Markers + reference

Epipactis

8 species · Orchidaceae · Asparagales

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Species 8
Genome length 159–160 kb
Candidate markers 275
Primer pairs 100

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 275 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 944 0.0152 0.99 59.7 yes View details
trnS-GCU-trnG-GCC LSC 765 0.0141 1.00 62.5 yes View details
petN-psbM LSC 729 0.0157 1.00 54.2 yes View details
trnE-UUC-trnT-GGU LSC 1547 0.0103 1.00 53.4 yes View details
clpP-psbB LSC 959 0.0128 0.98 68.4 yes View details
psbB-psbT LSC 319 0.0290 1.00 61.1 yes View details
rpl16 LSC 1587 0.0079 1.00 42.9 yes View details
ndhA SSC 2200 0.0064 1.00 41.8 yes View details
rpl32-ndhF SSC 1230 0.0151 1.00 60.6 yes View details
petA-psbJ LSC 835 0.0123 1.00 67.1 yes View details
trnT-UGU-trnL-UAA LSC 1041 0.0093 0.98 64.8 yes View details
atpB-rbcL LSC 984 0.0115 0.99 62.6 yes View details
rpl16-rps3 LSC 176 0.0308 0.99 61.1 yes View details
psbL-psbF LSC 22 0.0503 1.00 61.0 yes View details
psbA-trnK-UUU LSC 246 0.0247 1.00 60.7 yes View details
psbE-petL LSC 1348 0.0090 0.99 59.8 yes View details
matK-trnK-UUU LSC 880 0.0059 1.00 57.1 yes View details
trnL-UAG-rpl32 SSC 705 0.0106 1.00 56.0 yes View details
psaJ-rpl33 LSC 491 0.0060 1.00 55.4 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbA-trnK-UUU_p1 psbA-trnK-UUU TAGGCTTGTACTTTCGCGTC ACTCCATCCGACTAGTTCCG 303–334 1.000 82.5
psbA-trnK-UUU_p2 psbA-trnK-UUU TAGGCTTGTACTTTCGCGTC ACTAGTTCCGGGTTCGAGTC 293–324 1.000 80.8
psbA-trnK-UUU_p3 psbA-trnK-UUU TAGGCTTGTACTTTCGCGTC GACTAGTTCCGGGTTCGAGT 294–325 1.000 80.8
psbA-trnK-UUU_p4 psbA-trnK-UUU TAGGCTTGTACTTTCGCGTC ATCCGACTAGTTCCGGGTTC 298–329 1.000 80.3
psbA-trnK-UUU_p5 psbA-trnK-UUU GCTTGTACTTTCGCGTCTCT ACTCCATCCGACTAGTTCCG 300–331 1.000 80.2
trnK-UUU_p1 trnK-UUU TGCCAATGTCAACCAATCAA TCCTCACTCCATATTGGCTCT 2971–2990 0.750 48.6
trnK-UUU_p2 trnK-UUU TGCCAATGTCAACCAATCAA TCTCCTCACTCCATATTGGCT 2973–2992 0.750 48.6
trnK-UUU_p3 trnK-UUU TGCCAATGTCAACCAATCAAA TCCTCACTCCATATTGGCTCT 2971–2990 0.750 46.8
trnK-UUU_p4 trnK-UUU TGCCAATGTCAACCAATCAAA TCTCCTCACTCCATATTGGCT 2973–2992 0.750 46.8
trnK-UUU_p5 trnK-UUU ATGCCAATGTCAACCAATCA TCCTCACTCCATATTGGCTCT 2972–2991 0.750 46.8
matK-trnK-UUU_p1 matK-trnK-UUU TCCTTGTAATTCTGCCATTTACA TCCGGGTTGCTAACTCAATG 906–949 1.000 45.8
matK-trnK-UUU_p2 matK-trnK-UUU TCCTTGTAATTCTGCCATTTACA CGGGTTGCTAACTCAATGGT 904–947 1.000 45.4
matK-trnK-UUU_p3 matK-trnK-UUU TCCTTGTAATTCTGCCATTTACA GATCCGGGTTGCTAACTCAA 908–951 1.000 45.4
matK-trnK-UUU_p4 matK-trnK-UUU TCCTTGTAATTCTGCCATTTACA TTGATCCGGGTTGCTAACTC 910–953 1.000 45.4
matK-trnK-UUU_p5 matK-trnK-UUU CCTTGTAATTCTGCCATTTACA TCCGGGTTGCTAACTCAATG 905–948 1.000 45.4
rps16-trnQ-UUG_p1 rps16-trnQ-UUG ATCCACAGCCAATCATGTCC GAGGTTCGAATCCTTCCGTC 999–1041 1.000 85.6
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 976–1018 1.000 85.1
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CCACAGCCAATCATGTCCTT GAGGTTCGAATCCTTCCGTC 997–1039 1.000 84.8
rps16-trnQ-UUG_p4 rps16-trnQ-UUG ATCCACAGCCAATCATGTCC CTCGGAGGTTCGAATCCTTC 1003–1045 1.000 84.5
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 987–1029 1.000 84.5
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC TTAGTCCCCTCAGCCATCTC ACGAATCACACTTTTACCACT 781–843 1.000 56.9
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC TTTAGTCCCCTCAGCCATCT ACGAATCACACTTTTACCACT 782–844 1.000 56.4
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC TTAGTCCCCTCAGCCATCTC AGAACGAATCACACTTTTACCAC 784–846 1.000 55.8
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC TTAGTCCCCTCAGCCATCTC GAACGAATCACACTTTTACCACT 783–845 1.000 55.8
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC CGGAGAGAGAGGGATTCGAA ACGAATCACACTTTTACCACT 846–908 1.000 55.6
petN-psbM_p1 petN-psbM TCCTATTTTGACTCTGCGCC CGTTTATTGCTACTGCGCTG 984–1000 1.000 83.2
petN-psbM_p2 petN-psbM TAGTAAGTCTCGCTTGGGCT CGTTTATTGCTACTGCGCTG 883–899 1.000 82.6
petN-psbM_p3 petN-psbM TTGACTCTGCGCCATTGATT CGTTTATTGCTACTGCGCTG 977–993 1.000 82.0
petN-psbM_p4 petN-psbM TTTGACTCTGCGCCATTGAT CGTTTATTGCTACTGCGCTG 978–994 1.000 82.0
petN-psbM_p5 petN-psbM TCCTATTTTGACTCTGCGCC AGCGGGAAAATGAAATGGGA 1276–1292 0.875 76.3

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (8)

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

Species Accession Length (bp) Link
Epipactis albensis NC_041182.1 159763 View on NCBI ↗
Epipactis atrorubens NC_041183.1 159790 View on NCBI ↗
Epipactis gigantea NC_041184.1 158977 View on NCBI ↗
Epipactis helleborine NC_041185.1 159822 View on NCBI ↗
Epipactis microphylla NC_041186.1 159236 View on NCBI ↗
Epipactis palustris NC_041187.1 159134 View on NCBI ↗
Epipactis purpurata NC_041188.1 159864 View on NCBI ↗
Epipactis veratrifolia NC_030708.1 159719 View on NCBI ↗