Markers + reference

Tropaeolum

2 species · Tropaeolaceae · Brassicales

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Species 2
Genome length 152–153 kb
Candidate markers 267
Primer pairs 75

Genome-wide nucleotide diversity

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

Candidate markers

7 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 715 0.0751 0.99 77.1 yes View details
psbE-petL LSC 1238 0.0602 0.97 77.7 yes View details
ycf1 IRb 1104 0.0155 0.99 53.2 no View details
ndhF-rpl32 SSC 966 0.0789 0.98 80.6 yes View details
rpl32-trnL-UAG SSC 928 0.0936 0.96 84.0 yes View details
rps15-ycf1 SSC 364 0.1009 0.93 77.2 yes View details
ycf1 SSC 5493 0.0591 0.99 68.6 yes View details
trnE-UUC-trnT-GGU LSC 609 0.0612 0.97 81.4 yes View details
trnF-GAA-ndhJ LSC 562 0.0625 0.83 81.4 yes View details
ndhC-trnV-UAC LSC 752 0.0498 0.96 79.9 yes View details
trnS-GCU-trnG-UCC LSC 531 0.0667 0.96 79.3 yes View details
psaA-pafI LSC 705 0.0449 0.98 79.3 yes View details
trnP-UGG-psaJ LSC 344 0.0539 0.97 79.3 yes View details
trnC-GCA-petN LSC 663 0.0553 0.98 78.9 yes View details
trnS-GGA-rps4 LSC 296 0.0616 0.93 78.7 yes View details
psbK-psbI LSC 428 0.0742 0.98 78.6 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 75 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG AAAAAGGGGTTTGTTGCTGC 1553–1639 1.000 84.4
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG AAAGGGGTTTGTTGCTGCTA 1551–1637 1.000 84.1
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCAGGATCAGTCGTGGTCTT AAAAAGGGGTTTGTTGCTGC 1549–1635 1.000 84.0
trnK-UUU-rps16_p4 trnK-UUU-rps16 TTTGTGCCGATTCGAAAACG AAAAAGGGGTTTGTTGCTGC 1640 0.500 59.5
trnK-UUU-rps16_p5 trnK-UUU-rps16 TTTGTGCCGATTCGAAAACG AAAGGGGTTTGTTGCTGCTA 1638 0.500 59.2
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG GGAATCCGAAGATGAAGAGGG 526–528 1.000 76.8
psbK-psbI_p2 psbK-psbI GTTTGGCAAGCTGCTGTAAG CCGAAGATGAAGAGGGAAACA 521–523 1.000 75.2
psbK-psbI_p3 psbK-psbI TGGCAAGCTGCTGTAAGTTT GGAATCCGAAGATGAAGAGGG 523–525 1.000 74.8
psbK-psbI_p4 psbK-psbI TTGGCAAGCTGCTGTAAGTT GGAATCCGAAGATGAAGAGGG 524–526 1.000 74.8
psbK-psbI_p5 psbK-psbI TTTGGCAAGCTGCTGTAAGT GGAATCCGAAGATGAAGAGGG 525–527 1.000 74.8
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA GGGCGAATCACACTTTTACC 602–642 1.000 79.7
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC GGGCGAATCACACTTTTACC 601–641 1.000 79.7
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC AGGAAACGGAAAGAGAGGGA GGGCGAATCACACTTTTACC 661–701 1.000 78.9
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA GGGCGAATCACACTTTTACC 656–696 1.000 78.0
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA GGCGAATCACACTTTTACCAC 601–641 1.000 77.5
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGCCCAAGCGAGACTTACTA 719–741 1.000 83.4
trnC-GCA-petN_p2 trnC-GCA-petN GGGGGACTGCAAATCCTTTT AGCCCAAGCGAGACTTACTA 737–759 1.000 81.1
trnC-GCA-petN_p3 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG GCCCAAGCGAGACTTACTAT 718–740 1.000 77.5
trnC-GCA-petN_p4 trnC-GCA-petN CCAGTTCAAATCCGGGTGTC AGCCCAAGCGAGACTTACTA 714–736 1.000 77.4
trnC-GCA-petN_p5 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG ATTAAAGCAGCCCAAGCGAG 727–749 1.000 77.3
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA GAACCGATGACTTACGCCTT 713–726 1.000 85.0
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA CCATGGCGTTACTCTACCAC 692–705 1.000 84.8
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA TGGCGTTACTCTACCACTGA 689–702 1.000 84.6
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA GAACCGATGACTTACGCCTT 691–704 1.000 84.4
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA CCGATGACTTACGCCTTACC 710–723 1.000 83.9
psaA-pafI_p1 psaA-pafI TTACGGGATCCCTATCGACC GGAAACAGGCTATAGCGCTT 829–843 1.000 83.4
psaA-pafI_p2 psaA-pafI TGAGAAATGACCCGGTTTGG GGAAACAGGCTATAGCGCTT 870–884 1.000 83.1
psaA-pafI_p3 psaA-pafI GCCCATTCCTCGAAAGAAGT GGAAACAGGCTATAGCGCTT 851–865 1.000 83.0
psaA-pafI_p4 psaA-pafI TTACGGGATCCCTATCGACC AATTGCGGAGGCTTGGTTTA 867–881 1.000 82.9
psaA-pafI_p5 psaA-pafI TGAGAAATGACCCGGTTTGG AATTGCGGAGGCTTGGTTTA 908–922 1.000 82.6

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
Tropaeolum majus NC_066011.1 152313 View on NCBI ↗
Tropaeolum pentaphyllum NC_050975.1 152954 View on NCBI ↗