Markers + reference

Pleione

20 species · Orchidaceae · Asparagales

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Species 20
Genome length 158–160 kb
Candidate markers 276
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 276 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 1138 0.0126 0.99 70.9 yes View details
trnS-GCU-trnG-GCC LSC 992 0.0172 0.99 69.3 yes View details
rpoB-trnC-GCA LSC 1458 0.0103 0.99 61.7 yes View details
trnC-GCA-petN LSC 826 0.0115 1.00 66.5 yes View details
trnE-UUC-trnT-GGU LSC 1297 0.0152 0.99 71.9 yes View details
atpB-rbcL LSC 992 0.0157 1.00 57.7 yes View details
clpP-psbB LSC 743 0.0126 0.99 61.3 yes View details
psbB-psbT LSC 524 0.0119 0.92 52.9 yes View details
ycf1 IRb 1029 0.0045 1.00 46.1 no View details
ndhF-rpl32 SSC 996 0.0141 0.93 71.0 yes View details
psaC-ndhE SSC 735 0.0194 1.00 65.8 yes View details
ycf1 SSC 5559 0.0094 1.00 48.9 yes View details
psbT-psbN LSC 70 0.0720 1.00 73.3 yes View details
trnT-UGU-trnL-UAA LSC 553 0.0127 0.99 65.4 yes View details
petA-psbJ LSC 1035 0.0124 0.99 64.8 yes View details
psaJ-rpl33 LSC 582 0.0122 1.00 64.6 yes View details
trnF-GAA-ndhJ LSC 605 0.0122 1.00 61.3 yes View details
psbA-trnK-UUU LSC 251 0.0103 0.99 61.1 yes View details
rpl32-trnL-UAG SSC 655 0.0137 1.00 60.8 yes View details
trnW-CCA-trnP-UGG LSC 172 0.0133 1.00 60.0 yes View details
psbK-psbI LSC 478 0.0103 1.00 59.5 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 TCGTGTGCAATGAAAACTGC 405–424 1.000 82.9
psbA-trnK-UUU_p2 psbA-trnK-UUU TAGGCTTGTACTTTCGCGTC AATGAAAACTGCAAGCACGG 397–416 1.000 82.8
psbA-trnK-UUU_p3 psbA-trnK-UUU TAGGCTTGTACTTTCGCGTC CGTGTGCAATGAAAACTGCA 404–423 1.000 82.5
psbA-trnK-UUU_p4 psbA-trnK-UUU TAGGCTTGTACTTTCGCGTC AAAACTGCAAGCACGGTTTG 393–412 1.000 81.1
psbA-trnK-UUU_p5 psbA-trnK-UUU GCTTGTACTTTCGCGTCTCT TCGTGTGCAATGAAAACTGC 402–421 1.000 80.6
rps16-trnQ-UUG_p1 rps16-trnQ-UUG ATCCACAGCCAATCATGTCC GAGGTTCGAATCCTTCCGTC 622–1249 1.000 87.5
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 599–1226 1.000 86.9
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CCACAGCCAATCATGTCCTT GAGGTTCGAATCCTTCCGTC 620–1247 1.000 86.7
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 610–1237 1.000 86.4
rps16-trnQ-UUG_p5 rps16-trnQ-UUG GGATGTCAGAATCCACAGCC GAGGTTCGAATCCTTCCGTC 632–1259 1.000 85.4
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG ACGCCCCGGATCATTAGATA 80–607 1.000 86.3
psbK-psbI_p2 psbK-psbI GTTTGGCAAGCTGCTGTAAG TACGCCCCGGATCATTAGAT 80–608 1.000 86.3
psbK-psbI_p3 psbK-psbI AATCGTAGACGTTATGCCGG ACGCCCCGGATCATTAGATA 80–659 1.000 85.5
psbK-psbI_p4 psbK-psbI AATCGTAGACGTTATGCCGG TACGCCCCGGATCATTAGAT 80–660 1.000 85.5
psbK-psbI_p5 psbK-psbI CGTTATGCCGGTTATCCCTT ACGCCCCGGATCATTAGATA 80–650 1.000 84.5
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA ACGAATCACACTTTTACCACT 80–1133 1.000 61.2
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC ACGAATCACACTTTTACCACT 80–1132 1.000 61.2
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA AGAACGAATCACACTTTTACCAC 80–1136 1.000 60.1
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA GAACGAATCACACTTTTACCACT 80–1135 1.000 60.1
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC GAACGAATCACACTTTTACCACT 80–1134 1.000 60.1
rpoB-trnC-GCA_p1 rpoB-trnC-GCA AATTCTTCCGTCAAGCCCTG TAAAGGATTTGCAGTCCCCC 80–1634 1.000 81.8
rpoB-trnC-GCA_p2 rpoB-trnC-GCA AATTCTTCCGTCAAGCCCTG CGACACCCAGATTCGAACTG 80–1658 1.000 80.7
rpoB-trnC-GCA_p3 rpoB-trnC-GCA AATTCTTCCGTCAAGCCCTG TTTTTGATCAGGCGACACCC 80–1670 1.000 79.8
rpoB-trnC-GCA_p4 rpoB-trnC-GCA AAATTCTTCCGTCAAGCCCT TAAAGGATTTGCAGTCCCCC 80–1635 1.000 78.5
rpoB-trnC-GCA_p5 rpoB-trnC-GCA AATTCTTCCGTCAAGCCCTG ATAAAGGATTTGCAGTCCCCC 80–1635 1.000 77.7
trnC-GCA-petN_p1 trnC-GCA-petN CCAGTTCGAATCTGGGTGTC GCTCTAAAGCCCACTCCTTC 80–970 1.000 85.2
trnC-GCA-petN_p2 trnC-GCA-petN CCAGTTCGAATCTGGGTGTC AGCCCAAGCGAGACTTACTA 80–904 1.000 84.5
trnC-GCA-petN_p3 trnC-GCA-petN GGGGGACTGCAAATCCTTTA GCTCTAAAGCCCACTCCTTC 80–993 1.000 83.1
trnC-GCA-petN_p4 trnC-GCA-petN GGGGGACTGCAAATCCTTTA AGCCCAAGCGAGACTTACTA 80–927 1.000 82.3
trnC-GCA-petN_p5 trnC-GCA-petN CCAGTTCGAATCTGGGTGTC CCTTCCCCATACTACAAGCG 80–954 0.950 81.5

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (20)

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

Species Accession Length (bp) Link
Pleione albiflora NC_063635.1 158432 View on NCBI ↗
Pleione arunachalensis NC_063638.1 158440 View on NCBI ↗
Pleione aurita NC_063659.1 158984 View on NCBI ↗
Pleione bulbocodioides NC_036342.1 159269 View on NCBI ↗
Pleione coronaria NC_063639.1 158072 View on NCBI ↗
Pleione dilamellata NC_063656.1 159251 View on NCBI ↗
Pleione formosana NC_042197.1 159843 View on NCBI ↗
Pleione grandiflora NC_063651.1 158872 View on NCBI ↗
Pleione hookeriana NC_063652.1 157962 View on NCBI ↗
Pleione hui PP856694.1 159037 View on NCBI ↗
Pleione humilis NC_063640.1 158472 View on NCBI ↗
Pleione limprichtii NC_063641.1 159265 View on NCBI ↗
Pleione maculata MT954966.1 158287 View on NCBI ↗
Pleione microphylla NC_063657.1 158808 View on NCBI ↗
Pleione praecox NC_063653.1 157822 View on NCBI ↗
Pleione saxicola NC_063642.1 158976 View on NCBI ↗
Pleione scopulorum NC_063643.1 158870 View on NCBI ↗
Pleione vietnamensis NC_063654.1 157964 View on NCBI ↗
Pleione x taliensis MZ958822.2 159234 View on NCBI ↗
Pleione yunnanensis NC_063655.1 158802 View on NCBI ↗