 yes View details
psaJ-rpl33 LSC 542 0.0100 0.99 69.1 yes View details
ndhG-ndhI SSC 636 0.0101 0.93 53.8 yes View details
rps16-trnQ-UUG LSC 891 0.0056 1.00 67.7 yes View details
rpl32-trnL-UAG SSC 1176 0.0049 0.99 66.2 yes View details
ccsA-ndhD SSC 248 0.0175 1.00 65.7 yes View details
rps16 LSC 1119 0.0054 0.99 63.2 yes View details
atpH-atpI LSC 811 0.0033 1.00 62.1 yes View details
petN-psbM LSC 1214 0.0039 0.99 61.9 yes View details
rpoB-trnC-GCA LSC 796 0.0025 1.00 61.5 yes View details
matK-trnK-UUU LSC 723 0.0037 1.00 61.1 yes View details
psbC-trnS-UGA LSC 285 0.0152 0.92 60.9 yes View details
psbM-trnD-GUC LSC 892 0.0030 1.00 60.8 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
matK-trnK-UUU_p1 matK-trnK-UUU ACCGGGTTGTTGCGATATAC TTGGTCTTCGGGTTGCTAAC 820 1.000 79.0
matK-trnK-UUU_p2 matK-trnK-UUU CGGGTTGTTGCGATATACCA TTGGTCTTCGGGTTGCTAAC 818 1.000 79.0
matK-trnK-UUU_p3 matK-trnK-UUU ACCGGGTTGTTGCGATATAC AACGGTAGAGTACTCGGCTT 798 1.000 78.6
matK-trnK-UUU_p4 matK-trnK-UUU ACCGGGTTGTTGCGATATAC ACGGTAGAGTACTCGGCTTT 797 1.000 78.6
matK-trnK-UUU_p5 matK-trnK-UUU CGGGTTGTTGCGATATACCA ACGGTAGAGTACTCGGCTTT 795 1.000 78.6
rps16_p1 rps16 ATACACAAAGGACAAGGGGG ACCGTTTCCAAATCAAGAGGA 1245–1259 1.000 62.3
rps16_p2 rps16 GATACACAAAGGACAAGGGGG ACCGTTTCCAAATCAAGAGGA 1246–1260 1.000 59.2
rps16_p3 rps16 ATACACAAAGGACAAGGGGG ACCGTTTCCAAATCAAGAGG 1245–1259 1.000 57.8
rps16_p4 rps16 TTTACCCCCACCCTCTTTTT ACCGTTTCCAAATCAAGAGGA 1168–1180 1.000 57.6
rps16_p5 rps16 ATACACAAAGGACAAGGGGG ACCGTTTCCAAATCAAGAGGAA 1245–1259 1.000 56.9
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 949–982 1.000 82.8
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AGACAGCGGTGGATAGAAGA GAGGTTCGAATCCTTCCGTC 996–1029 1.000 82.7
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CGAAATAGACAGCGGTGGAT GAGGTTCGAATCCTTCCGTC 1002–1035 1.000 82.1
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AGACAGCGAAATAGACAGCG GAGGTTCGAATCCTTCCGTC 1023 0.333 52.0
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AGACAGCGAAATAGACAGCG TAAAAATCGAAGTGGGGCGT 1083 0.333 51.1
psbK-psbI_p1 psbK-psbI CTTTTGTTTGGCAAGCTGCT TAAAGCGGCGGATTGCTAAT 1015–1103 1.000 83.2
psbK-psbI_p2 psbK-psbI GTTTGGCAAGCTGCTGTAAG TAAAGCGGCGGATTGCTAAT 1010–1098 1.000 83.2
psbK-psbI_p3 psbK-psbI TTCTCTGGGACGGAAGGATT TAAAGCGGCGGATTGCTAAT 1594–1682 1.000 82.0
psbK-psbI_p4 psbK-psbI GCCGGTCATACCCGTTTTAT TAAAGCGGCGGATTGCTAAT 1047–1088 0.667 69.9
psbK-psbI_p5 psbK-psbI GCCGGTCATACCCGTTTTAT ATTGGGAGAGATGGCTGAGT 1071–1112 0.667 69.3
atpH-atpI_p1 atpH-atpI AACAGAAGCGGCAGAAATCA TTTTTGCAACTTTAGCCGCC 897–902 1.000 79.2
atpH-atpI_p2 atpH-atpI AACAGAAGCGGCAGAAATCA TAGCCGCCGCTTATATAGGT 885–890 1.000 79.1
atpH-atpI_p3 atpH-atpI CAGCAGCAATAACAGAAGCG TTTTTGCAACTTTAGCCGCC 907–912 1.000 78.7
atpH-atpI_p4 atpH-atpI CAGCAGCAATAACAGAAGCG TAGCCGCCGCTTATATAGGT 895–900 1.000 78.5
atpH-atpI_p5 atpH-atpI GCCAATCCAGCAGCAATAAC TTTTTGCAACTTTAGCCGCC 914–919 1.000 78.3
atpI-rps2_p1 atpI-rps2 CTTGTCCGTGGACTTGGAAA GTGTTCGCAATTTGTGAGGG 473–492 1.000 84.8
atpI-rps2_p2 atpI-rps2 CTTCCACACCGGATACTTCG GTGTTCGCAATTTGTGAGGG 422–441 1.000 84.6
atpI-rps2_p3 atpI-rps2 TCCACACCGGATACTTCGTA GTGTTCGCAATTTGTGAGGG 420–439 1.000 84.3
atpI-rps2_p4 atpI-rps2 ATGTTGGCCTACTTCCACAC GTGTTCGCAATTTGTGAGGG 433–452 1.000 83.6
atpI-rps2_p5 atpI-rps2 GTACTTGTCCGTGGACTTGG GTGTTCGCAATTTGTGAGGG 476–495 1.000 83.4

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.

Species Accession Length (bp) Link
Lasianthus attenuatus OR490208.1 160164 View on NCBI ↗
Lasianthus henryi OR490209.1 160240 View on NCBI ↗
Lasianthus hookeri OR490210.1 160246 View on NCBI ↗