Markers + reference

Vrydagzynea

2 species · Orchidaceae · Asparagales

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Species 2
Genome length 152–152 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
trnK-UUU-rps16 LSC 576 0.0330 1.00 68.7 yes View details
rps16-trnQ-UUG LSC 535 0.0287 0.98 67.0 yes View details
trnS-GCU-trnG-GCC LSC 490 0.0292 0.98 65.2 yes View details
petN-psbM LSC 538 0.0243 0.99 59.6 yes View details
trnD-GUC-trnY-GUA LSC 283 0.0424 1.00 63.1 yes View details
trnS-UGA-psbZ LSC 231 0.0346 1.00 59.3 yes View details
rps4-trnT-UGU LSC 313 0.0321 1.00 60.2 yes View details
rpl32-trnL-UAG SSC 368 0.0168 0.97 57.6 yes View details
ndhG SSC 531 0.0169 1.00 52.1 yes View details
psbF-psbE LSC 10 0.1000 1.00 79.0 yes View details
ndhF-rpl32 SSC 179 0.0565 0.69 77.5 yes View details
rrn16-trnI-GAU IRb 302 0.0331 1.00 71.6 yes View details
trnI-GAU-rrn16 IRa 302 0.0331 1.00 71.6 yes View details
trnL-UAG-ccsA SSC 116 0.0517 1.00 67.5 yes View details
psbK-psbI LSC 451 0.0200 1.00 67.4 yes View details
rpl33-rps18 LSC 169 0.0240 0.99 67.4 yes View details
trnF-GAA-ndhJ LSC 567 0.0159 1.00 67.2 yes View details
psaA-ycf3 LSC 698 0.0089 0.97 66.9 yes View details
trnT-GGU-psbD LSC 1005 0.0139 1.00 66.2 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 GCTCAACCCACAGGAACT 697–709 1.000 55.0
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GCTCAACCCACAGGAACT 696–708 1.000 55.0
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCAGTCGCGGTCTTAGAAAC GCTCAACCCACAGGAACT 778–790 1.000 53.4
trnK-UUU-rps16_p4 trnK-UUU-rps16 CAGTCGCGGTCTTAGAAACT GCTCAACCCACAGGAACT 777–789 1.000 53.3
trnK-UUU-rps16_p5 trnK-UUU-rps16 TACCGTTGAGTTAGCAACCC GCTCAACCCACAGGAACT 683–695 1.000 52.7
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA ACAAAAGAAGAATGGGGCGT 657–669 1.000 82.6
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA ACGGGTTTTGGTCCTGTTAC 620–632 1.000 82.1
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 597–609 1.000 81.9
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CTCGGAGGTTCGAATCCTTC 601–613 1.000 80.8
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CGGGTTTTGGTCCTGTTACT 619–631 1.000 80.2
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG TTCTTCACGCCCAGGATTAC 589–601 1.000 77.7
psbK-psbI_p2 psbK-psbI TGGCAAGCTGCTGTAAGTTT TTCTTCACGCCCAGGATTAC 586–598 1.000 75.7
psbK-psbI_p3 psbK-psbI TTGGCAAGCTGCTGTAAGTT TTCTTCACGCCCAGGATTAC 587–599 1.000 75.7
psbK-psbI_p4 psbK-psbI TTTGGCAAGCTGCTGTAAGT TTCTTCACGCCCAGGATTAC 588–600 1.000 75.7
psbK-psbI_p5 psbK-psbI GTTTGGCAAGCTGCTGTAAG GGATTACGTCCCGGATCATT 576–588 1.000 74.3
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA ACGAATCACACTTTTACCACT 549–559 1.000 55.1
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC ACGAATCACACTTTTACCACT 548–558 1.000 55.1
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC GTTATCAGGGGAGTCGGAGA ACGAATCACACTTTTACCACT 616–626 1.000 54.3
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC AGTTATCAGGGGAGTCGGAG ACGAATCACACTTTTACCACT 617–627 1.000 54.2
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA GAACGAATCACACTTTTACCACT 551–561 1.000 54.1
petN-psbM_p1 petN-psbM AGTATGGGGAAGGAGTGGAC ACGTCAAAACAGTCAGCCAA 592–642 1.000 79.1
petN-psbM_p2 petN-psbM GTATGGGGAAGGAGTGGACT ACGTCAAAACAGTCAGCCAA 591–641 1.000 79.1
petN-psbM_p3 petN-psbM ATGGGGAAGGAGTGGACTTT ACGTCAAAACAGTCAGCCAA 589–639 1.000 78.1
petN-psbM_p4 petN-psbM TGGGGAAGGAGTGGACTTTA ACGTCAAAACAGTCAGCCAA 588–638 1.000 76.6
petN-psbM_p5 petN-psbM GTATGGGGAAGGAGTGGACT TACGTCAAAACAGTCAGCCA 592–642 1.000 76.3
trnD-GUC-trnY-GUA_p1 trnD-GUC-trnY-GUA ATTCCAATTCGGGACTGACG ATTCCTTCTTCCTGGGTCGA 463–465 1.000 81.8
trnD-GUC-trnY-GUA_p2 trnD-GUC-trnY-GUA ATTCCAATTCGGGACTGACG TTCCTTCTTCCTGGGTCGAT 462–464 1.000 81.8
trnD-GUC-trnY-GUA_p3 trnD-GUC-trnY-GUA ATTCCAATTCGGGACTGACG GAACCGATGACTTACGCCTT 1053–1055 1.000 81.0
trnD-GUC-trnY-GUA_p4 trnD-GUC-trnY-GUA ATTCCAATTCGGGACTGACG CCATGGCGTTACTCTACCAC 1032–1034 1.000 80.6
trnD-GUC-trnY-GUA_p5 trnD-GUC-trnY-GUA AAAGAAAGGGGCGGGTTAAG GAACCGATGACTTACGCCTT 1630 0.500 59.3

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
Vrydagzynea nuda MW589534.1 152308 View on NCBI ↗
Vrydagzynea tristriata MW589535.1 152222 View on NCBI ↗