Markers + reference

Glochidion

4 species · Phyllanthaceae · Malpighiales

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Species 4
Genome length 157–157 kb
Candidate markers 268
Primer pairs 105

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 9 remaining regions by MarkerSeek score (out of 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 280 0.0089 1.00 44.7 yes View details
rps16 LSC 1144 0.0022 1.00 47.9 yes View details
trnR-UCU-atpA LSC 277 0.0126 1.00 50.7 yes View details
psbC LSC 1422 0.0004 1.00 40.4 yes View details
psbC-trnS-UGA LSC 227 0.0213 0.96 59.7 yes View details
trnM-CAU-atpE LSC 247 0.0081 1.00 37.2 yes View details
cemA LSC 690 0.0031 1.00 54.9 yes View details
petA-psbJ LSC 911 0.0115 1.00 57.4 yes View details
trnL-CAA-ndhB IRb 567 0.0009 1.00 40.3 yes View details
ndhD SSC 1521 0.0014 1.00 54.4 yes View details
ndhB-trnL-CAA IRa 567 0.0009 1.00 40.3 yes View details
rps16-trnQ-UUG LSC 936 0.0023 1.00 65.5 yes View details
trnS-GCU-trnG-UCC LSC 762 0.0026 1.00 64.9 yes View details
ndhA SSC 2250 0.0016 1.00 62.2 yes View details
psbE-petL LSC 1074 0.0009 0.99 62.1 yes View details
rbcL-accD LSC 774 0.0024 1.00 61.8 yes View details
atpH-atpI LSC 1146 0.0013 0.99 61.0 yes View details
psbM-trnD-GUC LSC 1145 0.0017 1.00 60.9 yes View details
atpA-atpF LSC 55 0.0242 1.00 60.7 yes View details
rpl32-trnL-UAG SSC 1045 0.0014 1.00 60.0 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
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCTCTAGACCTAGCTGCTGT 347 1.000 79.6
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCTCTAGACCTAGCTGCTGT 361 1.000 79.5
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCTCTAGACCTAGCTGCTGT 360 1.000 79.5
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCTCTAGACCTAGCTGCTGT 362 1.000 79.5
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 350 1.000 79.5
trnK-UUU_p1 trnK-UUU CCCAAGCACACGAATTCTCT TGTTCCCAATCATTAGGATTTCA 2935–2944 1.000 40.5
trnK-UUU_p2 trnK-UUU CTCCCAAGCACACGAATTCT TGTTCCCAATCATTAGGATTTCA 2937–2946 1.000 40.5
trnK-UUU_p3 trnK-UUU TCCCAAGCACACGAATTCTC TGTTCCCAATCATTAGGATTTCA 2936–2945 1.000 40.5
trnK-UUU_p4 trnK-UUU TGAATGGCGTTGAAGTGAGT TGTTCCCAATCATTAGGATTTCA 2785–2794 1.000 40.5
trnK-UUU_p5 trnK-UUU ACTCCCAAGCACACGAATTC TGTTCCCAATCATTAGGATTTCA 2938–2947 1.000 40.5
rps16_p1 rps16 GGGGGATAGTAGAGAAAAGGT CTGGATTACTATGTACCCGCG 1309–1315 1.000 46.5
rps16_p2 rps16 GGGGGATAGTAGAGAAAAGGT TGGATTACTATGTACCCGCG 1308–1314 1.000 46.2
rps16_p3 rps16 GGGGGATAGTAGAGAAAAGGTT CTGGATTACTATGTACCCGCG 1309–1315 1.000 44.6
rps16_p4 rps16 GGGGGATAGTAGAGAAAAGGTT TGGATTACTATGTACCCGCG 1308–1314 1.000 44.3
rps16_p5 rps16 GGGGGATAGTAGAGAAAAGGT GGATTACTATGTACCCGCGA 1307–1313 1.000 43.9
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CCACAACCGATCATGTCCTT GAGGTTCGAATCCTTCCGTC 1030–1289 1.000 82.8
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1009–1268 1.000 82.6
rps16-trnQ-UUG_p3 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1020–1279 1.000 82.0
rps16-trnQ-UUG_p4 rps16-trnQ-UUG ATCCACAACCGATCATGTCC GAGGTTCGAATCCTTCCGTC 1032–1291 1.000 81.0
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CCACAACCGATCATGTCCTT TTCGGAGGTTCGAATCCTTC 1034–1293 1.000 78.0
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA TGAACGAATCACACTTTTACCAC 826–834 1.000 55.7
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC TGAACGAATCACACTTTTACCAC 825–833 1.000 55.7
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA TGAACCGAGAGATCCTTTAACT 860–868 1.000 55.5
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC TGAACCGAGAGATCCTTTAACT 859–867 1.000 55.5
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA ACGAATCACACTTTTACCACT 823–831 1.000 54.8
trnR-UCU-atpA_p1 trnR-UCU-atpA AAGCGTCCATCGTCTAATGG TCAAGAACAGCTGGAACGTT 386–415 1.000 78.6
trnR-UCU-atpA_p2 trnR-UCU-atpA AAGCGTCCATCGTCTAATGG TTCAAGAACAGCTGGAACGT 387–416 1.000 78.6
trnR-UCU-atpA_p3 trnR-UCU-atpA GGAAAAGCGTCCATCGTCTA TCAAGAACAGCTGGAACGTT 390–419 1.000 78.1
trnR-UCU-atpA_p4 trnR-UCU-atpA GGAAAAGCGTCCATCGTCTA TTCAAGAACAGCTGGAACGT 391–420 1.000 78.1
trnR-UCU-atpA_p5 trnR-UCU-atpA AAGCGTCCATCGTCTAATGG GGAAGCCCTTTTGAAAGAAGC 410–439 1.000 72.8

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (4)

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

Species Accession Length (bp) Link
Glochidion chodoense NC_042906.1 157085 View on NCBI ↗
Glochidion eriocarpum NC_086713.1 157460 View on NCBI ↗
Glochidion lanceolarium NC_086709.1 157219 View on NCBI ↗
Glochidion puberum PV700501.1 157133 View on NCBI ↗