Markers + reference

Vanda

9 species · Orchidaceae · Asparagales

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Species 9
Genome length 146–149 kb
Candidate markers 264
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 264 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 871 0.0203 0.98 64.6 yes View details
trnS-GCU-trnG-GCC LSC 1209 0.0248 0.96 67.7 yes View details
rpoB-trnC-GCA LSC 1620 0.0129 0.94 57.8 yes View details
petN-psbM LSC 811 0.0197 0.98 59.6 yes View details
ndhC-trnV-UAC LSC 709 0.0335 0.94 65.8 yes View details
clpP-psbB LSC 740 0.0670 1.00 89.3 yes View details
rpl16 LSC 1620 0.0191 0.99 58.0 yes View details
trnN-GUU-rpl32 IRb 797 0.0506 0.99 84.5 yes View details
psaC-ndhE SSC 615 0.0259 0.99 63.7 yes View details
psbB-psbT LSC 459 0.0256 0.92 66.9 yes View details
trnT-UGU-trnL-UAA LSC 510 0.0199 0.99 59.9 yes View details
atpB-rbcL LSC 1012 0.0130 0.93 59.7 yes View details
psbC-trnS-UGA LSC 145 0.0195 1.00 59.4 yes View details
trnT-GGU-psbD LSC 1012 0.0088 0.95 58.9 yes View details
trnE-UUC-trnT-GGU LSC 750 0.0131 0.99 58.7 yes View details
ndhI-rps15 SSC 131 0.0373 0.98 58.2 yes View details
matK-trnK-UUU LSC 1141 0.0158 0.99 57.3 yes View details
psbM-trnD-GUC LSC 1153 0.0149 0.99 57.3 yes View details
psbL-psbF LSC 22 0.0202 1.00 56.0 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
matK-trnK-UUU_p1 matK-trnK-UUU TCCTGAAGGAGTAGCGGATA GGTAGAGTACTCGGCTTTTA 1207–1280 1.000 47.3
matK-trnK-UUU_p2 matK-trnK-UUU TCCTGAAGGAGTAGCGGATA GGTAGAGTACTCGGCTTTTAA 1207–1280 1.000 47.3
matK-trnK-UUU_p3 matK-trnK-UUU TCCTGAAGGAGTAGCGGATAT GGTAGAGTACTCGGCTTTTA 1207–1280 1.000 47.3
matK-trnK-UUU_p4 matK-trnK-UUU TCCTGAAGGAGTAGCGGATAT GGTAGAGTACTCGGCTTTTAA 1207–1280 1.000 47.3
matK-trnK-UUU_p5 matK-trnK-UUU TCCTGAAGGAGTAGCGGAT GGTAGAGTACTCGGCTTTTA 1207–1280 1.000 47.3
rps16-trnQ-UUG_p1 rps16-trnQ-UUG ATCCACAGCCAATCATGTCC GAGGTTCGAATCCTTCCGTC 952–1039 1.000 86.4
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 929–1016 1.000 86.0
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CCACAGCCAATCATGTCCTT GAGGTTCGAATCCTTCCGTC 950–1037 1.000 85.7
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 940–1027 1.000 85.4
rps16-trnQ-UUG_p5 rps16-trnQ-UUG ATCCACAGCCAATCATGTCC CTCGGAGGTTCGAATCCTTC 956–1043 1.000 85.3
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA ACGAATCACACTTTTACCACT 1178–1278 1.000 61.6
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC ACGAATCACACTTTTACCACT 1177–1277 1.000 61.6
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA AGAACGAATCACACTTTTACCAC 1181–1281 1.000 60.5
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA GAACGAATCACACTTTTACCACT 1180–1280 1.000 60.5
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC GAACGAATCACACTTTTACCACT 1179–1279 1.000 60.5
rpoB-trnC-GCA_p1 rpoB-trnC-GCA GTGGACATTCCCTCATTTCCA CCGGGGATAAAGGATTTGCA 1468–1703 1.000 77.4
rpoB-trnC-GCA_p2 rpoB-trnC-GCA TGTGGACATTCCCTCATTTCC CCGGGGATAAAGGATTTGCA 1469–1704 1.000 77.4
rpoB-trnC-GCA_p3 rpoB-trnC-GCA GTGGACATTCCCTCATTTCCA ACCGGGGATAAAGGATTTGC 1469–1704 1.000 77.4
rpoB-trnC-GCA_p4 rpoB-trnC-GCA TGTGGACATTCCCTCATTTCC ACCGGGGATAAAGGATTTGC 1470–1705 1.000 77.4
rpoB-trnC-GCA_p5 rpoB-trnC-GCA GTGGACATTCCCTCATTTCCA TCGAACCGGGGATAAAGGAT 1473–1708 1.000 76.3
petN-psbM_p1 petN-psbM GGGGCATCATTCACATGGAT ACGTCAAAACAGTCAGCCAA 925–1011 1.000 86.0
petN-psbM_p2 petN-psbM GGGGCATCATTCACATGGAT ATTGCTACTGCGCTGTTCAT 977–1063 1.000 85.8
petN-psbM_p3 petN-psbM TCCTGTTTTGACTCTGCACC ACGTCAAAACAGTCAGCCAA 1010–1100 1.000 85.6
petN-psbM_p4 petN-psbM GGGGCATCATTCACATGGAT CGTTTATTGCTACTGCGCTG 982–1047 0.889 82.6
petN-psbM_p5 petN-psbM TCCTGTTTTGACTCTGCACC CGTTTATTGCTACTGCGCTG 1067–1136 0.889 82.3
psbM-trnD-GUC_p1 psbM-trnD-GUC CGCAGTAGCAATAAACGCAA CCATGCATATGGCTGGGATT 1254–1277 1.000 81.6
psbM-trnD-GUC_p2 psbM-trnD-GUC CGCAGTAGCAATAAACGCAA AGTTCAATCGGTCAGAGCAC 1232–1255 1.000 81.6
psbM-trnD-GUC_p3 psbM-trnD-GUC CGCAGTAGCAATAAACGCAA ATGCATATGGCTGGGATTGT 1252–1275 1.000 76.7
psbM-trnD-GUC_p4 psbM-trnD-GUC GCGCAGTAGCAATAAACGC CCATGCATATGGCTGGGATT 1255–1278 1.000 76.5
psbM-trnD-GUC_p5 psbM-trnD-GUC GCGCAGTAGCAATAAACGC AGTTCAATCGGTCAGAGCAC 1233–1256 1.000 76.5

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (9)

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

Species Accession Length (bp) Link
Vanda alpina PQ009216.1 149273 View on NCBI ↗
Vanda brunnea NC_041522.1 149216 View on NCBI ↗
Vanda coerulescens MN711650.1 149410 View on NCBI ↗
Vanda concolor NC_048458.1 149474 View on NCBI ↗
Vanda cristata PQ009219.1 146993 View on NCBI ↗
Vanda falcata NC_036372.1 146497 View on NCBI ↗
Vanda flabellata PP003956.1 148145 View on NCBI ↗
Vanda pumila PQ009220.1 149273 View on NCBI ↗
Vanda subconcolor NC_047413.1 149490 View on NCBI ↗