Markers + reference

Pogonia

2 species · Orchidaceae · Asparagales

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Species 2
Genome length 158–158 kb
Candidate markers 266
Primer pairs 80

Genome-wide nucleotide diversity

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

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 7 remaining regions by MarkerSeek score (out of 266 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0000 1.00 29.9 yes View details
rpoC2 LSC 4071 0.0005 1.00 54.2 yes View details
petD LSC 1460 0.0000 1.00 40.0 yes View details
rpoA LSC 1020 0.0010 1.00 59.3 yes View details
ndhA IRb 596 0.0052 0.96 65.6 yes View details
ndhD-ccsA SSC 313 0.0000 0.98 40.4 yes View details
ccsA SSC 933 0.0011 1.00 59.4 yes View details
ndhA IRa 442 0.0000 1.00 36.7 no View details
rpl32-ndhA SSC 1101 0.0000 0.98 61.0 yes View details
rps4 LSC 606 0.0016 1.00 59.7 yes View details
accD LSC 1641 0.0000 0.99 59.7 yes View details
matK-trnK(UUU) LSC 1324 0.0008 1.00 59.6 yes View details
rpl20-rps12 LSC 813 0.0012 1.00 59.5 yes View details
psbD-trnT(GGU) LSC 935 0.0011 1.00 59.4 yes View details
rbcL-accD LSC 875 0.0011 1.00 59.4 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 80 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbA_p1 psbA ACTGGGGGATTGTTACCTACA GTGCTTGGGAGTCCTTGAAA 1159 1.000 71.2
psbA_p2 psbA ACTGGGGGATTGTTACCTACA TGAATACGTGTGCTTGGGAG 1168 1.000 70.6
psbA_p3 psbA ACTGGGGGATTGTTACCTACA AATACGTGTGCTTGGGAGTC 1166 1.000 70.6
psbA_p4 psbA ACTGGGGGATTGTTACCTACA GAATACGTGTGCTTGGGAGT 1167 1.000 70.6
psbA_p5 psbA ACTGGGGGATTGTTACCTACA AGTGAATACGTGTGCTTGGG 1170 1.000 69.9
trnK(UUU)_p1 trnK(UUU) CGGAACTAGTCGGATGGAGT AGTAGTGGTAGTGGTTCAATTCA 193 1.000 45.0
trnK(UUU)_p2 trnK(UUU) CGGAACTAGTCGGATGGAGT AGTGGTAGTGGTTCAATTCA 190 1.000 45.0
trnK(UUU)_p3 trnK(UUU) CGGAACTAGTCGGATGGAGT GGTTCAATTCATTTAGTCGTCCA 181 1.000 44.6
trnK(UUU)_p4 trnK(UUU) CGGAACTAGTCGGATGGAGT TGGTTCAATTCATTTAGTCGTCC 182 1.000 44.6
trnK(UUU)_p5 trnK(UUU) ACTCGAACCCGGAACTAGTC AGTAGTGGTAGTGGTTCAATTCA 202 1.000 43.2
matK-trnK(UUU)_p1 matK-trnK(UUU) TCTTGCAGGAGAAGCGGATA GGTCCAGTTGATCAGTGCAA 1512–1558 1.000 75.4
matK-trnK(UUU)_p2 matK-trnK(UUU) TCTTGCAGGAGAAGCGGATA TTGGTCCAGTTGATCAGTGC 1514–1560 1.000 75.4
matK-trnK(UUU)_p3 matK-trnK(UUU) CTTGCAGGAGAAGCGGATAT GGTCCAGTTGATCAGTGCAA 1511–1557 1.000 75.2
matK-trnK(UUU)_p4 matK-trnK(UUU) CTTGCAGGAGAAGCGGATAT TTGGTCCAGTTGATCAGTGC 1513–1559 1.000 75.2
matK-trnK(UUU)_p5 matK-trnK(UUU) TCTTGCAGGAGAAGCGGATA ACGGTAGAGTACTCGGCTTT 1433–1478 1.000 74.9
psbD-trnT(GGU)_p1 psbD-trnT(GGU) AGGAAAGAGCAATATGCCGG GTGGTAGAGTAACGCCATGG 1113 1.000 79.3
psbD-trnT(GGU)_p2 psbD-trnT(GGU) GGAAAGAGCAATATGCCGGA GTGGTAGAGTAACGCCATGG 1112 1.000 79.3
psbD-trnT(GGU)_p3 psbD-trnT(GGU) AGGAAAGAGCAATATGCCGG TCAGTGGTAGAGTAACGCCA 1116 1.000 79.2
psbD-trnT(GGU)_p4 psbD-trnT(GGU) GGAAAGAGCAATATGCCGGA TCAGTGGTAGAGTAACGCCA 1115 1.000 79.1
psbD-trnT(GGU)_p5 psbD-trnT(GGU) GGACCAGCCTACAAAAACGA GTGGTAGAGTAACGCCATGG 1095 1.000 78.7
rpoC2_p1 rpoC2 GAACTCTTGGCACGTTGTTG TTTCAATTGAAGTGCTTTAAGCA 299 1.000 40.3
rpoC2_p2 rpoC2 AACATCAGGGAACTCTTGGC TTTCAATTGAAGTGCTTTAAGCA 308 1.000 40.3
rpoC2_p3 rpoC2 AACTCTTGGCACGTTGTTGA TTTCAATTGAAGTGCTTTAAGCA 298 1.000 40.3
rpoC2_p4 rpoC2 ACTCTTGGCACGTTGTTGAA TTTCAATTGAAGTGCTTTAAGCA 297 1.000 40.3
rpoC2_p5 rpoC2 CTTGGCACGTTGTTGAATCG TTTCAATTGAAGTGCTTTAAGCA 294 1.000 40.3
rps4_p1 rps4 TACTTCAGCGAAAGGAGTGC TGCTTTGTGGATACTGTAGCT 743 1.000 63.6
rps4_p2 rps4 TCAGCGAAAGGAGTGCAAAT TGCTTTGTGGATACTGTAGCT 739 1.000 63.4
rps4_p3 rps4 TACTTCAGCGAAAGGAGTGC TGTGGATACTGTAGCTCAGAGT 738 1.000 63.2
rps4_p4 rps4 TCAGCGAAAGGAGTGCAAAT TGTGGATACTGTAGCTCAGAGT 734 1.000 63.0
rps4_p5 rps4 TACTTCAGCGAAAGGAGTGC GCTTTGTGGATACTGTAGCTCA 742 1.000 62.4

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (2)

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

Species Accession Length (bp) Link
Pogonia japonica NC_046806.1 158200 View on NCBI ↗
Pogonia minor NC_046807.1 158170 View on NCBI ↗