Markers + reference

Yoania

4 species · Orchidaceae · Asparagales

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Species 4
Genome length 43–45 kb
Candidate markers 83
Primer pairs 70

Genome-wide nucleotide diversity

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

Candidate markers

4 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 83 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16 Genome 991 0.0389 0.99 73.6 yes View details
rrn16-rrn23 Genome 472 0.1133 0.83 75.3 yes View details
rrn5-ycf1 Genome 443 0.0862 0.98 81.3 yes View details
trnL-CAA-rps16 Genome 4243 0.0203 0.50 45.6 yes View details
rpl16-rps3 Genome 1173 0.0485 0.95 82.0 yes View details
clpP-rps11 Genome 276 0.0775 0.98 80.6 yes View details
rrn4.5-rrn5 Genome 140 0.1274 1.00 79.6 yes View details
rps16-trnQ-UUG Genome 336 0.0701 0.93 78.6 yes View details
trnE-UUC-trnfM-CAU Genome 80 0.0633 0.99 78.5 yes View details
rrn23-rrn4.5 Genome 103 0.0647 1.00 77.6 yes View details
rpl33-rps18 Genome 154 0.0649 0.96 77.3 yes View details
ycf1-rps12 Genome 1025 0.0408 0.96 76.9 yes View details
trnC-GCA-trnY-GUA Genome 497 0.0476 0.95 75.8 yes View details
trnfM-CAU-rps14 Genome 151 0.1157 0.87 75.1 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 70 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps16_p1 rps16 CTTGTCGGTTTAGCCCCTTT CGTGCGACTTGAAGGACATA 916–1010 1.000 87.3
rps16_p2 rps16 TTCCTTCTCTTCGGGATCGA CGTGCGACTTGAAGGACATA 813–907 1.000 87.3
rps16_p3 rps16 CGGTTTAGCCCCTTTGTCAA CGTGCGACTTGAAGGACATA 911–1005 1.000 84.9
rps16_p4 rps16 TTGTCGGTTTAGCCCCTTTG CGTGCGACTTGAAGGACATA 915–1009 1.000 84.9
rps16_p5 rps16 AGTTCTTGTCGGTTTAGCCC CGTGCGACTTGAAGGACATA 920–1014 0.750 74.6
rps16-trnQ-UUG_p1 rps16-trnQ-UUG TATGTCCTTCAAGTCGCACG CCTTACCACTTGGCCACG 390–490 1.000 75.2
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TATGTCCTTCAAGTCGCACG GTTGCCTTACCACTTGGCC 394–494 1.000 75.0
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CCTTACCACTTGGCCACG 380–480 1.000 74.4
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GTTGCCTTACCACTTGGCC 384–484 1.000 74.2
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TATGTCCTTCAAGTCGCACG GCCTTACCACTTGGCCAC 391–491 1.000 72.8
trnC-GCA-trnY-GUA_p1 trnC-GCA-trnY-GUA CCCCTACTTGCTGCATCAAA CATAACCTTGAGACCACGGG 1273–1477 1.000 86.4
trnC-GCA-trnY-GUA_p2 trnC-GCA-trnY-GUA CCCCTACTTGCTGCATCAAA CTTGAGACCACGGGTTCAAA 1267–1471 1.000 86.3
trnC-GCA-trnY-GUA_p3 trnC-GCA-trnY-GUA CCCCTACTTGCTGCATCAAA GGAGGTAACGGGGATTCAAC 1113–1313 1.000 86.2
trnC-GCA-trnY-GUA_p4 trnC-GCA-trnY-GUA CCCCTACTTGCTGCATCAAA AAGGAGGTAACGGGGATTCA 1115–1315 1.000 86.2
trnC-GCA-trnY-GUA_p5 trnC-GCA-trnY-GUA CCCCTACTTGCTGCATCAAA AGGAGGTAACGGGGATTCAA 1114–1314 1.000 86.2
trnE-UUC-trnfM-CAU_p1 trnE-UUC-trnfM-CAU TGTCCTGAACCACTAGACGA CTTGAGACCACGGGTTCAAA 140–151 1.000 83.5
trnE-UUC-trnfM-CAU_p2 trnE-UUC-trnfM-CAU TGTCCTGAACCACTAGACGA CATAACCTTGAGACCACGGG 146–157 1.000 83.4
trnE-UUC-trnfM-CAU_p3 trnE-UUC-trnfM-CAU TGTCCTGAACCACTAGACGA GTTCAAATCCTGTCTCCGCA 127–138 1.000 82.9
trnE-UUC-trnfM-CAU_p4 trnE-UUC-trnfM-CAU TGTCCTGAACCACTAGACGA CACGGGTTCAAATCCTGTCT 132–143 1.000 82.7
trnE-UUC-trnfM-CAU_p5 trnE-UUC-trnfM-CAU TGTCCTGAACCACTAGACGA TGAGACCACGGGTTCAAATC 138–149 1.000 82.5
trnfM-CAU-rps14_p1 trnfM-CAU-rps14 CCCGTGGTCTCAAGGTTATG CACGTAATAGTGCGCGGATA 342–377 1.000 91.5
trnfM-CAU-rps14_p2 trnfM-CAU-rps14 CCCGTGGTCTCAAGGTTATG ACGTAATAGTGCGCGGATAC 341–376 1.000 91.5
trnfM-CAU-rps14_p3 trnfM-CAU-rps14 AAGGTTATGAGCCTTGCGAG CACGTAATAGTGCGCGGATA 331–366 1.000 91.4
trnfM-CAU-rps14_p4 trnfM-CAU-rps14 AAGGTTATGAGCCTTGCGAG ACGTAATAGTGCGCGGATAC 330–365 1.000 91.4
trnfM-CAU-rps14_p5 trnfM-CAU-rps14 GTTGAATCCCCGTTACCTCC CACGTAATAGTGCGCGGATA 502–546 1.000 90.1
rpl33-rps18_p1 rpl33-rps18 CGAACTGAACTAAGAGCGCT TCGTCGTTTGTGGATCACTC 1162–1271 1.000 89.6
rpl33-rps18_p2 rpl33-rps18 GTTTTGGAGACCCACGTTCT TCGTCGTTTGTGGATCACTC 1184–1293 1.000 89.4
rpl33-rps18_p3 rpl33-rps18 GAAAAGGAGGTTCATGGCCA TCGTCGTTTGTGGATCACTC 979–1043 1.000 89.2
rpl33-rps18_p4 rpl33-rps18 TGAAAAGGAGGTTCATGGCC TCGTCGTTTGTGGATCACTC 980–1044 1.000 89.2
rpl33-rps18_p5 rpl33-rps18 AAAGGAGGTTCATGGCCAAG TCGTCGTTTGTGGATCACTC 977–1041 0.750 78.0

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
Yoania amagiensis NC_066820.1 44940 View on NCBI ↗
Yoania japonica OK514622.1 44079 View on NCBI ↗
Yoania prainii OK514624.1 43091 View on NCBI ↗
Yoania squamipes OK514620.1 44367 View on NCBI ↗