Markers + reference

Apostasia

2 species · Orchidaceae · Asparagales

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Species 2
Genome length 153–159 kb
Candidate markers 252
Primer pairs 90

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 252 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
matK-rps16 LSC 2249 0.0371 0.85 65.0 yes View details
rps16 LSC 1289 0.0305 0.97 65.1 yes View details
clpP LSC 2663 0.0234 0.98 57.5 yes View details
clpP-psbB LSC 729 0.0516 0.98 74.8 yes View details
psbB-psbT LSC 1285 0.0656 0.84 84.9 yes View details
petD LSC 1548 0.0233 0.91 66.4 yes View details
ycf1 IRb 1142 0.0414 0.99 68.5 yes View details
ndhI SSC 540 0.4000 1.00 77.5 yes View details
ycf1 SSC 5706 0.0169 0.99 48.7 no View details
psbT-psbN LSC 66 0.1061 1.00 84.0 yes View details
rps3-rpl22 LSC 113 0.2195 0.73 79.1 yes View details
rps4-trnT-UGU LSC 384 0.0507 0.92 78.8 yes View details
psbL-psbF LSC 22 0.0455 1.00 78.6 yes View details
atpI-atpH LSC 742 0.0279 0.97 77.9 yes View details
atpA-trnR-UCU LSC 46 0.1522 1.00 75.9 yes View details
rpoC1-rpoC2 LSC 241 0.0948 0.88 74.1 yes View details
rps16-trnQ-UUG LSC 626 0.0364 0.96 72.9 yes View details
psbK-psbI LSC 173 0.0299 0.97 72.9 yes View details
trnG-UCC-psbZ LSC 302 0.0321 0.93 72.8 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
matK-rps16_p1 matK-rps16 TCGCGACGAGAATGGAATTT TCATTTTTGCTCGAGCCGTA 2695–2870 1.000 85.7
matK-rps16_p2 matK-rps16 TCGCGACGAGAATGGAATTT TTTTTGCTCGAGCCGTATGA 2692–2867 1.000 85.7
matK-rps16_p3 matK-rps16 TCGCGACGAGAATGGAATTT TCGATCCCGAAGAGAAGGAA 2587–2763 1.000 85.4
matK-rps16_p4 matK-rps16 TCGCGACGAGAATGGAATTT GGTGCTCAACCTACAGGAAC 2481–2657 1.000 85.1
matK-rps16_p5 matK-rps16 ACTAATCGCGACGAGAATGG TTTTTGCTCGAGCCGTATGA 2697–2872 1.000 84.8
rps16_p1 rps16 TGGAATTGCGCTGTACAACT CAAGTGGTAAGGCAATGGGT 2666–2808 1.000 84.0
rps16_p2 rps16 GGAATTGCGCTGTACAACTG CAAGTGGTAAGGCAATGGGT 2665–2807 1.000 82.8
rps16_p3 rps16 GAATTGCGCTGTACAACTGC CAAGTGGTAAGGCAATGGGT 2664–2806 1.000 81.7
rps16_p4 rps16 TGGAATTGCGCTGTACAACT GGGGCCCCATTTTTACTCTT 2211 0.500 57.1
rps16_p5 rps16 GGAATTGCGCTGTACAACTG GGGGCCCCATTTTTACTCTT 2210 0.500 56.0
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CAAGTGGTAAGGCAATGGGT 752–774 1.000 84.2
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TCGGAGGTTCGAATCCTTTC 718–740 1.000 79.8
rps16-trnQ-UUG_p3 rps16-trnQ-UUG TATCCTTCAAGTCGCACGTT CAAGTGGTAAGGCAATGGGT 760–782 1.000 79.4
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA AAGTGGTAAGGCAATGGGTT 751–773 1.000 79.3
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA AGTGGTAAGGCAATGGGTTT 750–772 1.000 79.3
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG TTTTATTCCTCACGCCCAGG 316–637 1.000 80.4
psbK-psbI_p2 psbK-psbI ATGCCCCTTTCAATCCCATC TTTTATTCCTCACGCCCAGG 384–705 1.000 79.9
psbK-psbI_p3 psbK-psbI TTCACCAAATTACCCGAGGC TTTTATTCCTCACGCCCAGG 406–727 1.000 79.2
psbK-psbI_p4 psbK-psbI CCCATCGTAGACGTTATGCC TTTTATTCCTCACGCCCAGG 370–691 1.000 78.9
psbK-psbI_p5 psbK-psbI CACCAAATTACCCGAGGCAT TTTTATTCCTCACGCCCAGG 404–725 1.000 78.7
trnG-UCC-psbZ_p1 trnG-UCC-psbZ AATCGAACCCGCATCTTCTC CTTCCGATGGTTGGTCAAGT 447–464 1.000 83.5
trnG-UCC-psbZ_p2 trnG-UCC-psbZ GAATCGAACCCGCATCTTCT CTTCCGATGGTTGGTCAAGT 448–465 1.000 83.5
trnG-UCC-psbZ_p3 trnG-UCC-psbZ ACATTACTTCACCATGGGGC CTTCCGATGGTTGGTCAAGT 477–501 1.000 82.8
trnG-UCC-psbZ_p4 trnG-UCC-psbZ AATCGAACCCGCATCTTCTC TTGCTTCTTCCGATGGTTGG 453–470 1.000 81.2
trnG-UCC-psbZ_p5 trnG-UCC-psbZ GAATCGAACCCGCATCTTCT TTGCTTCTTCCGATGGTTGG 454–471 1.000 81.2
rpoC1-rpoC2_p1 rpoC1-rpoC2 TGATGGGGATCAAATGGCTG CCGCGTGTACATTCCCATAA 1084–1086 1.000 83.4
rpoC1-rpoC2_p2 rpoC1-rpoC2 GATGGGGATCAAATGGCTGT CCGCGTGTACATTCCCATAA 1083–1085 1.000 83.3
rpoC1-rpoC2_p3 rpoC1-rpoC2 TGATGGGGATCAAATGGCTG TCTAGCTCCCGAAAAGGACA 1215–1217 1.000 82.8
rpoC1-rpoC2_p4 rpoC1-rpoC2 TGATGGGGATCAAATGGCTG GTCTACGGGTGAGGTATCCA 1420–1422 1.000 82.3
rpoC1-rpoC2_p5 rpoC1-rpoC2 GATGGGGATCAAATGGCTGT GTCTACGGGTGAGGTATCCA 1419–1421 1.000 82.3

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
Apostasia fujianica NC_088545.1 153179 View on NCBI ↗
Apostasia odorata NC_030722.1 159285 View on NCBI ↗