Markers + reference

Cheirostylis

5 species · Orchidaceae · Asparagales

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Species 5
Genome length 147–152 kb
Candidate markers 272
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 272 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK_UUU-rps16 LSC 504 0.0862 0.99 81.8 yes View details
rps16-trnQ_UUG LSC 365 0.0722 0.99 80.3 yes View details
psbK-psbI LSC 361 0.0717 0.94 79.6 yes View details
trnC_GCA-petN LSC 866 0.0610 0.46 71.0 yes View details
trnF_GAA-ndhJ LSC 577 0.0684 0.73 76.9 yes View details
rbcL-accD LSC 790 0.0604 0.98 82.8 yes View details
accD LSC 1533 0.0695 0.99 83.9 yes View details
clpP LSC 2198 0.0649 1.00 83.1 yes View details
clpP-psbB LSC 593 0.0649 1.00 83.2 yes View details
ycf1 IRb 1089 0.0164 1.00 60.5 no View details
ndhF-rpl32 SSC 521 0.0673 0.99 77.2 yes View details
ycf1 SSC 5622 0.0423 1.00 71.2 yes View details
petA-psbJ LSC 629 0.0489 1.00 86.2 yes View details
trnL_UAA-trnF_GAA LSC 435 0.0701 0.99 85.9 yes View details
atpH-atpI LSC 499 0.0406 0.99 85.4 yes View details
ndhC-trnV_UAC LSC 637 0.0509 0.99 85.2 yes View details
trnT_GGU-psbD LSC 867 0.0524 1.00 84.4 yes View details
rpl32-trnL_UAG SSC 650 0.0557 1.00 84.3 yes View details
trnS_GCU-trnG_GCC LSC 509 0.0644 1.00 84.2 yes View details
ycf4-cemA LSC 706 0.0482 0.98 83.9 yes View details
trnT_UGU-trnL_UAA LSC 635 0.0489 0.99 83.1 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
trnK_UUU-rps16_p1 trnK_UUU-rps16 AAAGCCGAGTACTCTACCGT TCGATCCCGAAGAGAAGGAA 647–829 1.000 89.5
trnK_UUU-rps16_p2 trnK_UUU-rps16 AAGCCGAGTACTCTACCGTT TCGATCCCGAAGAGAAGGAA 646–828 1.000 89.5
trnK_UUU-rps16_p3 trnK_UUU-rps16 CCTTTCAGGATCAGTCGTGG TCGATCCCGAAGAGAAGGAA 738–809 0.800 80.9
trnK_UUU-rps16_p4 trnK_UUU-rps16 TCAGGATCAGTCGTGGTCTT TCGATCCCGAAGAGAAGGAA 734–805 0.800 80.5
trnK_UUU-rps16_p5 trnK_UUU-rps16 TTCAGGATCAGTCGTGGTCT TCGATCCCGAAGAGAAGGAA 735–806 0.800 80.5
rps16-trnQ_UUG_p1 rps16-trnQ_UUG AAGTCGCACGTTGCTTTCTA CTTACAGCAGCTTGCCAAAC 874–1201 1.000 90.4
rps16-trnQ_UUG_p2 rps16-trnQ_UUG AAGTTTTGCTCGAGCTCCAT CTTACAGCAGCTTGCCAAAC 1040–1367 1.000 90.0
rps16-trnQ_UUG_p3 rps16-trnQ_UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 428–605 1.000 89.2
rps16-trnQ_UUG_p4 rps16-trnQ_UUG AAGTCGCACGTTGCTTTCTA TTCGCCCTAGTGACAACATG 569–580 0.800 79.1
rps16-trnQ_UUG_p5 rps16-trnQ_UUG TCATGTCCTTCAAGTCGCAC CTTACAGCAGCTTGCCAAAC 885–1028 0.800 79.0
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG AGACGAAGAGTTTAAGAGTAAGCA 374–500 1.000 56.9
psbK-psbI_p2 psbK-psbI TGGCAAGCTGCTGTAAGTTT AGACGAAGAGTTTAAGAGTAAGCA 371–497 1.000 54.9
psbK-psbI_p3 psbK-psbI TTGGCAAGCTGCTGTAAGTT AGACGAAGAGTTTAAGAGTAAGCA 372–498 1.000 54.9
psbK-psbI_p4 psbK-psbI TTTGGCAAGCTGCTGTAAGT AGACGAAGAGTTTAAGAGTAAGCA 373–499 1.000 54.9
psbK-psbI_p5 psbK-psbI GTTTGGCAAGCTGCTGTAAG TGTGTAGACGAAGAGTTTAAGAGT 379–505 1.000 54.5
trnS_GCU-trnG_GCC_p1 trnS_GCU-trnG_GCC CAATCCGACGCTTTAGTCCA TACCACTAAACTATACCCGC 542–573 1.000 59.9
trnS_GCU-trnG_GCC_p2 trnS_GCU-trnG_GCC AATCCGACGCTTTAGTCCAC TACCACTAAACTATACCCGC 541–572 1.000 59.9
trnS_GCU-trnG_GCC_p3 trnS_GCU-trnG_GCC CAATCCGACGCTTTAGTCCA TTACCACTAAACTATACCCGC 543–574 1.000 58.8
trnS_GCU-trnG_GCC_p4 trnS_GCU-trnG_GCC AATCCGACGCTTTAGTCCAC TTACCACTAAACTATACCCGC 542–573 1.000 58.8
trnS_GCU-trnG_GCC_p5 trnS_GCU-trnG_GCC CAATCCGACGCTTTAGTCCA TTTACCACTAAACTATACCCGC 544–575 1.000 57.1
atpH-atpI_p1 atpH-atpI AGCCAATCCAGCAGCAATAA AACTTTGGCTGCGGCTTATA 589–615 1.000 87.7
atpH-atpI_p2 atpH-atpI GCCAATCCAGCAGCAATAAC AACTTTGGCTGCGGCTTATA 588–614 1.000 87.2
atpH-atpI_p3 atpH-atpI TCCAGCAGCAATAACGGAAG AACTTTGGCTGCGGCTTATA 583–609 1.000 86.9
atpH-atpI_p4 atpH-atpI AGCCAATCCAGCAGCAATAA GGCTGCGGCTTATATAGGTG 583–609 1.000 86.6
atpH-atpI_p5 atpH-atpI GCCAATCCAGCAGCAATAAC GGCTGCGGCTTATATAGGTG 582–608 1.000 86.1
trnC_GCA-petN_p1 trnC_GCA-petN AAGCACGATGATCCTAGGGA CGTTTATTGCTACTGCGCTG 1589–2156 1.000 90.7
trnC_GCA-petN_p2 trnC_GCA-petN AAGCACGATGATCCTAGGGA AGCCCAAGCGAGACTTACTA 901–1452 1.000 90.1
trnC_GCA-petN_p3 trnC_GCA-petN AAGCACGATGATCCTAGGGA CTAAAGCCCACTTCTTCCCC 964–1515 0.800 78.8
trnC_GCA-petN_p4 trnC_GCA-petN GGGTGTCGCCTAATCAACAA CGTTTATTGCTACTGCGCTG 1064–1624 0.800 77.7
trnC_GCA-petN_p5 trnC_GCA-petN GGGTGTCGCCTAATCAACAA CTAAAGCCCACTTCTTCCCC 439–983 0.800 77.0

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (5)

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

Species Accession Length (bp) Link
Cheirostylis chinensis MN641483.1 147218 View on NCBI ↗
Cheirostylis moniliformis MW589503.1 148762 View on NCBI ↗
Cheirostylis montana MW589504.1 147625 View on NCBI ↗
Cheirostylis sherriffii PX438587.1 152283 View on NCBI ↗
Cheirostylis thailandica MW589505.1 151115 View on NCBI ↗