Markers + reference

Schoenorchis

2 species · Orchidaceae · Asparagales

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Species 2
Genome length 143–147 kb
Candidate markers 261
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 261 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 906 0.0563 0.96 77.5 yes View details
trnS-GCU-trnG-GCC LSC 1151 0.0513 0.97 79.3 yes View details
ndhC-trnV-UAC LSC 652 0.0787 0.88 83.2 yes View details
atpB-rbcL LSC 911 0.0556 0.97 77.6 yes View details
rpl16 LSC 1769 0.0255 0.93 64.7 yes View details
trnN-GUU-rpl32 SSC 679 0.0421 0.95 73.0 yes View details
ndhD SSC 916 0.0304 0.65 58.0 yes View details
psaC-ndhE SSC 608 0.0445 0.92 74.2 yes View details
ycf1 SSC 5328 0.0289 0.99 56.9 yes View details
psbC-trnS-UGA LSC 156 0.0839 0.92 82.0 yes View details
trnG-GCC-trnR-UCU LSC 124 0.0887 1.00 81.0 yes View details
psbT-psbN LSC 62 0.0484 1.00 78.1 yes View details
trnL-CAA-rps7 IRb 728 0.0289 1.00 75.6 yes View details
rps7-trnL-CAA IRa 728 0.0289 1.00 75.6 yes View details
psbB-psbT LSC 391 0.0421 0.91 75.4 yes View details
rpoC1-rpoB LSC 26 0.1154 1.00 74.8 yes View details
petD-rpoA LSC 180 0.0615 0.99 74.0 yes View details
psbL-psbF LSC 22 0.0455 1.00 73.8 yes View details
ndhI-rps15 SSC 103 0.0737 0.92 72.9 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 976–979 1.000 85.3
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TAGCGGCACCATGTCCTATA 1110–1113 1.000 85.2
rps16-trnQ-UUG_p3 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC TAGCGGCACCATGTCCTATA 1121–1124 1.000 84.6
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CTTACAGCAGCTTGCCAAAC 1569–1602 1.000 83.4
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC CTTACAGCAGCTTGCCAAAC 1580–1613 1.000 82.9
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA ACGAATCACACTTTTACCACT 1220–1285 1.000 57.8
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC ACGAATCACACTTTTACCACT 1219–1284 1.000 57.8
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA AGAACGAATCACACTTTTACCAC 1223–1288 1.000 56.7
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA GAACGAATCACACTTTTACCACT 1222–1287 1.000 56.7
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC GAACGAATCACACTTTTACCACT 1221–1286 1.000 56.7
trnG-GCC-trnR-UCU_p1 trnG-GCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTTTGTCCTATCCA 204–205 1.000 57.6
trnG-GCC-trnR-UCU_p2 trnG-GCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTTTGTCCTATCCA 207–208 1.000 57.3
trnG-GCC-trnR-UCU_p3 trnG-GCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAATTGCGTCCAATAGGA 246–247 1.000 57.2
trnG-GCC-trnR-UCU_p4 trnG-GCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTTTGTCCT 210–211 1.000 57.2
trnG-GCC-trnR-UCU_p5 trnG-GCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAATTGCGTCCAATAGGA 249–250 1.000 56.9
rpoC1-rpoB_p1 rpoC1-rpoB GGGAAACTGGTCCAATTCGA CCAGATGGATAGGAAGGAAGC 100 1.000 69.5
rpoC1-rpoB_p2 rpoC1-rpoB TTGTTGAGGGGAAACTGGTC CCAGATGGATAGGAAGGAAGC 108 1.000 68.0
rpoC1-rpoB_p3 rpoC1-rpoB TGAGGGGAAACTGGTCCAAT CCAGATGGATAGGAAGGAAGC 104 1.000 66.6
rpoC1-rpoB_p4 rpoC1-rpoB AGGGGAAACTGGTCCAATTC CCAGATGGATAGGAAGGAAGC 102 1.000 66.2
rpoC1-rpoB_p5 rpoC1-rpoB GAGGGGAAACTGGTCCAATT CCAGATGGATAGGAAGGAAGC 103 1.000 66.2
psbC-trnS-UGA_p1 psbC-trnS-UGA CCTGTTCTTTCCATGACCCC GAGAGATGGCTGAGTGGTTG 265–278 1.000 85.9
psbC-trnS-UGA_p2 psbC-trnS-UGA CCTGTTCTTTCCATGACCCC ATAGCCCCGGTCTTGAAAAC 245–258 1.000 85.5
psbC-trnS-UGA_p3 psbC-trnS-UGA TTCCATGACCCCTCTTAGCT GAGAGATGGCTGAGTGGTTG 257–270 1.000 85.3
psbC-trnS-UGA_p4 psbC-trnS-UGA AGCGGGGTTTGAAAAAGGAA GAGAGATGGCTGAGTGGTTG 302–315 1.000 84.6
psbC-trnS-UGA_p5 psbC-trnS-UGA TTGTGGGACATTTGTGGCAT GAGAGATGGCTGAGTGGTTG 345–358 1.000 83.2
ndhC-trnV-UAC_p1 ndhC-trnV-UAC AGGAATGCCCAGAAAATCTCA AGAAGGTCTACGGTTCGAGT 700–708 1.000 73.6
ndhC-trnV-UAC_p2 ndhC-trnV-UAC AGGAATGCCCAGAAAATCTCA AGCCCAATGCAACAAAATGC 782–790 1.000 70.8
ndhC-trnV-UAC_p3 ndhC-trnV-UAC AGGAATGCCCAGAAAATCTCA GAAGGTCTACGGTTCGAGTC 699–707 1.000 70.8
ndhC-trnV-UAC_p4 ndhC-trnV-UAC AGGAATGCCCAGAAAATCTCA GTTCGAGTCCGTATAGCCCT 688–696 1.000 69.8
ndhC-trnV-UAC_p5 ndhC-trnV-UAC AGGAATGCCCAGAAAATCTCAT AGAAGGTCTACGGTTCGAGT 700–708 1.000 69.4

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
Schoenorchis seidenfadenii MN124434.1 142859 View on NCBI ↗
Schoenorchis tixieri MN124407.1 146692 View on NCBI ↗