Markers + reference

Thlaspi

2 species · Brassicaceae · Brassicales

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Species 2
Genome length 153–154 kb
Candidate markers 272
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 272 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-TTT-rps16 LSC 666 0.1305 0.92 85.8 yes View details
rps16-trnQ-TTG LSC 456 0.1244 0.93 84.9 yes View details
trnS-GCT-trnT-CGT LSC 595 0.1096 0.97 84.6 yes View details
trnR-TCT-atpA LSC 380 0.1297 0.77 74.4 yes View details
trnT-TGT-trnF-GAA LSC 685 0.0900 0.88 78.9 yes View details
ndhC-trnV-TAC LSC 853 0.0857 0.78 77.3 yes View details
petA-psbJ LSC 972 0.1048 0.62 70.3 yes View details
psbE-petL LSC 866 0.2634 0.80 80.8 yes View details
ycf1 SSC 1038 0.0194 0.99 56.3 no View details
ndhF-rpl32 SSC 820 0.0745 0.88 79.9 yes View details
rpl32-trnL-TAG SSC 675 0.1277 0.84 80.8 yes View details
ycf1 SSC 5328 0.0626 0.99 68.5 yes View details
trnT-GGT-psbD LSC 1155 0.0641 0.95 84.4 yes View details
trnF-GAA-ndhJ LSC 589 0.0716 0.93 83.9 yes View details
trnC-GCA-petN LSC 635 0.0718 0.97 82.7 yes View details
trnS-TGA-psbZ LSC 347 0.0636 0.95 80.7 yes View details
rpl16-rps3 LSC 181 0.0930 0.95 80.4 yes View details
trnY-GTA-trnE-TTC LSC 59 0.1186 1.00 80.1 yes View details
rbcL-accD LSC 710 0.0761 0.94 80.1 yes View details
rps4-trnT-TGT LSC 409 0.0699 0.94 79.8 yes View details
trnD-GTC-trnY-GTA LSC 440 0.0856 0.85 79.7 yes View details
psaA-ycf3 LSC 752 0.0567 0.94 79.2 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-TTT-rps16_p1 trnK-TTT-rps16 AACTCTACCGCAGATCTGGA ACGGAATTAAGTCTTAATAAAACGA 794–804 1.000 52.0
trnK-TTT-rps16_p2 trnK-TTT-rps16 AAAGCCGAGTACTCTACCGT ACGGAATTAAGTCTTAATAAAACGA 726–736 1.000 52.0
trnK-TTT-rps16_p3 trnK-TTT-rps16 AAGCCGAGTACTCTACCGTT ACGGAATTAAGTCTTAATAAAACGA 725–735 1.000 52.0
trnK-TTT-rps16_p4 trnK-TTT-rps16 TACCGTTGAGTTAGCAACCC ACGGAATTAAGTCTTAATAAAACGA 712–722 1.000 52.0
trnK-TTT-rps16_p5 trnK-TTT-rps16 AACTCTACCGCAGATCTGGA ACGGAATTAAGTCTTAATAAAACGAA 794–804 1.000 52.0
rps16-trnQ-TTG_p1 rps16-trnQ-TTG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 517–529 1.000 90.3
rps16-trnQ-TTG_p2 rps16-trnQ-TTG CCTTCAATTCAAGTCGCACG GAGGTTCGAATCCTTCCGTC 527–539 1.000 89.5
rps16-trnQ-TTG_p3 rps16-trnQ-TTG TCAATTCAAGTCGCACGTTG GAGGTTCGAATCCTTCCGTC 524–536 1.000 86.1
rps16-trnQ-TTG_p4 rps16-trnQ-TTG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 521–533 1.000 85.5
rps16-trnQ-TTG_p5 rps16-trnQ-TTG AAGTCGCACGTTGCTTTCTA TAAGGCAACGGGTTTTGGTC 547–559 1.000 85.1
trnS-GCT-trnT-CGT_p1 trnS-GCT-trnT-CGT CCAACGCTTTAGTCCACTCA ACGAATCACACTTTTACCACT 660–748 1.000 59.8
trnS-GCT-trnT-CGT_p2 trnS-GCT-trnT-CGT AACGCTTTAGTCCACTCAGC ACGAATCACACTTTTACCACT 658–746 1.000 59.5
trnS-GCT-trnT-CGT_p3 trnS-GCT-trnT-CGT CCAACGCTTTAGTCCACTCA GAACGAATCACACTTTTACCACT 662–750 1.000 58.7
trnS-GCT-trnT-CGT_p4 trnS-GCT-trnT-CGT AACGCTTTAGTCCACTCAGC GAACGAATCACACTTTTACCACT 660–748 1.000 58.5
trnS-GCT-trnT-CGT_p5 trnS-GCT-trnT-CGT CCAACGCTTTAGTCCACTCA AACGAATCACACTTTTACCACT 661–749 1.000 57.9
trnR-TCT-atpA_p1 trnR-TCT-atpA AGCCTTCCAAGCTAACGATG ACGAATAAACCGCAGTTCCA 706–773 1.000 89.3
trnR-TCT-atpA_p2 trnR-TCT-atpA ACCCTTAGCCTTCCAAGCTA ACGAATAAACCGCAGTTCCA 712–779 1.000 89.2
trnR-TCT-atpA_p3 trnR-TCT-atpA AGCCTTCCAAGCTAACGATG GAGACCCAGTCAGGAGATGT 1144–1211 1.000 87.3
trnR-TCT-atpA_p4 trnR-TCT-atpA ACCCTTAGCCTTCCAAGCTA GAGACCCAGTCAGGAGATGT 1150–1217 1.000 87.3
trnR-TCT-atpA_p5 trnR-TCT-atpA AAACCCTTAGCCTTCCAAGC GAGACCCAGTCAGGAGATGT 1152–1219 1.000 86.9
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGCCCATGCGAGACTTACTA 679–691 1.000 85.3
trnC-GCA-petN_p2 trnC-GCA-petN GGGGGACTGCAAATCCTTTT AGCCCATGCGAGACTTACTA 697–709 1.000 82.9
trnC-GCA-petN_p3 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG ATTAAACCAGCCCATGCGAG 687–699 1.000 82.1
trnC-GCA-petN_p4 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG ACCATTAAACCAGCCCATGC 690–702 1.000 80.5
trnC-GCA-petN_p5 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG GCCCATGCGAGACTTACTAT 678–690 1.000 80.5
trnD-GTC-trnY-GTA_p1 trnD-GTC-trnY-GTA CGGTGCTCTGACCAATTGAA TGGCAATATGTCTACGCTGG 446–510 1.000 83.6
trnD-GTC-trnY-GTA_p2 trnD-GTC-trnY-GTA CGGTGCTCTGACCAATTGAA GGCAATATGTCTACGCTGGT 445–509 1.000 83.6
trnD-GTC-trnY-GTA_p3 trnD-GTC-trnY-GTA CGGTGCTCTGACCAATTGAA GGGGACGGACTGTAAATTCG 467–531 1.000 82.5
trnD-GTC-trnY-GTA_p4 trnD-GTC-trnY-GTA CGGTGCTCTGACCAATTGAA GGGACGGACTGTAAATTCGT 466–530 1.000 82.3
trnD-GTC-trnY-GTA_p5 trnD-GTC-trnY-GTA CGGTGCTCTGACCAATTGAA GATTCTTCCTGGGTCGATGC 500–564 1.000 81.7

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
Thlaspi arvense NC_034362.1 153892 View on NCBI ↗
Thlaspi praecox PP165062.1 152969 View on NCBI ↗