Markers + reference

Tacca

2 species · Taccaceae · Dioscoreales

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Species 2
Genome length 162–162 kb
Candidate markers 273
Primer pairs 110

Genome-wide nucleotide diversity

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

Candidate markers

13 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 273 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-trnQ-UUG LSC 1157 0.0622 0.97 81.4 yes View details
psbK-psbI LSC 419 0.0638 0.90 79.2 yes View details
trnS-GCU-trnG-UCC LSC 1019 0.0536 0.44 71.3 yes View details
atpF LSC 1494 0.0356 0.96 68.1 yes View details
atpF-atpH LSC 426 0.0851 0.99 76.3 yes View details
trnT-GGU-psbD LSC 1049 0.0418 0.98 70.0 yes View details
ndhC-trnV-UAC LSC 795 0.0835 0.99 80.2 yes View details
ycf4-cemA LSC 795 0.0487 0.96 77.2 yes View details
ndhF-rpl32 SSC 727 0.0831 0.81 76.0 yes View details
rpl32-trnL-UAG SSC 729 0.0501 0.96 77.5 yes View details
ndhD SSC 1335 0.0292 1.00 61.8 yes View details
psaC-ndhE SSC 436 0.0769 0.98 80.8 yes View details
ndhI SSC 543 0.0203 1.00 54.4 yes View details
atpH-atpI LSC 788 0.0429 0.98 80.3 yes View details
petA-psbJ LSC 852 0.0473 0.92 79.8 yes View details
accD-psaI LSC 487 0.0490 0.96 79.7 yes View details
rpl2-rpl23 IRb 18 0.0556 1.00 79.5 yes View details
rpl23-rpl2 IRa 18 0.0556 1.00 79.5 yes View details
rpoC1-rpoB LSC 5 0.2000 1.00 78.8 yes View details
trnT-UGU-trnL-UAA LSC 939 0.0407 0.97 77.9 yes View details
trnW-CCA-trnP-UGG LSC 161 0.0596 0.94 77.9 yes View details
psbT-psbN LSC 66 0.1333 0.91 77.5 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 110 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-trnQ-UUG_p1 trnK-UUU-trnQ-UUG AAAGCCGAGTACTCTACCGT GAGGTTCGAATCCTTCCGTC 1215–2317 1.000 82.7
trnK-UUU-trnQ-UUG_p2 trnK-UUU-trnQ-UUG AAGCCGAGTACTCTACCGTT GAGGTTCGAATCCTTCCGTC 1214–2316 1.000 82.7
trnK-UUU-trnQ-UUG_p3 trnK-UUU-trnQ-UUG TCGTTGCCTCATCCAAATGT GAGGTTCGAATCCTTCCGTC 1258–2360 1.000 82.3
trnK-UUU-trnQ-UUG_p4 trnK-UUU-trnQ-UUG CGTTGCCTCATCCAAATGTG GAGGTTCGAATCCTTCCGTC 1257–2359 1.000 81.8
trnK-UUU-trnQ-UUG_p5 trnK-UUU-trnQ-UUG AAGCCGAGTACTCTACCGTT CTCGGAGGTTCGAATCCTTC 1218–2320 1.000 81.6
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG TCACCACTGTGTAAACAAAGAGT 465–486 1.000 62.3
psbK-psbI_p2 psbK-psbI GTTTGGCAAGCTGCTGTAAG CACCACTGTGTAAACAAAGAGT 464–485 1.000 61.8
psbK-psbI_p3 psbK-psbI AATCGTAGACGTTATGCCCG TCACCACTGTGTAAACAAAGAGT 517–538 1.000 61.3
psbK-psbI_p4 psbK-psbI AATCGTAGACGTTATGCCCG CACCACTGTGTAAACAAAGAGT 516–537 1.000 60.8
psbK-psbI_p5 psbK-psbI ATGCCCGTCATACCTGTACT TCACCACTGTGTAAACAAAGAGT 504–525 1.000 60.8
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAGATTAGCAATCCACCGCT ACGAATCGCACTTTTACCACT 546–1096 1.000 76.1
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC CAGATTAGCAATCCACCGCT ACGAATCGCACTTTTACCAC 546–1096 1.000 76.1
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CAATCCACCGCTTTAGTCCA ACGAATCGCACTTTTACCACT 538–1088 1.000 75.6
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AATCCACCGCTTTAGTCCAC ACGAATCGCACTTTTACCACT 537–1087 1.000 75.6
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC CAATCCACCGCTTTAGTCCA ACGAATCGCACTTTTACCAC 538–1088 1.000 75.5
atpF_p1 atpF CCGCCATCACTTCATCAAGA AAGCCGTAGAAGGTATTGCG 2233–2288 1.000 85.0
atpF_p2 atpF CACTAATTCACCCGCCATCA AAGCCGTAGAAGGTATTGCG 2244–2299 1.000 84.9
atpF_p3 atpF ACTAATTCACCCGCCATCAC AAGCCGTAGAAGGTATTGCG 2243–2298 1.000 84.9
atpF_p4 atpF GCCCTGTTTGAAGAGGTTCA AAGCCGTAGAAGGTATTGCG 2533–2588 1.000 84.6
atpF_p5 atpF GCCCTGTTTGAAGAGGTTCA GCTCGCTTTCTTCCTTCTCA 2207–2268 1.000 84.6
atpF-atpH_p1 atpF-atpH GAGGAAACAAAAGAATCGGT AATTTACGGGCTGGTCGTG 513–518 1.000 46.1
atpF-atpH_p2 atpF-atpH GAGGAAACAAAAGAATCGGT AACAATTTACGGGCTGGTCG 516–521 1.000 46.0
atpF-atpH_p3 atpF-atpH GAGGAAACAAAAGAATCGGTTACA AACAATTTACGGGCTGGTCG 516–521 1.000 46.0
atpF-atpH_p4 atpF-atpH GAGGAAACAAAAGAATCGGTT AACAATTTACGGGCTGGTCG 516–521 1.000 46.0
atpF-atpH_p5 atpF-atpH AGGAAACAAAAGAATCGGTTACA AACAATTTACGGGCTGGTCG 515–520 1.000 46.0
atpH-atpI_p1 atpH-atpI AACAGAAGCGGCAGAAATCA TTTTGCAACTTTAGCTGCGG 865–873 1.000 82.8
atpH-atpI_p2 atpH-atpI CGCAATACCTTCTACGGCTT TTTTGCAACTTTAGCTGCGG 955–963 1.000 82.7
atpH-atpI_p3 atpH-atpI AACAGAAGCGGCAGAAATCA CGAATCCATGGAGGGTCATC 835–843 1.000 82.6
atpH-atpI_p4 atpH-atpI CGCAATACCTTCTACGGCTT CGAATCCATGGAGGGTCATC 925–933 1.000 82.5
atpH-atpI_p5 atpH-atpI AGCCAATCCAGCAGCAATAA TTTTGCAACTTTAGCTGCGG 883–891 1.000 82.4

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
Tacca leontopetaloides NC_036658.1 162477 View on NCBI ↗
Tacca plantaginea NC_085341.1 162149 View on NCBI ↗