Markers + reference

Pomatocalpa

2 species · Orchidaceae · Asparagales

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Species 2
Genome length 147–148 kb
Candidate markers 252
Primer pairs 70

Genome-wide nucleotide diversity

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

Candidate markers

6 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 252 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnN-GUU-ycf1 SSC 5917 0.4281 0.93 76.8 yes View details
ycf1-rps15 SSC 450 0.4810 0.99 76.3 yes View details
rps15 SSC 363 0.4818 0.83 75.4 yes View details
ndhG-psaC SSC 937 0.4702 0.84 80.6 yes View details
psaC-ndhD SSC 896 0.4565 0.94 83.2 yes View details
ndhD-ccsA SSC 1145 0.4598 0.85 80.7 yes View details
trnL-UAG-trnN-GUU SSC 1568 0.3228 0.93 82.8 yes View details
ycf1 SSC 69 0.5846 0.94 77.1 yes View details
ndhD SSC 231 0.4332 0.94 77.1 yes View details
ndhG SSC 267 0.4980 0.96 77.0 yes View details
ccsA SSC 276 0.4339 0.88 75.4 yes View details
ccsA-trnL-UAG SSC 150 0.4041 0.97 75.1 yes View details
rps15-ndhG SSC 106 0.4239 0.87 75.0 yes View details
psbK-psbI LSC 485 0.0252 0.98 72.6 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
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG GCCCCGGATCGTTAGATAAG 594–603 1.000 79.4
psbK-psbI_p2 psbK-psbI GTTTGGCAAGCTGCTGTAAG TTCTTCACGCCCAGGATTAC 614–623 1.000 79.1
psbK-psbI_p3 psbK-psbI TGGCAAGCTGCTGTAAGTTT GCCCCGGATCGTTAGATAAG 591–600 1.000 77.4
psbK-psbI_p4 psbK-psbI TTGGCAAGCTGCTGTAAGTT GCCCCGGATCGTTAGATAAG 592–601 1.000 77.4
psbK-psbI_p5 psbK-psbI TTTGGCAAGCTGCTGTAAGT GCCCCGGATCGTTAGATAAG 593–602 1.000 77.4
trnN-GUU-ycf1_p1 trnN-GUU-ycf1 GCCGTCAGACAAGGAAGAAT AGATTGCGACGAAAATCCGA 1369 0.500 59.2
trnN-GUU-ycf1_p2 trnN-GUU-ycf1 ACGGAAGAAGAGGGCAAAAG AGATTGCGACGAAAATCCGA 1303 0.500 59.1
trnN-GUU-ycf1_p3 trnN-GUU-ycf1 GAAACGGAAGAAGAGGGCAA AGATTGCGACGAAAATCCGA 1306 0.500 59.1
trnN-GUU-ycf1_p4 trnN-GUU-ycf1 GCCGTCAGACAAGGAAGAAT TCCTCGATATGGTCCGTTGA 835 0.500 58.7
trnN-GUU-ycf1_p5 trnN-GUU-ycf1 ACGGAAGAAGAGGGCAAAAG TCCTCGATATGGTCCGTTGA 769 0.500 58.7
ycf1_p1 ycf1 TTGCACGACACTAGCAACAT ATTCGTAGACCCCTTTGTGA 986 0.500 44.4
ycf1_p2 ycf1 TTGCACGACACTAGCAACAT TTCGTAGACCCCTTTGTGAT 985 0.500 44.4
ycf1_p3 ycf1 TTGCACGACACTAGCAACAT TCCACTCTTCCTAATGCACA 542 0.500 44.3
ycf1_p4 ycf1 AGGGACCTAGTTCTTGCAGA ATTCGTAGACCCCTTTGTGA 1180 0.500 42.7
ycf1_p5 ycf1 AGGGACCTAGTTCTTGCAGA TTCGTAGACCCCTTTGTGAT 1179 0.500 42.7
ycf1-rps15_p1 ycf1-rps15 TTGCACGACACTAGCAACAT AAATAAGGAACTGCGTGGCA 1484 0.500 58.3
ycf1-rps15_p2 ycf1-rps15 TTGCACGACACTAGCAACAT TGTCCAATGTACCTTGTGGC 1250 0.500 58.3
ycf1-rps15_p3 ycf1-rps15 TTGCACGACACTAGCAACAT CCAATGTACCTTGTGGCTCA 1247 0.500 57.4
ycf1-rps15_p4 ycf1-rps15 TTGCACGACACTAGCAACAT GTCCAATGTACCTTGTGGCT 1249 0.500 57.4
ycf1-rps15_p5 ycf1-rps15 TTGCACGACACTAGCAACAT CCGTTCATAAACAGCACAGC 1534 0.500 57.0
rps15_p1 rps15 CCCCAGACGTCGTAGAGAAT AAATAAGGAACTGCGTGGCA 1401 0.500 54.4
rps15_p2 rps15 CCCCAGACGTCGTAGAGAAT TGTCCAATGTACCTTGTGGC 1167 0.500 54.4
rps15_p3 rps15 ATTCTATCCCCCAGACGTCG AAATAAGGAACTGCGTGGCA 1409 0.500 53.9
rps15_p4 rps15 ATTCTATCCCCCAGACGTCG TGTCCAATGTACCTTGTGGC 1175 0.500 53.9
rps15_p5 rps15 CCCCAGACGTCGTAGAGAAT CCAATGTACCTTGTGGCTCA 1164 0.500 53.5
rps15-ndhG_p1 rps15-ndhG ATCACAAAGGGGTCTACGAA AAATAAGGAACTGCGTGGCA 519 0.500 44.6
rps15-ndhG_p2 rps15-ndhG TCACAAAGGGGTCTACGAAT AAATAAGGAACTGCGTGGCA 518 0.500 44.6
rps15-ndhG_p3 rps15-ndhG TGTGCATTAGGAAGAGTGGA AAATAAGGAACTGCGTGGCA 962 0.500 44.5
rps15-ndhG_p4 rps15-ndhG ATCACAAAGGGGTCTACGAA CCGTTCATAAACAGCACAGC 569 0.500 43.4
rps15-ndhG_p5 rps15-ndhG TCACAAAGGGGTCTACGAAT CCGTTCATAAACAGCACAGC 568 0.500 43.4

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
Pomatocalpa diffusum NC_086716.1 148198 View on NCBI ↗
Pomatocalpa spicatum MN124411.1 147413 View on NCBI ↗