Markers + reference

Phalaenopsis

14 species · Orchidaceae · Asparagales

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Species 14
Genome length 145–149 kb
Candidate markers 288
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 288 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
PhapfoPp003 LSC 2968 0.0233 0.99 62.2 yes View details
rps16-PhapfoPt001 LSC 865 0.0359 0.99 74.7 yes View details
PhapfoPt002-PhapfoPt003 LSC 1330 0.0833 0.88 78.9 yes View details
rpoB-PhapfoPt005 LSC 1533 0.0335 0.99 71.3 yes View details
PhapfoPt008-PhapfoPt009 LSC 819 0.0438 0.97 78.9 yes View details
ndhK LSC 1511 0.0606 0.61 68.8 yes View details
clpP-psbB LSC 622 0.0408 0.98 74.3 yes View details
PhapfoPp092-PhapfoPp093 SSC 327 0.0485 0.91 71.3 yes View details
psaC-ndhE SSC 723 0.0498 0.56 67.9 yes View details
PhapfoPt014-PhapfoPt015 LSC 632 0.0381 0.94 75.7 yes View details
matK-rps16 LSC 1628 0.0336 0.98 74.1 yes View details
ccsA-ndhD SSC 343 0.0428 0.95 70.7 yes View details
ndhD SSC 1089 0.0304 1.00 70.6 yes View details
PhapfoPt003-PhapfoPt004 LSC 142 0.0625 0.90 70.3 yes View details
PhapfoPt004-atpA LSC 171 0.0553 0.89 70.0 yes View details
rps2-rpoC2 LSC 206 0.0389 1.00 68.6 yes View details
psbI-PhapfoPt002 LSC 191 0.0503 0.88 68.1 yes View details
rps19-psbA LSC 405 0.0396 0.86 67.6 no View details
rpoA-rps11 LSC 83 0.0386 1.00 67.0 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
PhapfoPp003_p1 PhapfoPp003 CAGAACGGCGTATGTGTGTA TCTTAGTGCCTGATGTGGGA 693–718 0.429 65.8
PhapfoPp003_p2 PhapfoPp003 CAGAACGGCGTATGTGTGTA AGTGCCTGATGTGGGAAAAG 689–714 0.429 65.5
PhapfoPp003_p3 PhapfoPp003 CAGAACGGCGTATGTGTGTA GCAACGAGCTTCCCTTCTTA 759–784 0.429 65.2
PhapfoPp003_p4 PhapfoPp003 CAGAACGGCGTATGTGTGTA CCTGATGTGGGAAAAGGGTC 685–710 0.429 64.9
PhapfoPp003_p5 PhapfoPp003 CAGAACGGCGTATGTGTGTA ATAAGACCGCGACTGATCCT 958–1020 0.429 63.2
matK-rps16_p1 matK-rps16 TCTTGTGCAGCGAAAATCCA TCGATCCCGAAGAGAAGGAA 2094–2185 1.000 86.8
matK-rps16_p2 matK-rps16 TCTTGTGCAGCGAAAATCCA GCTCAACCCACAGAAACTGT 1985–2076 1.000 85.6
matK-rps16_p3 matK-rps16 TCTTGTGCAGCGAAAATCCA TGCTCAACCCACAGAAACTG 1986–2077 1.000 85.6
matK-rps16_p4 matK-rps16 CTTGTGCAGCGAAAATCCAT TCGATCCCGAAGAGAAGGAA 2093–2184 1.000 84.8
matK-rps16_p5 matK-rps16 TCTTGTGCAGCGAAAATCCA GTGCTCAACCCACAGAAACT 2000–2076 0.643 68.1
rps16-PhapfoPt001_p1 rps16-PhapfoPt001 TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 849–994 1.000 89.6
rps16-PhapfoPt001_p2 rps16-PhapfoPt001 TCATGTCCTTCAAGTCGCAC CTCGGAGGTTCGAATCCTTC 853–998 1.000 88.5
rps16-PhapfoPt001_p3 rps16-PhapfoPt001 AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 838–983 0.929 87.1
rps16-PhapfoPt001_p4 rps16-PhapfoPt001 AAGTCGCACGTTGCTTTCTA CTCGGAGGTTCGAATCCTTC 842–987 0.929 86.0
rps16-PhapfoPt001_p5 rps16-PhapfoPt001 AAGTCGCACGTTGCTTTCTA TACTCGGAGGTTCGAATCCT 844–989 0.929 84.2
psbI-PhapfoPt002_p1 psbI-PhapfoPt002 GTAATCCTGGGCGTGAAGAA GGGTTCGAATCCCTCTCTCT 194–237 0.929 84.2
psbI-PhapfoPt002_p2 psbI-PhapfoPt002 GTAATCCTGGGCGTGAAGAA TTCGAATCCCTCTCTCTCCG 191–234 0.929 83.4
psbI-PhapfoPt002_p3 psbI-PhapfoPt002 GTAATCCTGGGCGTGAAGAAT GGGTTCGAATCCCTCTCTCT 194–237 0.929 78.8
psbI-PhapfoPt002_p4 psbI-PhapfoPt002 GTAATCCTGGGCGTGAAGAAT TTCGAATCCCTCTCTCTCCG 191–234 0.929 77.9
psbI-PhapfoPt002_p5 psbI-PhapfoPt002 CGTAATCCTGGGCGTGAAG GGGTTCGAATCCCTCTCTCT 195–238 0.929 76.8
PhapfoPt002-PhapfoPt003_p1 PhapfoPt002-PhapfoPt003 CAATCCGACGCTTTAGTCCA ACGAATCACACTTTTACCACT 871–1419 1.000 63.7
PhapfoPt002-PhapfoPt003_p2 PhapfoPt002-PhapfoPt003 AATCCGACGCTTTAGTCCAC ACGAATCACACTTTTACCACT 870–1418 1.000 63.7
PhapfoPt002-PhapfoPt003_p3 PhapfoPt002-PhapfoPt003 CAATCCGACGCTTTAGTCCA AGAACGAATCACACTTTTACCAC 874–1422 1.000 62.6
PhapfoPt002-PhapfoPt003_p4 PhapfoPt002-PhapfoPt003 CAATCCGACGCTTTAGTCCA GAACGAATCACACTTTTACCACT 873–1421 1.000 62.6
PhapfoPt002-PhapfoPt003_p5 PhapfoPt002-PhapfoPt003 AATCCGACGCTTTAGTCCAC GAACGAATCACACTTTTACCACT 872–1420 1.000 62.6
PhapfoPt003-PhapfoPt004_p1 PhapfoPt003-PhapfoPt004 AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 201–223 1.000 75.3
PhapfoPt003-PhapfoPt004_p2 PhapfoPt003-PhapfoPt004 CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 204–226 1.000 75.1
PhapfoPt003-PhapfoPt004_p3 PhapfoPt003-PhapfoPt004 AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 207–229 1.000 74.7
PhapfoPt003-PhapfoPt004_p4 PhapfoPt003-PhapfoPt004 CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 210–232 1.000 74.5
PhapfoPt003-PhapfoPt004_p5 PhapfoPt003-PhapfoPt004 CCAACGTCGACTATAACCCC AGAAGACCTCTGTCCTATCCA 222–244 1.000 73.9

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (14)

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

Species Accession Length (bp) Link
Phalaenopsis aphrodite subsp. formosana NC_007499.1 148964 View on NCBI ↗
Phalaenopsis braceana NC_072257.1 145874 View on NCBI ↗
Phalaenopsis deliciosa NC_067938.1 148090 View on NCBI ↗
Phalaenopsis equestris NC_017609.1 148959 View on NCBI ↗
Phalaenopsis hybrid cultivar NC_025593.1 148918 View on NCBI ↗
Phalaenopsis hygrochila MN124430.1 147298 View on NCBI ↗
Phalaenopsis japonica NC_046808.1 146942 View on NCBI ↗
Phalaenopsis lobbii NC_059699.1 144607 View on NCBI ↗
Phalaenopsis malipoensis NC_060875.1 144528 View on NCBI ↗
Phalaenopsis parishii MZ681480.1 147508 View on NCBI ↗
Phalaenopsis stobartiana NC_059917.1 145900 View on NCBI ↗
Phalaenopsis subparishii NC_085592.1 147584 View on NCBI ↗
Phalaenopsis wilsonii NC_057488.1 145373 View on NCBI ↗
Phalaenopsis yingjiangensis NC_067617.1 147316 View on NCBI ↗