Markers + reference

Homalium

3 species · Salicaceae · Malpighiales

Back to catalogue

Species 3
Genome length 157–158 kb
Candidate markers 259
Primer pairs 95

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 259 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-trnH LSC 1274 0.0085 0.98 66.4 yes View details
atpH-atpI LSC 1028 0.0110 1.00 54.8 yes View details
psbZ-trnG LSC 492 0.0276 0.96 62.9 yes View details
ycf4-cemA LSC 399 0.0623 0.80 75.6 yes View details
petA-psbJ LSC 959 0.0146 1.00 60.3 yes View details
psbE-petL LSC 1130 0.0250 0.95 73.8 yes View details
rpl22 LSC 390 0.0120 1.00 35.1 yes View details
rps19 IRb 279 0.0024 1.00 32.4 no View details
ndhF SSC 2280 0.0082 1.00 48.2 yes View details
rps19 IRa 279 0.0024 1.00 32.4 yes View details
rps19-trnH IRa 319 0.0406 0.77 72.9 no View details
ycf1-ndhF SSC 94 0.1190 0.60 67.6 yes View details
trnF-ndhJ LSC 765 0.0076 0.92 66.9 yes View details
trnR-trnN IRb 671 0.0050 1.00 66.1 yes View details
trnN-trnR IRa 671 0.0040 1.00 65.5 yes View details
atpB-rbcL LSC 792 0.0061 0.97 65.4 yes View details
matK-trnK LSC 766 0.0210 1.00 65.2 yes View details
trnH-psbA LSC 259 0.0170 0.91 64.3 yes View details
psaA-ycf3 LSC 651 0.0020 1.00 63.6 yes View details
ndhC-trnV LSC 1153 0.0006 0.97 62.4 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-psbA_p1 trnH-psbA GATCCACTTGGCTACATCCG CCTCTAGACCTAGCTGCTGT 325–336 1.000 83.9
trnH-psbA_p2 trnH-psbA CAATCCACTGCCTTGATCCA CCTCTAGACCTAGCTGCTGT 339–350 1.000 83.8
trnH-psbA_p3 trnH-psbA AATCCACTGCCTTGATCCAC CCTCTAGACCTAGCTGCTGT 338–349 1.000 83.8
trnH-psbA_p4 trnH-psbA ACAATCCACTGCCTTGATCC CCTCTAGACCTAGCTGCTGT 340–351 1.000 83.8
trnH-psbA_p5 trnH-psbA GATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 328–339 1.000 83.8
trnK_p1 trnK GGACTCCCAAGCACATGAAT TGTGTCGTACGATTCAATCTCT 2926–3000 0.667 46.0
trnK_p2 trnK GGACTCCCAAGCACATGAAT TGTGTCGTACGATTCAATCTCTT 2926–3000 0.667 43.1
trnK_p3 trnK GGACTCCCAAGCACATGAAT TGTGTCGTACGATTCAATCTC 2926–3000 0.667 42.5
trnK_p4 trnK GGACTCCCAAGCACATGAAT GTGTCGTACGATTCAATCTCT 2925–2999 0.667 40.2
trnK_p5 trnK GGACTCCCAAGCACATGAAT TGTGTCGTACGATTCAATCT 2926–3000 0.667 40.1
matK-trnK_p1 matK-trnK TTCTTTGAGATTTCTCTATTTTCA TGGGGTTGCTAACTCAATGG 756–837 1.000 45.8
matK-trnK_p2 matK-trnK TTCTTTGAGATTTCTCTATTTTCA GGGGTTGCTAACTCAATGGT 755–836 1.000 45.8
matK-trnK_p3 matK-trnK TCTTTGAGATTTCTCTATTTTCAT TGGGGTTGCTAACTCAATGG 755–836 1.000 45.8
matK-trnK_p4 matK-trnK TCTTTGAGATTTCTCTATTTTCAT GGGGTTGCTAACTCAATGGT 754–835 1.000 45.8
matK-trnK_p5 matK-trnK TCTAAATTTCTTTGAGATTTCTCT TGGGGTTGCTAACTCAATGG 763–844 1.000 45.8
trnK-trnH_p1 trnK-trnH AAAGCTGTTAGCCGCACTTA GAGGTTCGAATCCTTCCGTC 1352–2146 1.000 80.1
trnK-trnH_p2 trnK-trnH AAGCTGTTAGCCGCACTTAA GAGGTTCGAATCCTTCCGTC 1351–2145 1.000 80.1
trnK-trnH_p3 trnK-trnH AGCTGTTAGCCGCACTTAAA GAGGTTCGAATCCTTCCGTC 1350–2144 1.000 80.1
trnK-trnH_p4 trnK-trnH TAAAAGCTGTTAGCCGCACT GAGGTTCGAATCCTTCCGTC 1354–2148 1.000 80.1
trnK-trnH_p5 trnK-trnH GTTAGCCGCACTTAAAAGCC GAGGTTCGAATCCTTCCGTC 1346–2140 1.000 79.4
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT GTGAATCCTTGGAGGGACAC 1086–1242 1.000 83.3
atpH-atpI_p2 atpH-atpI AGCGGCAGAAATCAATGGAT GTGAATCCTTGGAGGGACAC 1078–1234 1.000 83.2
atpH-atpI_p3 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTGCAACTTTAGCTGCGG 1115–1271 1.000 83.1
atpH-atpI_p4 atpH-atpI AGCGGCAGAAATCAATGGAT TTTTGCAACTTTAGCTGCGG 1107–1263 1.000 82.9
atpH-atpI_p5 atpH-atpI GTCCAATAGAAGCAAGCCCA GTGAATCCTTGGAGGGACAC 1124–1280 1.000 82.5
psbZ-trnG_p1 psbZ-trnG TAGGAGTTGATACCGTCGCT TTCTTCTCTTCATCACGCGG 1274–1350 1.000 85.0
psbZ-trnG_p2 psbZ-trnG TAGGAGTTGATACCGTCGCT TGGAAAGTTACAAGCCCCAC 1596–1672 1.000 84.9
psbZ-trnG_p3 psbZ-trnG CAAGACCGGAGCTATCAACC TTCTTCTCTTCATCACGCGG 1367–1443 1.000 84.8
psbZ-trnG_p4 psbZ-trnG TAGGAGTTGATACCGTCGCT GAAAGTTACAAGCCCCACCA 1594–1670 0.667 70.2
psbZ-trnG_p5 psbZ-trnG CGAATAAAGTGGGAAGGGGG TTCTTCTCTTCATCACGCGG 1142–1166 0.667 69.3

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
Homalium ceylanicum NC_045235.1 156551 View on NCBI ↗
Homalium cochinchinense NC_045919.1 157116 View on NCBI ↗
Homalium hainanense NC_054193.1 157852 View on NCBI ↗