Markers + reference

Leptodermis

9 species · Rubiaceae · Gentianales

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Species 9
Genome length 154–155 kb
Candidate markers 265
Primer pairs 100

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 265 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 1413 0.0102 0.96 54.8 yes View details
trnS-GCU-trnG-GCC LSC 591 0.0120 0.99 49.9 yes View details
rps2-rpoC2 LSC 226 0.0268 0.99 52.4 yes View details
petN-psbM LSC 690 0.0082 0.99 42.8 yes View details
trnT-UGU-trnL-UAA LSC 728 0.0086 1.00 42.1 yes View details
psbE-petL LSC 1090 0.0065 1.00 44.7 yes View details
trnP-UGG-psaJ LSC 396 0.0065 1.00 52.1 yes View details
ndhF SSC 2283 0.0041 1.00 44.3 yes View details
rpl32-trnL-UAG SSC 688 0.0118 1.00 48.8 yes View details
ycf1 SSC 5613 0.0039 1.00 38.1 yes View details
psbF-psbE LSC 9 0.0617 1.00 63.1 yes View details
trnK-UUU-rps16 LSC 831 0.0043 0.99 58.6 yes View details
accD-psaI LSC 724 0.0077 1.00 56.9 yes View details
atpH-atpI LSC 1019 0.0040 1.00 56.1 yes View details
petG-trnW-CCA LSC 152 0.0235 0.93 55.4 yes View details
ndhA SSC 2233 0.0047 0.99 54.6 yes View details
infA-rps8 LSC 172 0.0128 0.98 53.6 yes View details
trnE-UUC-trnT-GGU LSC 906 0.0060 0.98 52.9 yes View details
rrn16-trnE-UUC IRb 304 0.0083 0.98 52.9 yes View details
trnE-UUC-rrn16 IRa 304 0.0083 0.98 52.9 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
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TGCTCAACTTACAGGAACCG 940–960 1.000 80.7
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TGCTCAACTTACAGGAACCG 939–959 1.000 80.7
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT GCTCAACTTACAGGAACCGT 939–959 1.000 80.7
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GCTCAACTTACAGGAACCGT 938–958 1.000 80.7
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT ACAGGAACCGTTCAGGATCT 929–949 1.000 79.2
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1417–1486 1.000 84.5
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 1421–1490 1.000 79.8
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TAAGGCAACGGGTTTTGGTC 1447–1516 1.000 79.6
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG GAGGTTCGAATCCTTCCGTC 1409–1478 1.000 79.3
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AGTCGCACGTTGCTTTCTAC GAGGTTCGAATCCTTCCGTC 1416–1485 1.000 78.7
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA AAACCGAAAGCAAAGACCCT 703–868 1.000 82.9
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA AACCGAAAGCAAAGACCCTT 702–867 1.000 82.9
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA ACCGAAAGCAAAGACCCTTT 701–866 1.000 82.9
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC AACCGAAAGCAAAGACCCTT 701–866 1.000 82.9
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC ACCGAAAGCAAAGACCCTTT 700–865 1.000 82.9
atpH-atpI_p1 atpH-atpI CAAACCAGCAGCAATAACGG TTTTTGCAACTTTAGCCGCG 1120–1160 1.000 76.8
atpH-atpI_p2 atpH-atpI CCAAACCAGCAGCAATAACG TTTTTGCAACTTTAGCCGCG 1121–1161 1.000 76.8
atpH-atpI_p3 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTTGCAACTTTAGCCGCG 1107–1147 1.000 76.7
atpH-atpI_p4 atpH-atpI TCCGATAGAAGCAAGCCCTA TTTTTGCAACTTTAGCCGCG 1144–1184 1.000 76.3
atpH-atpI_p5 atpH-atpI AACCAGCAGCAATAACGGAA TTTTTGCAACTTTAGCCGCG 1118–1158 1.000 76.2
rps2-rpoC2_p1 rps2-rpoC2 CCTGCCTCCATCATCTCTTC TCCATGATACATCAGAACAGTCT 321–326 1.000 45.7
rps2-rpoC2_p2 rps2-rpoC2 ATGGCCAAAATGAACCCCTG TCCATGATACATCAGAACAGTCT 337–342 1.000 44.1
rps2-rpoC2_p3 rps2-rpoC2 CATGGCCAAAATGAACCCCT TCCATGATACATCAGAACAGTCT 338–343 1.000 44.1
rps2-rpoC2_p4 rps2-rpoC2 CCCTGCCTCCATCATCTCTT TCCATGATACATCAGAACAGTCT 322–327 1.000 43.7
rps2-rpoC2_p5 rps2-rpoC2 CCTGCCTCCATCATCTCTTC TCCTTTCAAAGAGTTTCCATGA 336–341 1.000 43.6
petN-psbM_p1 petN-psbM CGCTTTGGCACAGAGATAGT CTATGAAAGGAAAGGGGGCC 1829–1861 1.000 81.9
petN-psbM_p2 petN-psbM CGCTTTGGCACAGAGATAGT GGCTATGAAAGGAAAGGGGG 1831–1863 1.000 81.8
petN-psbM_p3 petN-psbM CGCTTTGGCACAGAGATAGT GATTGGGTCCCGAATCGAAA 1495–1521 1.000 81.5
petN-psbM_p4 petN-psbM CGCTTTGGCACAGAGATAGT TTTTTGGCAGGAAAAGGGGT 1751–1784 1.000 81.1
petN-psbM_p5 petN-psbM TAGTAAGTCTCGCTTGGGCT GATTGGGTCCCGAATCGAAA 1084–1110 1.000 80.6

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (9)

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

Species Accession Length (bp) Link
Leptodermis forrestii NC_063327.1 154369 View on NCBI ↗
Leptodermis gracilis NC_063325.1 154783 View on NCBI ↗
Leptodermis hirsutiflora NC_063324.1 154639 View on NCBI ↗
Leptodermis hirsutiflora var. ciliata MT674516.1 154619 View on NCBI ↗
Leptodermis kumaonensis NC_063323.1 154789 View on NCBI ↗
Leptodermis ludlowii NC_063326.1 154403 View on NCBI ↗
Leptodermis pilosa var. acanthoclada MT677907.1 154794 View on NCBI ↗
Leptodermis rehderiana PV370340.1 154345 View on NCBI ↗
Leptodermis scabrida NC_049160.1 154783 View on NCBI ↗