Markers + reference

Bulbophyllum

19 species · Orchidaceae · Asparagales

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Species 19
Genome length 150–166 kb
Candidate markers 261
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 261 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 853 0.0469 0.98 82.9 yes View details
trnS-GCU-trnG-UCC LSC 921 0.0574 0.96 85.1 yes View details
petN-psbM LSC 756 0.0422 1.00 81.1 yes View details
psbM-trnD-GUC LSC 1081 0.0408 0.98 80.5 yes View details
trnE-UUC-trnT-GGU LSC 1197 0.0452 0.98 84.5 yes View details
atpB-rbcL LSC 1022 0.0347 1.00 77.3 yes View details
psaJ-rpl33 LSC 608 0.0520 0.94 82.4 yes View details
clpP-psbB LSC 683 0.0518 0.95 86.9 yes View details
psbB-psbT LSC 490 0.0606 0.97 80.7 yes View details
ycf1 SSC 5487 0.0283 1.00 68.9 yes View details
psaA-ycf3 LSC 555 0.0307 0.98 81.4 yes View details
rpl16-rps3 LSC 179 0.0517 0.99 80.5 yes View details
rpl32-trnL-UAG SSC 540 0.0439 0.99 80.5 yes View details
accD-psaI LSC 836 0.0379 1.00 79.8 yes View details
trnC-GCA-petN LSC 788 0.0253 0.99 79.4 yes View details
psbI-trnS-GCU LSC 172 0.0502 0.98 78.4 yes View details
matK-trnK-UUU LSC 1069 0.0361 0.98 77.9 yes View details
psaI-ycf4 LSC 412 0.0325 1.00 77.9 yes View details
psbK-psbI LSC 498 0.0378 0.97 77.7 yes View details
psbE-petL LSC 1099 0.0277 0.99 77.6 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU_p1 trnK-UUU ACTTTGGTTGGTATGGGTTGA TCGATCATATCTACATTTTATATTGA 2986–2998 0.105 5.7
trnK-UUU_p2 trnK-UUU ACTTTGGTTGGTATGGGTTGA TTCGATCATATCTACATTTTATATTGA 2987–2999 0.105 5.7
trnK-UUU_p3 trnK-UUU ACTTTGGTTGGTATGGGTTGA CGATCATATCTACATTTTATATTGA 2985–2997 0.105 5.7
trnK-UUU_p4 trnK-UUU ACTTTGGTTGGTATGGGTTGA TCGATCATATCTACATTTTATATTG 2986–2998 0.105 5.7
trnK-UUU_p5 trnK-UUU ACTTTGGTTGGTATGGGTTGA TCGATCATATCTACATTTTATATTGAT 2986–2998 0.105 5.7
matK-trnK-UUU_p1 matK-trnK-UUU AATTCTCGTGCCCCCAAAAT AACGGTAGAGTACTCGGCTT 1275–1422 0.789 81.7
matK-trnK-UUU_p2 matK-trnK-UUU AATTCTCGTGCCCCCAAAAT ACGGTAGAGTACTCGGCTTT 1274–1421 0.789 81.7
matK-trnK-UUU_p3 matK-trnK-UUU ATTCTCGTGCCCCCAAAATT AACGGTAGAGTACTCGGCTT 1274–1421 0.737 79.6
matK-trnK-UUU_p4 matK-trnK-UUU ATTCTCGTGCCCCCAAAATT ACGGTAGAGTACTCGGCTTT 1273–1420 0.737 79.6
matK-trnK-UUU_p5 matK-trnK-UUU ATTCTCGTGCCCCCAAAATT GTGCTAAACCCACAGGAACT 1903–2068 0.737 78.8
rps16-trnQ-UUG_p1 rps16-trnQ-UUG ATCCACAGCCAATCATGTCC GAGGTTCGAATCCTTCCGTC 848–1142 1.000 90.9
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 825–1119 1.000 90.3
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CCACAGCCAATCATGTCCTT GAGGTTCGAATCCTTCCGTC 846–1140 1.000 90.1
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 836–1130 1.000 89.8
rps16-trnQ-UUG_p5 rps16-trnQ-UUG ATCATGTCCTTCAAGTCGCA GAGGTTCGAATCCTTCCGTC 837–1131 1.000 85.2
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG ACGCCCCGGATCATTAGATA 565–629 1.000 91.0
psbK-psbI_p2 psbK-psbI GTTTGGCAAGCTGCTGTAAG TACGCCCCGGATCATTAGAT 566–630 1.000 91.0
psbK-psbI_p3 psbK-psbI GTTTGGCAAGCTGCTGTAAG TTACGCCCCGGATCATTAGA 567–631 1.000 89.2
psbK-psbI_p4 psbK-psbI TGGCAAGCTGCTGTAAGTTT ACGCCCCGGATCATTAGATA 562–626 1.000 89.0
psbK-psbI_p5 psbK-psbI TGGCAAGCTGCTGTAAGTTT TACGCCCCGGATCATTAGAT 563–627 1.000 89.0
psbI-trnS-GCU_p1 psbI-trnS-GCU GTTTGGCAAGCTGCTGTAAG TGGACTAAAGCGTCGGATTG 818–892 1.000 91.5
psbI-trnS-GCU_p2 psbI-trnS-GCU ATCTAATGATCCGGGGCGTA TGGACTAAAGCGTCGGATTG 272–285 1.000 91.4
psbI-trnS-GCU_p3 psbI-trnS-GCU TATCTAATGATCCGGGGCGT TGGACTAAAGCGTCGGATTG 273–286 1.000 91.4
psbI-trnS-GCU_p4 psbI-trnS-GCU GTTTGGCAAGCTGCTGTAAG GTGGACTAAAGCGTCGGATT 839–893 0.842 85.2
psbI-trnS-GCU_p5 psbI-trnS-GCU ATCTAATGATCCGGGGCGTA GTGGACTAAAGCGTCGGATT 278–286 0.842 84.5
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC GCTTTAGTCCACTCAGCCAT ACGAATCACACTTTTACCACT 928–1157 1.000 60.4
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AGTCCACTCAGCCATCTCTC ACGAATCACACTTTTACCACT 923–1152 1.000 59.6
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC GCTTTAGTCCACTCAGCCAT AGAACGAATCACACTTTTACCAC 931–1160 1.000 59.4
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC GCTTTAGTCCACTCAGCCAT GAACGAATCACACTTTTACCACT 930–1159 1.000 59.4
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AGTCCACTCAGCCATCTCTC GAACGAATCACACTTTTACCACT 925–1154 1.000 58.5

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (19)

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

Species Accession Length (bp) Link
Bulbophyllum albociliatum NC_070215.1 151046 View on NCBI ↗
Bulbophyllum ambrosia NC_088536.1 158026 View on NCBI ↗
Bulbophyllum chondriophorum PQ276426.1 151023 View on NCBI ↗
Bulbophyllum crassipes NC_088537.1 165812 View on NCBI ↗
Bulbophyllum farreri NC_088538.1 157339 View on NCBI ↗
Bulbophyllum flammuliferum NC_084215.1 156822 View on NCBI ↗
Bulbophyllum gedangense MW161053.1 158524 View on NCBI ↗
Bulbophyllum inconspicuum NC_046811.1 149548 View on NCBI ↗
Bulbophyllum lingii MW161052.1 156689 View on NCBI ↗
Bulbophyllum menghaiense MW161050.1 156550 View on NCBI ↗
Bulbophyllum pentaneurum MW161051.1 156182 View on NCBI ↗
Bulbophyllum pilopetalum OM459712.1 151148 View on NCBI ↗
Bulbophyllum pingnanense MW822749.1 151224 View on NCBI ↗
Bulbophyllum reptans NC_058531.1 158389 View on NCBI ↗
Bulbophyllum shanicum NC_088539.1 158009 View on NCBI ↗
Bulbophyllum tianguii NC_060701.1 151953 View on NCBI ↗
Bulbophyllum triste NC_088540.1 157429 View on NCBI ↗
Bulbophyllum violaceolabellum NC_088541.1 157811 View on NCBI ↗
Bulbophyllum wolongense ON357877.1 157496 View on NCBI ↗