Markers + reference

Lovoa

2 species · Meliaceae · Sapindales

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Species 2
Genome length 159–159 kb
Candidate markers 257
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 257 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-rps16 LSC 861 0.0175 0.99 59.8 yes View details
rps16-trnQ LSC 1360 0.0148 0.99 66.3 yes View details
trnS-trnG LSC 760 0.0146 0.99 55.8 yes View details
trnT-psbD LSC 1243 0.0185 1.00 62.0 yes View details
ndhC-trnV LSC 908 0.0210 0.99 58.1 yes View details
ycf4-cemA LSC 569 0.0516 0.99 80.5 yes View details
psbE-petL LSC 1271 0.0142 1.00 59.5 yes View details
trnP-psaJ LSC 351 0.0456 1.00 76.2 yes View details
rps3 LSC 660 0.0091 1.00 49.1 yes View details
ccsA-ndhD SSC 340 0.0446 0.92 67.9 yes View details
psbT-psbN LSC 60 0.0333 1.00 71.7 yes View details
rpoB-trnC LSC 967 0.0103 1.00 64.7 yes View details
ndhE-ndhG SSC 241 0.0207 1.00 64.4 yes View details
trnW-trnP LSC 183 0.0176 0.93 63.9 yes View details
rpl20-rps12 LSC 763 0.0066 1.00 62.6 yes View details
rbcL LSC 1428 0.0063 1.00 62.4 yes View details
petA-psbJ LSC 1069 0.0112 1.00 62.3 yes View details
trnF-ndhJ LSC 427 0.0164 1.00 61.9 yes View details
rps4-trnT LSC 362 0.0138 1.00 61.7 yes View details
psbC LSC 1422 0.0049 1.00 61.6 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
trnK_p1 trnK CTCCGTGTCAACCAATAGCA CGTTGTGCAATTCAATCGCT 2788–2808 1.000 80.5
trnK_p2 trnK GACGGTTTTCGGTACTGGTT CGTTGTGCAATTCAATCGCT 2975–2995 1.000 80.3
trnK_p3 trnK GGACTCCCAAGCACACAAAT CGTTGTGCAATTCAATCGCT 2864–2884 1.000 78.2
trnK_p4 trnK TCTCCGTGTCAACCAATAGC CGTTGTGCAATTCAATCGCT 2789–2809 1.000 78.2
trnK_p5 trnK AAGACGGTTTTCGGTACTGG CGTTGTGCAATTCAATCGCT 2997 0.500 58.5
trnK-rps16_p1 trnK-rps16 AGCCGTACTTAAAAGCCGAG ATTTTCTTGAGAAGGGCGCT 1006–1010 1.000 80.0
trnK-rps16_p2 trnK-rps16 AAAGCCGAGTACTCTACCGT ATTTTCTTGAGAAGGGCGCT 995–999 1.000 78.7
trnK-rps16_p3 trnK-rps16 AAGCCGAGTACTCTACCGTT ATTTTCTTGAGAAGGGCGCT 994–998 1.000 78.7
trnK-rps16_p4 trnK-rps16 AGCCGTACTTAAAAGCCGAG CGCTCAACCTACAGGAATCG 990–994 1.000 78.1
trnK-rps16_p5 trnK-rps16 AGCCGTACTTAAAAGCCGAG TCAAAGAAGGCAGGGGTTTT 959–963 1.000 77.9
rps16-trnQ_p1 rps16-trnQ TCCATAGCGGATCATGTCCT GAAATTGAAATGGGGCGTGG 1504–1513 1.000 81.3
rps16-trnQ_p2 rps16-trnQ GCGGATCATGTCCTTCAAGT GAAATTGAAATGGGGCGTGG 1498–1507 1.000 81.2
rps16-trnQ_p3 rps16-trnQ TCCATAGCGGATCATGTCCT GAGGTTCGAATCCTTCCGTC 1446–1455 1.000 80.9
rps16-trnQ_p4 rps16-trnQ GCGGATCATGTCCTTCAAGT GAGGTTCGAATCCTTCCGTC 1440–1449 1.000 80.8
rps16-trnQ_p5 rps16-trnQ AAGTCGCACGTTGCTTTCTA GAAATTGAAATGGGGCGTGG 1482–1491 1.000 80.4
trnS-trnG_p1 trnS-trnG TAAGCCACTCAGCCATCTCT CGAACGAATCACACTTTTACCA 819–838 1.000 58.7
trnS-trnG_p2 trnS-trnG TAAGCCACTCAGCCATCTCT TCGAACGAATCACACTTTTACC 820–839 1.000 56.6
trnS-trnG_p3 trnS-trnG GCTTTAAGCCACTCAGCCAT CGAACGAATCACACTTTTACCA 823–842 1.000 55.4
trnS-trnG_p4 trnS-trnG ACTCGTACACCGGATTAGCA CGAACGAATCACACTTTTACCA 850–869 1.000 55.4
trnS-trnG_p5 trnS-trnG CTCGTACACCGGATTAGCAA CGAACGAATCACACTTTTACCA 849–868 1.000 55.1
rpoB-trnC_p1 rpoB-trnC ATTCCCGCATTTCCATCTCC GGCGAGTTATACCAGCCAAA 1113–1186 1.000 80.3
rpoB-trnC_p2 rpoB-trnC ATTCCCGCATTTCCATCTCC AAAAGGATTTGCAGTCCCCC 1037–1110 1.000 77.8
rpoB-trnC_p3 rpoB-trnC GCATTTCCATCTCCGAGCAT GGCGAGTTATACCAGCCAAA 1107–1180 1.000 77.3
rpoB-trnC_p4 rpoB-trnC ACATTCCCGCATTTCCATCT GGCGAGTTATACCAGCCAAA 1115–1188 1.000 76.9
rpoB-trnC_p5 rpoB-trnC AGACATTCCCGCATTTCCAT GGCGAGTTATACCAGCCAAA 1117–1190 1.000 76.9
trnT-psbD_p1 trnT-psbD GTGGTAGAGTAACGCCATGG ACAAAAACGAAACGGTCCCT 1393–1395 1.000 78.8
trnT-psbD_p2 trnT-psbD TCAGTGGTAGAGTAACGCCA ACAAAAACGAAACGGTCCCT 1396–1398 1.000 78.7
trnT-psbD_p3 trnT-psbD ACGGCCCTTTTAACTCAGTG ACAAAAACGAAACGGTCCCT 1410–1412 1.000 78.5
trnT-psbD_p4 trnT-psbD GTGGTAGAGTAACGCCATGG CCCTTCGTAACCAGTCATCC 1377–1379 1.000 78.3
trnT-psbD_p5 trnT-psbD TCAGTGGTAGAGTAACGCCA CCCTTCGTAACCAGTCATCC 1380–1382 1.000 78.2

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
Lovoa swynnertonii MZ274130.1 158881 View on NCBI ↗
Lovoa trichilioides MZ274129.1 159381 View on NCBI ↗