Markers + reference

Ophiorrhiza

3 species · Rubiaceae · Gentianales

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Species 3
Genome length 154–154 kb
Candidate markers 273
Primer pairs 100

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 10 remaining regions by MarkerSeek score (out of 273 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0006 1.00 33.6 yes View details
rps16-trnQ-UUG LSC 969 0.0217 1.00 64.4 yes View details
trnS-GCU-trnG-GCC LSC 559 0.0203 1.00 59.2 yes View details
psbM-trnD-GUC LSC 884 0.0747 1.00 89.7 yes View details
psaA-ycf3 LSC 809 0.0135 0.98 59.3 yes View details
ndhC-trnV-UAC LSC 436 0.0292 1.00 62.5 yes View details
petA-psbJ LSC 1003 0.0349 0.98 73.7 yes View details
ycf1 IRb 756 0.0035 0.99 46.7 no View details
ndhF SSC 2256 0.0092 0.99 49.3 yes View details
rpl32-trnL-UAG SSC 857 0.0170 0.98 60.0 yes View details
ycf1 SSC 5607 0.0104 1.00 50.3 yes View details
trnY-GUA-trnE-UUC LSC 59 0.0565 1.00 78.9 yes View details
trnH-GUG-psbA LSC 230 0.0667 1.00 76.1 yes View details
infA LSC 159 0.0252 1.00 67.5 yes View details
accD-psaI LSC 787 0.0129 0.99 66.5 yes View details
trnR-ACG-trnN-GUU IRb 422 0.0095 1.00 66.1 yes View details
trnN-GUU-trnR-ACG IRa 422 0.0095 1.00 66.1 yes View details
petN-psbM LSC 709 0.0085 1.00 65.9 yes View details
trnT-UGU-trnL-UAA LSC 778 0.0091 0.99 65.5 yes View details
trnT-GGU-psbD LSC 1237 0.0075 1.00 64.2 yes View details
atpH-atpI LSC 1027 0.0052 1.00 63.1 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
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 300–310 1.000 84.4
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TTCCCTCTAGACCTAGCTGC 314–324 1.000 84.1
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TTCCCTCTAGACCTAGCTGC 313–323 1.000 84.1
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TTCCCTCTAGACCTAGCTGC 315–325 1.000 84.1
trnH-GUG-psbA_p5 trnH-GUG-psbA GCCTTGATCCACTTGGCTAC TTCCCTCTAGACCTAGCTGC 305–315 1.000 80.4
psbA_p1 psbA ACTCCTATACAATAAGACCGGA ATTTGTGTGCTTGGGAGTCC 1144 1.000 41.3
psbA_p2 psbA AACTCCTATACAATAAGACCGGA ATTTGTGTGCTTGGGAGTCC 1145 1.000 40.1
psbA_p3 psbA ACTCCTATACAATAAGACCGGAT ATTTGTGTGCTTGGGAGTCC 1144 1.000 40.1
psbA_p4 psbA ACTCCTATACAATAAGACCGG ATTTGTGTGCTTGGGAGTCC 1144 1.000 40.1
psbA_p5 psbA ACTCCTATACAATAAGACCGGA AGAATTTGTGTGCTTGGGAGT 1147 1.000 40.1
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1042–1679 1.000 80.8
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATTCCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1053–1690 1.000 80.4
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 1046–1683 1.000 76.1
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TAAGGCAACGGGTTTTGGTC 1072–1709 1.000 76.0
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TCATTCCCTTCAAGTCGCAC TTCGGAGGTTCGAATCCTTC 1057–1694 1.000 75.7
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC ATTAGCAATCCGCCGCTTTA ACGAATCACACTTTTACCACT 633–676 1.000 53.5
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC ACGGAAAGAGAGGGATTCGA ACGAATCACACTTTTACCACT 682–725 1.000 52.4
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC ATTAGCAATCCGCCGCTTTA AACGAATCACACTTTTACCACT 634–677 1.000 51.6
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC TGGAAACGGAAAGAGAGGGA ACGAATCACACTTTTACCACT 687–730 1.000 51.4
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC ACGGAAAGAGAGGGATTCGA AACGAATCACACTTTTACCACT 683–726 1.000 50.5
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTTGCAACTTTAGCCGCG 1109–1115 1.000 76.8
atpH-atpI_p2 atpH-atpI TACCCTCTACAGCTTGACCC TTTTTGCAACTTTAGCCGCG 1192–1198 1.000 76.0
atpH-atpI_p3 atpH-atpI GCGATACCCTCTACAGCTTG TTTTTGCAACTTTAGCCGCG 1196–1202 1.000 75.9
atpH-atpI_p4 atpH-atpI AATAACGGAAGCGGCAGAAA TTTTTGCAACTTTAGCCGCG 1110–1116 1.000 75.7
atpH-atpI_p5 atpH-atpI GCCAATCCAGCAGCAATAAC TTTTTGCAACTTTAGCCGCG 1124–1130 1.000 75.4
petN-psbM_p1 petN-psbM ACTCGTAGTGTGGGGAAGAA TCATTCTAGTTCCTACGGCCT 787–836 1.000 74.6
petN-psbM_p2 petN-psbM TCGTAGTGTGGGGAAGAAGT TCATTCTAGTTCCTACGGCCT 785–834 1.000 74.6
petN-psbM_p3 petN-psbM ACTCGTAGTGTGGGGAAGAA TCTAGTTCCTACGGCCTTTCT 783–832 1.000 74.1
petN-psbM_p4 petN-psbM TCGTAGTGTGGGGAAGAAGT TCTAGTTCCTACGGCCTTTCT 781–830 1.000 74.1
petN-psbM_p5 petN-psbM CGTAGTGTGGGGAAGAAGTG TCATTCTAGTTCCTACGGCCT 784–833 1.000 74.0

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
Ophiorrhiza densa NC_058252.1 154079 View on NCBI ↗
Ophiorrhiza guizhouensis PX023271.1 154134 View on NCBI ↗
Ophiorrhiza pumila NC_057496.1 154385 View on NCBI ↗