Markers + reference

Erysimum

10 species · Brassicaceae · Brassicales

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Species 10
Genome length 154–155 kb
Candidate markers 270
Primer pairs 105

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 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-CAC-psbA LSC 297 0.0139 0.98 58.7 yes View details
trnR-AGA-atpA LSC 289 0.0072 1.00 46.3 yes View details
trnT-ACA-trnL-UUA LSC 696 0.0041 1.00 55.1 yes View details
trnL-UUA-trnF-UUC LSC 401 0.0173 1.00 63.3 yes View details
trnF-UUC-ndhJ LSC 611 0.0019 1.00 41.0 yes View details
rbcL-accD LSC 688 0.0077 1.00 59.1 yes View details
ycf4-cemA LSC 421 0.0059 1.00 46.5 yes View details
petA-psbJ LSC 982 0.0034 1.00 55.1 yes View details
ycf1 IRb 1032 0.0000 1.00 35.8 no View details
ndhF SSC 2241 0.0031 1.00 42.6 yes View details
ndhF-rpl32 SSC 826 0.0044 1.00 47.3 yes View details
ndhA SSC 2146 0.0018 1.00 44.3 yes View details
ycf1 SSC 5376 0.0024 1.00 48.5 yes View details
trnG-GGA-trnR-AGA LSC 164 0.0244 0.99 65.8 yes View details
psbM-trnD-GAC LSC 1001 0.0038 1.00 57.4 yes View details
psaA-ycf3 LSC 708 0.0030 1.00 56.1 yes View details
psbE-petL LSC 1239 0.0025 1.00 54.4 yes View details
rpl32-trnL-CUA SSC 729 0.0040 1.00 52.6 yes View details
rpoB-trnC-UGC LSC 1077 0.0025 0.99 52.5 yes View details
psaJ-rpl33 LSC 450 0.0031 0.97 51.7 yes View details
trnD-GAC-trnY-UAC LSC 441 0.0035 1.00 51.5 yes View details
psaI-ycf4 LSC 398 0.0021 1.00 51.5 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-CAC-psbA_p1 trnH-CAC-psbA CTGCCTTAATCCACTTGGCT GCTGTTGAGGCTCCATCTAC 333–372 1.000 85.7
trnH-CAC-psbA_p2 trnH-CAC-psbA CTGCCTTAATCCACTTGGCT GAGGCTCCATCTACAAACGG 327–366 1.000 85.7
trnH-CAC-psbA_p3 trnH-CAC-psbA CTGCCTTAATCCACTTGGCT CCTCTAGACCTAGCTGCTGT 348–387 1.000 85.5
trnH-CAC-psbA_p4 trnH-CAC-psbA ACTGCCTTAATCCACTTGGC GCTGTTGAGGCTCCATCTAC 334–373 1.000 85.5
trnH-CAC-psbA_p5 trnH-CAC-psbA CTGCCTTAATCCACTTGGCT TTCCCTCTAGACCTAGCTGC 351–390 1.000 85.4
trnG-GGA-trnR-AGA_p1 trnG-GGA-trnR-AGA AGCCTTCCAAGCTAACGATG TGATATTGCGTCCAATAGGA 283–290 1.000 51.4
trnG-GGA-trnR-AGA_p2 trnG-GGA-trnR-AGA ACCCTTAGCCTTCCAAGCTA TGATATTGCGTCCAATAGGA 289–296 1.000 51.2
trnG-GGA-trnR-AGA_p3 trnG-GGA-trnR-AGA CGACGTCGACTAAAACCCTT TGATATTGCGTCCAATAGGA 303–310 1.000 50.9
trnG-GGA-trnR-AGA_p4 trnG-GGA-trnR-AGA AAACCCTTAGCCTTCCAAGC TGATATTGCGTCCAATAGGA 291–298 1.000 50.9
trnG-GGA-trnR-AGA_p5 trnG-GGA-trnR-AGA AGCCTTCCAAGCTAACGATG TTGATATTGCGTCCAATAGGA 284–291 1.000 50.3
trnR-AGA-atpA_p1 trnR-AGA-atpA GCGAAAAGCGTCCATTGTC ACATTAACCGCTGAAGCAGA 443–452 1.000 71.0
trnR-AGA-atpA_p2 trnR-AGA-atpA GCGAAAAGCGTCCATTGTC AGACATTAACCGCTGAAGCA 445–454 1.000 71.0
trnR-AGA-atpA_p3 trnR-AGA-atpA GCGAAAAGCGTCCATTGTC GACATTAACCGCTGAAGCAG 444–453 1.000 68.3
trnR-AGA-atpA_p4 trnR-AGA-atpA GCGAAAAGCGTCCATTGTC TAACCGCTGAAGCAGAAAGC 439–448 1.000 68.1
trnR-AGA-atpA_p5 trnR-AGA-atpA GCGAAAAGCGTCCATTGTC ACCAAGACATTAACCGCTGA 449–458 1.000 68.0
rpoB-trnC-UGC_p1 rpoB-trnC-UGC GTTCCCTCTTTTCCATCCCC CCGGATTTGAACTGGGGAAA 1163–1166 1.000 79.5
rpoB-trnC-UGC_p2 rpoB-trnC-UGC CCCTCTTTTCCATCCCCAAG CCGGATTTGAACTGGGGAAA 1160–1163 1.000 79.5
rpoB-trnC-UGC_p3 rpoB-trnC-UGC CTCTTTTCCATCCCCAAGCA CCGGATTTGAACTGGGGAAA 1158–1161 1.000 78.9
rpoB-trnC-UGC_p4 rpoB-trnC-UGC TCCCTCTTTTCCATCCCCAA CCGGATTTGAACTGGGGAAA 1161–1164 1.000 78.8
rpoB-trnC-UGC_p5 rpoB-trnC-UGC TTCCCTCTTTTCCATCCCCA CCGGATTTGAACTGGGGAAA 1162–1165 1.000 78.8
psbM-trnD-GAC_p1 psbM-trnD-GAC AGGAACGAGAATGAAGAGTGC TTCAATTGGTCAGAGCACCG 1111–1122 1.000 70.5
psbM-trnD-GAC_p2 psbM-trnD-GAC ACGAGAATGAAGAGTGCAGT TTCAATTGGTCAGAGCACCG 1107–1118 1.000 69.8
psbM-trnD-GAC_p3 psbM-trnD-GAC GGAACGAGAATGAAGAGTGCA TTCAATTGGTCAGAGCACCG 1110–1121 1.000 68.3
psbM-trnD-GAC_p4 psbM-trnD-GAC AACGAGAATGAAGAGTGCAGT TTCAATTGGTCAGAGCACCG 1108–1119 1.000 67.6
psbM-trnD-GAC_p5 psbM-trnD-GAC GGAACGAGAATGAAGAGTGC TTCAATTGGTCAGAGCACCG 1110–1121 1.000 67.1
trnD-GAC-trnY-UAC_p1 trnD-GAC-trnY-UAC TGATGTATTGAATCCGCCGG TGGCAATATGTCTACGCTGG 571–572 1.000 78.1
trnD-GAC-trnY-UAC_p2 trnD-GAC-trnY-UAC TGATGTATTGAATCCGCCGG GGCAATATGTCTACGCTGGT 570–571 1.000 78.1
trnD-GAC-trnY-UAC_p3 trnD-GAC-trnY-UAC TGATGTATTGAATCCGCCGG GGGGACGGACTGTAAATTCG 592–593 1.000 77.2
trnD-GAC-trnY-UAC_p4 trnD-GAC-trnY-UAC TGATGTATTGAATCCGCCGG GGGACGGACTGTAAATTCGT 591–592 1.000 77.0
trnD-GAC-trnY-UAC_p5 trnD-GAC-trnY-UAC TGATGTATTGAATCCGCCGG GATTCTTCCTGGGTCGATGC 625–626 1.000 76.7

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (10)

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

Species Accession Length (bp) Link
Erysimum bicolor NC_049635.1 154344 View on NCBI ↗
Erysimum flavum NC_081120.1 154631 View on NCBI ↗
Erysimum flavum subsp. altaicum OQ644460.1 154580 View on NCBI ↗
Erysimum funiculosum PP234512.1 154293 View on NCBI ↗
Erysimum hieraciifolium NC_081121.1 154581 View on NCBI ↗
Erysimum menziesii PX508916.1 154668 View on NCBI ↗
Erysimum odoratum NC_049638.1 154703 View on NCBI ↗
Erysimum quadrangulum NC_081122.1 154582 View on NCBI ↗
Erysimum siliculosum NC_081123.1 154490 View on NCBI ↗
Erysimum sisymbrioides NC_081124.1 154662 View on NCBI ↗