Markers + reference

Zeuxine

3 species · Orchidaceae · Asparagales

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Species 3
Genome length 151–152 kb
Candidate markers 274
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 274 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 592 0.0920 0.99 83.1 yes View details
atpF LSC 1362 0.0237 0.99 63.8 yes View details
ycf3-trnS-GGA LSC 595 0.0611 1.00 87.9 yes View details
accD LSC 1863 0.0382 0.95 70.5 yes View details
accD-psaI LSC 687 0.0960 0.96 84.7 yes View details
petA-psbJ LSC 935 0.0504 1.00 80.7 yes View details
clpP-psbB LSC 530 0.0627 0.99 81.3 yes View details
ycf1 IRb 873 0.0141 1.00 52.7 no View details
ndhF-rpl32 SSC 778 0.0860 0.98 83.8 yes View details
ccsA-ndhD SSC 267 0.0886 1.00 72.6 yes View details
ycf1 SSC 5310 0.0362 1.00 61.3 yes View details
trnT-UGU-trnL-UAA LSC 942 0.0472 0.98 81.9 yes View details
rps16-trnQ-UUG LSC 506 0.0569 1.00 81.7 yes View details
psbK-psbI LSC 426 0.0536 0.99 81.6 yes View details
ndhI-ndhA SSC 102 0.0458 1.00 79.4 yes View details
trnS-GCU-trnG-GCC LSC 407 0.0590 1.00 79.3 yes View details
psbC-trnS-UGA LSC 140 0.0657 0.94 78.9 yes View details
psbI-trnS-GCU LSC 133 0.0909 0.99 78.6 yes View details
trnC-GCA-petN LSC 863 0.0457 1.00 78.5 yes View details
trnF-GAA-ndhJ LSC 551 0.0459 0.99 78.1 yes View details
trnL-UAA-trnF-GAA LSC 305 0.0699 0.95 78.0 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT GCAAAGACAACGAATTCCGG 1133–1255 1.000 88.6
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GCAAAGACAACGAATTCCGG 1132–1254 1.000 88.6
trnK-UUU-rps16_p3 trnK-UUU-rps16 ATACCCCGGAGACAGATAGC GCAAAGACAACGAATTCCGG 1929 0.333 52.5
trnK-UUU-rps16_p4 trnK-UUU-rps16 ATACCCCGGAGACAGATAGC TCGATCCCGAAGAGAAGGAA 1531 0.333 51.6
trnK-UUU-rps16_p5 trnK-UUU-rps16 ATACCCCGGAGACAGATAGC GTGCAAAGCAAAGACAACGA 1936 0.333 51.2
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 541–602 1.000 88.0
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 552–613 1.000 87.4
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG GAGGTTCGAATCCTTCCGTC 533–594 1.000 82.9
rps16-trnQ-UUG_p4 rps16-trnQ-UUG ATCATGTCCTTCAAGTCGCA GAGGTTCGAATCCTTCCGTC 553–614 1.000 82.8
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AGTCGCACGTTGCTTTCTAC GAGGTTCGAATCCTTCCGTC 540–601 1.000 82.2
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG ACTACTGTGTAGACGAAGAGT 491–522 1.000 60.8
psbK-psbI_p2 psbK-psbI GTTTGGCAAGCTGCTGTAAG ACTACTGTGTAGACGAAGAGTT 491–522 1.000 58.9
psbK-psbI_p3 psbK-psbI TGGCAAGCTGCTGTAAGTTT ACTACTGTGTAGACGAAGAGT 488–519 1.000 58.8
psbK-psbI_p4 psbK-psbI TTGGCAAGCTGCTGTAAGTT ACTACTGTGTAGACGAAGAGT 489–520 1.000 58.8
psbK-psbI_p5 psbK-psbI TTTGGCAAGCTGCTGTAAGT ACTACTGTGTAGACGAAGAGT 490–521 1.000 58.8
psbI-trnS-GCU_p1 psbI-trnS-GCU GTTTGGCAAGCTGCTGTAAG TGGACTAAAGCGTCGGATTG 773–821 1.000 89.0
psbI-trnS-GCU_p2 psbI-trnS-GCU GTTTGGCAAGCTGCTGTAAG GTGGACTAAAGCGTCGGATT 774–822 1.000 89.0
psbI-trnS-GCU_p3 psbI-trnS-GCU TTTTCTTCGCCAAATTGCCC TGGACTAAAGCGTCGGATTG 868–916 1.000 87.3
psbI-trnS-GCU_p4 psbI-trnS-GCU TTTTCTTCGCCAAATTGCCC GTGGACTAAAGCGTCGGATT 869–917 1.000 87.3
psbI-trnS-GCU_p5 psbI-trnS-GCU GTTTGGCAAGCTGCTGTAAG ACAAAAGAAGTACTGGCCCG 997–1053 0.667 68.2
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA ACGAATCACACTTTTACCACT 476–552 1.000 59.0
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC ACGAATCACACTTTTACCACT 475–551 1.000 59.0
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA GAACGAATCACACTTTTACCACT 478–554 1.000 57.9
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC GAACGAATCACACTTTTACCACT 477–553 1.000 57.9
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA AGAACGAATCACACTTTTACCAC 479–555 1.000 57.8
atpF_p1 atpF CACTTGAAGTACGGTACCGG ATTTATGGACTGGTCGTGGC 1842–1878 1.000 86.4
atpF_p2 atpF CCACTTGAAGTACGGTACCG ATTTATGGACTGGTCGTGGC 1843–1879 1.000 86.3
atpF_p3 atpF GCTCGAAGGGTTCCCATTAG ATTTATGGACTGGTCGTGGC 1754–1790 1.000 86.2
atpF_p4 atpF CACTTGAAGTACGGTACCGG GAGACAACCAGAAGCAGAGG 1915–1951 1.000 85.7
atpF_p5 atpF CCCCTCCTTCCTGGAAAGTA ATTTATGGACTGGTCGTGGC 2389–2425 1.000 85.0

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

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

Species Accession Length (bp) Link
Zeuxine affinis MW589536.1 151301 View on NCBI ↗
Zeuxine flava MW589537.1 152079 View on NCBI ↗
Zeuxine nervosa MW589538.1 151647 View on NCBI ↗