Markers + reference

Horsfieldia

4 species · Myristicaceae · Magnoliales

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Species 4
Genome length 156–156 kb
Candidate markers 260
Primer pairs 95

Genome-wide nucleotide diversity

Sliding-window nucleotide diversity
Sliding-window nucleotide diversity (π) across the plastome.

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 260 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 299 0.0390 1.00 55.6 yes View details
trnK-UUU-rps16 LSC 975 0.0104 1.00 55.9 yes View details
rps16-trnQ-UUG LSC 965 0.0159 1.00 58.5 yes View details
petN-psbM LSC 875 0.0223 0.99 59.2 yes View details
trnT-GGU-psbD LSC 1458 0.0096 1.00 49.3 yes View details
ndhC-trnV-UAC LSC 1901 0.0154 0.99 49.3 yes View details
petA-psbJ LSC 1198 0.0132 1.00 63.1 yes View details
ndhF SSC 2226 0.0067 1.00 37.6 yes View details
trnN-GUU-trnR-ACG SSC 628 0.0317 0.99 58.1 yes View details
rpoC1-rpoB LSC 26 0.0833 1.00 71.4 yes View details
rrn5-ndhF IRb 71 0.0606 0.93 67.0 yes View details
atpB-rbcL LSC 762 0.0059 0.96 65.9 yes View details
psbT-psbN LSC 59 0.0339 1.00 62.2 yes View details
atpH-atpI LSC 1040 0.0083 1.00 54.9 yes View details
trnE-UUC-trnT-GGU LSC 534 0.0066 1.00 52.6 yes View details
rpoC2-rpoC1 LSC 162 0.0134 1.00 52.2 yes View details
psbM-trnD-GUC LSC 993 0.0082 1.00 51.8 yes View details
trnS-GCU-trnG-UCC LSC 892 0.0075 1.00 51.5 yes View details
psbI-trnS-GCU LSC 139 0.0084 1.00 51.3 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-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG CTGATGGTATGCCCCTAGGA 878–888 1.000 81.1
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCTCTGGACCTAGCTGCTAT 366–376 0.750 71.7
trnH-GUG-psbA_p3 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCTCTGGACCTAGCTGCTAT 380–390 0.750 71.6
trnH-GUG-psbA_p4 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCTCTGGACCTAGCTGCTAT 379–389 0.750 71.6
trnH-GUG-psbA_p5 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCTCTGGACCTAGCTGCTAT 381–391 0.750 71.5
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG TCTTTTTCGAGCCGTACGAG 1065–1278 1.000 84.9
trnK-UUU-rps16_p2 trnK-UUU-rps16 ACACATCTGTATCCACCCCA TCTTTTTCGAGCCGTACGAG 1415–1630 1.000 84.6
trnK-UUU-rps16_p3 trnK-UUU-rps16 GGAGTCCAATCAACGGATCC TCTTTTTCGAGCCGTACGAG 1566–1781 1.000 84.4
trnK-UUU-rps16_p4 trnK-UUU-rps16 GGGAGTCCAATCAACGGATC TCTTTTTCGAGCCGTACGAG 1567–1782 1.000 84.4
trnK-UUU-rps16_p5 trnK-UUU-rps16 ACCCGATCGCTCTTTTGATC TCTTTTTCGAGCCGTACGAG 1468–1683 1.000 84.4
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1034–1042 1.000 81.1
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CTCGGAGGTTCGAATCCTTC 1038–1046 1.000 80.0
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CCGATCGTGTCCTTCAAGTC GAGGTTCGAATCCTTCCGTC 1049–1057 1.000 79.2
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TACTCGGAGGTTCGAATCCT 1040–1048 1.000 78.3
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA ACTCGGAGGTTCGAATCCTT 1039–1047 1.000 78.2
psbI-trnS-GCU_p1 psbI-trnS-GCU CGTAATCCTGGACGTGAGGA TGGACTAAAGCGACGGATTG 231–236 1.000 75.2
psbI-trnS-GCU_p2 psbI-trnS-GCU CGTAATCCTGGACGTGAGGA GTGGACTAAAGCGACGGATT 232–237 1.000 75.1
psbI-trnS-GCU_p3 psbI-trnS-GCU CGTAATCCTGGACGTGAGGA TAGGAGAGATGGCTGAGTGG 248–253 1.000 74.4
psbI-trnS-GCU_p4 psbI-trnS-GCU CGTAATCCTGGACGTGAGGA CGAGTTATTCGTACCGAGGG 198–203 1.000 72.4
psbI-trnS-GCU_p5 psbI-trnS-GCU CGTAATCCTGGACGTGAGGA CTGAGTGGACTAAAGCGACG 236–241 1.000 72.1
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGTCGCTTTAGTCCA AATCAAACCGAAAGACCCCC 1004–1015 1.000 80.4
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGTCGCTTTAGTCCAC AATCAAACCGAAAGACCCCC 1003–1014 1.000 80.4
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CAAGTGATCAGAGGGAACGG AATCAAACCGAAAGACCCCC 1074–1085 1.000 80.3
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CAATCCGTCGCTTTAGTCCA AACCGAAAGACCCCCTAACT 999–1010 1.000 79.0
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AATCCGTCGCTTTAGTCCAC AACCGAAAGACCCCCTAACT 998–1009 1.000 79.0
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTTGCAACTTTAGCCGCG 1128–1162 1.000 76.6
atpH-atpI_p2 atpH-atpI ATAACGGAAGCGGCAGAAAT CAAGCGGGATTCAAGCTCTT 1149–1183 1.000 76.4
atpH-atpI_p3 atpH-atpI CAGTACCTTGACCAACTCCG TTTTTGCAACTTTAGCCGCG 1187–1221 1.000 76.2
atpH-atpI_p4 atpH-atpI CAGTACCTTGACCAACTCCG CAAGCGGGATTCAAGCTCTT 1208–1242 1.000 76.0
atpH-atpI_p5 atpH-atpI GATACCTTCTACGGCTTGGC TTTTTGCAACTTTAGCCGCG 1213–1247 1.000 75.8

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
Horsfieldia amygdalina NC_060835.1 155682 View on NCBI ↗
Horsfieldia hainanensis NC_060833.1 155774 View on NCBI ↗
Horsfieldia prainii NC_060834.1 155696 View on NCBI ↗
Horsfieldia tetratepala NC_060836.1 155770 View on NCBI ↗