Markers + reference

Neuwiedia

2 species · Orchidaceae · Asparagales

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Species 2
Genome length 161–163 kb
Candidate markers 262
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 9 remaining regions by MarkerSeek score (out of 262 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
matK-rps16 LSC 2638 0.0899 0.89 92.2 yes View details
trnC-GCA-petN LSC 656 0.1046 0.93 93.9 yes View details
trnE-UUC-trnT-GGU LSC 543 0.0714 0.93 85.8 yes View details
trnT-GGU-psbD LSC 1090 0.0421 0.92 79.3 yes View details
trnT-UGU-trnL-UAA LSC 771 0.4695 0.85 95.8 yes View details
atpB-rbcL LSC 1125 0.0641 0.89 91.5 yes View details
clpP LSC 2790 0.0189 0.70 64.1 yes View details
rpl32-trnL-UAG SSC 797 0.1971 0.79 93.8 yes View details
ndhH-rps15 SSC 137 0.2137 0.85 89.6 yes View details
trnM-CAU-atpE LSC 188 0.0529 0.90 84.5 yes View details
petN-psbM LSC 1212 0.0375 0.97 83.4 yes View details
rps19-psbA IRa 549 0.0347 0.79 77.0 no View details
rpoB-trnC-GCA LSC 1187 0.0232 0.94 76.6 yes View details
ndhF-rpl32 SSC 684 0.0282 0.83 75.8 yes View details
rbcL-accD LSC 1142 0.0256 0.99 74.0 yes View details
petA-psbJ LSC 1389 0.0206 0.84 71.9 yes View details
psbH-petB LSC 723 0.0154 0.90 70.8 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
matK-rps16_p1 matK-rps16 TCCTGAAGGAGTAGCGGATA GGTGCTCAACCTACAGGAAC 2767–2796 1.000 80.2
matK-rps16_p2 matK-rps16 TCCTGAAGGAGTAGCGGATAT GGTGCTCAACCTACAGGAAC 2767–2796 1.000 76.4
matK-rps16_p3 matK-rps16 TCCTGAAGGAGTAGCGGATA GTGCTCAACCTACAGGAACT 2766–2795 1.000 75.0
matK-rps16_p4 matK-rps16 TCCTGAAGGAGTAGCGGAT GGTGCTCAACCTACAGGAAC 2767–2796 1.000 73.2
matK-rps16_p5 matK-rps16 CCTGAAGGAGTAGCGGATAT GGTGCTCAACCTACAGGAAC 2766–2795 1.000 71.8
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CGCCAAGCCCTGATTAATGA AAAGGATTTGCAGTCCCCTG 1326–1338 1.000 82.4
rpoB-trnC-GCA_p2 rpoB-trnC-GCA CGCCAAGCCCTGATTAATGA CGACACCCAGATTCGAACTG 1351–1363 1.000 77.7
rpoB-trnC-GCA_p3 rpoB-trnC-GCA ATGAAATTCTTCCGCCAAGC AAAGGATTTGCAGTCCCCTG 1338–1350 1.000 77.4
rpoB-trnC-GCA_p4 rpoB-trnC-GCA CGCCAAGCCCTGATTAATGA TTTGTTGATCAGGCGACACC 1364–1376 1.000 76.7
rpoB-trnC-GCA_p5 rpoB-trnC-GCA GTGGACATTCCCTCATTTCCA AAAGGATTTGCAGTCCCCTG 1262–1274 1.000 76.4
trnC-GCA-petN_p1 trnC-GCA-petN CCAGTTCGAATCTGGGTGTC AGCCCAAGCGAGACTTACTA 707–713 1.000 87.8
trnC-GCA-petN_p2 trnC-GCA-petN CAGTTCGAATCTGGGTGTCG AGCCCAAGCGAGACTTACTA 706–712 1.000 84.8
trnC-GCA-petN_p3 trnC-GCA-petN TAGGAAATTTGGCGGCATGG AGCCCAAGCGAGACTTACTA 764–770 1.000 82.3
trnC-GCA-petN_p4 trnC-GCA-petN CCAGTTCGAATCTGGGTGTC GCCCAAGCGAGACTTACTAT 706–712 1.000 81.9
trnC-GCA-petN_p5 trnC-GCA-petN TTAGGAAATTTGGCGGCATG AGCCCAAGCGAGACTTACTA 765–771 1.000 81.8
petN-psbM_p1 petN-psbM TAGTAAGTCTCGCTTGGGCT CTTGCGCTTATTGCTACTGC 1385–1782 1.000 82.3
petN-psbM_p2 petN-psbM TAGTAAGTCTCGCTTGGGCT ATTGCTACTGCGCTGTTCAT 1376–1773 1.000 81.0
petN-psbM_p3 petN-psbM TAGTAAGTCTCGCTTGGGCT TATTGCTACTGCGCTGTTCA 1377–1774 1.000 80.0
petN-psbM_p4 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCGCTGTTCATTT 1374–1771 1.000 79.2
petN-psbM_p5 petN-psbM TAGTAAGTCTCGCTTGGGCT TTGCTACTGCGCTGTTCATT 1375–1772 1.000 79.2
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU AGAGAGATGTCCTGGACCAC CCATGGCGTTACTCTACCAC 611–663 1.000 86.9
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU GAGAGATGTCCTGGACCACT CCATGGCGTTACTCTACCAC 610–662 1.000 86.9
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU AGAGAGATGTCCTGGACCAC TGGCGTTACTCTACCACTGA 608–660 1.000 86.7
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU GAGAGATGTCCTGGACCACT TGGCGTTACTCTACCACTGA 607–659 1.000 86.7
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA CCATGGCGTTACTCTACCAC 626–678 1.000 86.5
trnT-GGU-psbD_p1 trnT-GGU-psbD AATTGAAGAAAACGGGCCCT GGACCAGCCTACAAAAACGA 1221–1279 1.000 85.7
trnT-GGU-psbD_p2 trnT-GGU-psbD ATTGAAGAAAACGGGCCCTT GGACCAGCCTACAAAAACGA 1220–1278 1.000 85.7
trnT-GGU-psbD_p3 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG GGACCAGCCTACAAAAACGA 1192–1250 1.000 85.3
trnT-GGU-psbD_p4 trnT-GGU-psbD TCAGTGGTAGAGTAACGCCA GGACCAGCCTACAAAAACGA 1195–1253 1.000 85.2
trnT-GGU-psbD_p5 trnT-GGU-psbD AACGGGCCCTTTTAACTCAG GGACCAGCCTACAAAAACGA 1211–1269 1.000 85.0

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
Neuwiedia malipoensis NC_088553.1 163193 View on NCBI ↗
Neuwiedia zollingeri var. singapureana LC199503.1 161068 View on NCBI ↗