Markers + reference

Orchis

2 species · Orchidaceae · Asparagales

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Species 2
Genome length 152–152 kb
Candidate markers 269
Primer pairs 80

Genome-wide nucleotide diversity

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

Candidate markers

5 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 269 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps2 LSC 711 0.0014 1.00 59.6 yes View details
rpoC1 LSC 2791 0.0004 1.00 56.3 yes View details
rpoB-trnC-GCA LSC 1215 0.0016 1.00 59.7 yes View details
psbM-trnD-GUC LSC 815 0.0012 1.00 53.7 yes View details
rps15 SSC 273 0.0000 1.00 32.4 yes View details
trnH-GUG-rpl2 IRb 43 0.0233 1.00 65.9 yes View details
rpl2-trnH-GUG IRa 43 0.0233 1.00 65.9 yes View details
matK-trnK-UUU LSC 1044 0.0019 1.00 59.9 yes View details
trnT-GGU-psbD LSC 1009 0.0010 1.00 59.3 yes View details
accD LSC 1449 0.0007 1.00 59.1 yes View details
psaJ-rpl33 LSC 559 0.0000 0.99 59.1 yes View details
matK LSC 1551 0.0006 1.00 59.0 yes View details
rpl20-rps12 LSC 783 0.0000 1.00 58.9 yes View details
trnT-UGU-trnL-UAA LSC 995 0.0000 1.00 58.8 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
trnK-UUU_p1 trnK-UUU TGCTAATGTCAACCAATCAA CAGTTGTGCAGTGCAATTTCA 2997–2998 1.000 40.1
trnK-UUU_p2 trnK-UUU TGCTAATGTCAACCAATCAA AGTTGTGCAGTGCAATTTCA 2996–2997 1.000 40.1
trnK-UUU_p3 trnK-UUU TGCTAATGTCAACCAATCAAA CAGTTGTGCAGTGCAATTTCA 2997–2998 1.000 40.1
trnK-UUU_p4 trnK-UUU TGCTAATGTCAACCAATCAAA AGTTGTGCAGTGCAATTTCA 2996–2997 1.000 40.1
trnK-UUU_p5 trnK-UUU ATGCTAATGTCAACCAATCA CAGTTGTGCAGTGCAATTTCA 2998–2999 1.000 40.1
matK_p1 matK GCACACGACTTTCCCTATGT TACACATACGCCGTTCTGAC 1764 1.000 77.1
matK_p2 matK GCACACGACTTTCCCTATGT ACGCCGTTCTGACCATATTG 1757 1.000 76.5
matK_p3 matK GCACACGACTTTCCCTATGT CATACGCCGTTCTGACCATA 1760 1.000 75.3
matK_p4 matK GCACACGACTTTCCCTATGT GCCGTTCTGACCATATTGCA 1755 1.000 74.3
matK_p5 matK GCACACGACTTTCCCTATGT CATACGCCGTTCTGACCATAT 1760 1.000 71.1
matK-trnK-UUU_p1 matK-trnK-UUU TCCTGAAGGAGTAGCGGATA ATCCGGGTTGCTAACTCAAC 1168–1169 1.000 70.9
matK-trnK-UUU_p2 matK-trnK-UUU TCCTGAAGGAGTAGCGGATA AACGGTAGAGTACTCGGCTT 1151–1152 1.000 70.4
matK-trnK-UUU_p3 matK-trnK-UUU TCCTGAAGGAGTAGCGGATA ACGGTAGAGTACTCGGCTTT 1150–1151 1.000 70.4
matK-trnK-UUU_p4 matK-trnK-UUU TCCTGAAGGAGTAGCGGATA GATCCGGGTTGCTAACTCAA 1169–1170 1.000 68.6
matK-trnK-UUU_p5 matK-trnK-UUU TCCTGAAGGAGTAGCGGATA TTGATCCGGGTTGCTAACTC 1171–1172 1.000 68.6
trnG-UCC_p1 trnG-UCC AAATACGTGTGAATGCCGGA TGCATGTTAAAATGAATAGCATCT 937–946 1.000 40.8
trnG-UCC_p2 trnG-UCC AATACGTGTGAATGCCGGAA AGATGCATGTTAAAATGAATAGCA 939–948 1.000 40.8
trnG-UCC_p3 trnG-UCC AATACGTGTGAATGCCGGAA TGCATGTTAAAATGAATAGCATCT 936–945 1.000 40.8
trnG-UCC_p4 trnG-UCC TACGTGTGAATGCCGGAATT AGATGCATGTTAAAATGAATAGCA 937–946 1.000 40.8
trnG-UCC_p5 trnG-UCC TACGTGTGAATGCCGGAATT TGCATGTTAAAATGAATAGCATCT 934–943 1.000 40.8
rps2_p1 rps2 TCAAAGAAAGTTCACCAAAAACGA ATCCTGGTAGAAGGTTCCGT 855 1.000 46.0
rps2_p2 rps2 AGAAAGTTCACCAAAAACGAAC ATCCTGGTAGAAGGTTCCGT 851 1.000 45.9
rps2_p3 rps2 TCACCAAAAACGAACTAATTGGA ATCCTGGTAGAAGGTTCCGT 844 1.000 45.4
rps2_p4 rps2 TCAAAGAAAGTTCACCAAAAACGA TCCTGGTAGAAGGTTCCGTC 854 1.000 44.4
rps2_p5 rps2 AGAAAGTTCACCAAAAACGAAC TCCTGGTAGAAGGTTCCGTC 850 1.000 44.3
rpoC1_p1 rpoC1 ACACGAGTATGGGCATCACT TTGCTCGTTCGAGAACTACG 2971 1.000 73.3
rpoC1_p2 rpoC1 TACACGAGTATGGGCATCAC TTGCTCGTTCGAGAACTACG 2972 1.000 72.6
rpoC1_p3 rpoC1 TTACACGAGTATGGGCATCAC TTGCTCGTTCGAGAACTACG 2973 1.000 70.3
rpoC1_p4 rpoC1 CACGAGTATGGGCATCACTA TTGCTCGTTCGAGAACTACG 2970 1.000 70.3
rpoC1_p5 rpoC1 ACACGAGTATGGGCATCACT GCTCGTTCGAGAACTACGAT 2969 1.000 69.9

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
Orchis militaris NC_084283.1 152302 View on NCBI ↗
Orchis purpurea PP484634.1 152284 View on NCBI ↗