Markers + reference

Alyssum

4 species · Brassicaceae · Brassicales

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Species 4
Genome length 150–152 kb
Candidate markers 271
Primer pairs 85

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 9 remaining regions by MarkerSeek score (out of 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-CAC-psbA LSC 377 0.1176 0.96 75.9 yes View details
trnK-AAA-rps16 LSC 721 0.0634 0.92 80.7 yes View details
rps16-trnQ-CAA LSC 680 0.0471 0.93 78.7 yes View details
trnS-AGC-trnG-GGA LSC 738 0.0576 0.85 80.7 yes View details
trnT-ACA-trnL-UUA LSC 779 0.0527 0.94 86.3 yes View details
rpl16 LSC 1403 0.0383 0.97 73.3 yes View details
ycf1 IRb 936 0.0192 0.99 47.8 no View details
ndhF-rpl32 SSC 710 0.0512 0.96 78.4 yes View details
ycf1 SSC 5208 0.0518 0.99 73.6 yes View details
ndhC-trnV-GUA LSC 736 0.0349 0.99 74.6 yes View details
psbM-trnD-GAC LSC 1039 0.0450 0.95 72.1 yes View details
ndhE-ndhG SSC 274 0.0432 0.96 71.1 yes View details
petA-psbJ LSC 963 0.0355 0.88 70.7 yes View details
trnW-UGG-trnP-CCA LSC 189 0.0441 0.96 69.4 yes View details
psaJ-rpl33 LSC 427 0.0528 0.91 67.9 yes View details
trnR-AGA-atpA LSC 237 0.0633 0.87 67.2 yes View details
atpH-atpI LSC 473 0.0296 0.96 67.2 yes View details
trnG-GGA-trnR-AGA LSC 176 0.0480 0.86 67.0 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 85 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 402–435 1.000 90.5
trnH-CAC-psbA_p2 trnH-CAC-psbA CTGCCTTAATCCACTTGGCT CCTCTAGACCTAGCTGCTGT 417–450 1.000 90.4
trnH-CAC-psbA_p3 trnH-CAC-psbA CTGCCTTAATCCACTTGGCT TTCCCTCTAGACCTAGCTGC 420–453 1.000 90.3
trnH-CAC-psbA_p4 trnH-CAC-psbA ACTGCCTTAATCCACTTGGC GCTGTTGAGGCTCCATCTAC 403–436 1.000 90.3
trnH-CAC-psbA_p5 trnH-CAC-psbA ACTGCCTTAATCCACTTGGC CCTCTAGACCTAGCTGCTGT 418–451 1.000 90.2
trnK-AAA-rps16_p1 trnK-AAA-rps16 CCTTTCAGGATCAGTCGTGG GCCTTGTTGCTGTCGTTTTT 1358–1424 1.000 90.0
trnK-AAA-rps16_p2 trnK-AAA-rps16 TCGACACCGAAAACAAGGTT GCCTTGTTGCTGTCGTTTTT 1450–1516 1.000 89.8
trnK-AAA-rps16_p3 trnK-AAA-rps16 TGGTCTTACAAACGCTACCG GCCTTGTTGCTGTCGTTTTT 1341–1407 1.000 89.6
trnK-AAA-rps16_p4 trnK-AAA-rps16 TCAGGATCAGTCGTGGTCTT GCCTTGTTGCTGTCGTTTTT 1354–1420 1.000 89.4
trnK-AAA-rps16_p5 trnK-AAA-rps16 TTCAGGATCAGTCGTGGTCT GCCTTGTTGCTGTCGTTTTT 1355–1421 1.000 89.4
rps16-trnQ-CAA_p1 rps16-trnQ-CAA GCAAGCTCTATACGCGTCTT CAAAACCCTAGCACCACTGT 1116 0.250 48.6
rps16-trnQ-CAA_p2 rps16-trnQ-CAA GCAAGCTCTATACGCGTCTT TGGCGACTAAAAAGGTGCTT 1469 0.250 48.5
rps16-trnQ-CAA_p3 rps16-trnQ-CAA GCAAGCTCTATACGCGTCTT TGTCAAAACCCTAGCACCAC 1119 0.250 48.5
rps16-trnQ-CAA_p4 rps16-trnQ-CAA GCAAGCTCTATACGCGTCTT TTGGCGACTAAAAAGGTGCT 1470 0.250 48.5
rps16-trnQ-CAA_p5 rps16-trnQ-CAA GCGCCCTTTTCAGTAAATCG CAAAACCCTAGCACCACTGT 986 0.250 48.5
trnS-AGC-trnG-GGA_p1 trnS-AGC-trnG-GGA CCAACGCTTTAGTCCACTCA GGAACGAATCACACTTTTACCA 661–807 1.000 64.5
trnS-AGC-trnG-GGA_p2 trnS-AGC-trnG-GGA AACGCTTTAGTCCACTCAGC GGAACGAATCACACTTTTACCA 659–805 1.000 64.2
trnS-AGC-trnG-GGA_p3 trnS-AGC-trnG-GGA CCAACGCTTTAGTCCACTCA GGAACGAATCACACTTTTACCAC 661–807 1.000 63.4
trnS-AGC-trnG-GGA_p4 trnS-AGC-trnG-GGA AACGCTTTAGTCCACTCAGC GGAACGAATCACACTTTTACCAC 659–805 1.000 63.1
trnS-AGC-trnG-GGA_p5 trnS-AGC-trnG-GGA CCAACGCTTTAGTCCACTCA AGGAACGAATCACACTTTTACCA 662–808 1.000 62.9
trnG-GGA-trnR-AGA_p1 trnG-GGA-trnR-AGA AGCCTTCCAAGCTAACGATG TGGTATTGCGTCCAATAGGA 274–303 1.000 74.0
trnG-GGA-trnR-AGA_p2 trnG-GGA-trnR-AGA ACCCTTAGCCTTCCAAGCTA TGGTATTGCGTCCAATAGGA 280–309 1.000 73.9
trnG-GGA-trnR-AGA_p3 trnG-GGA-trnR-AGA CGACGTCGACTAAAACCCTT TGGTATTGCGTCCAATAGGA 294–323 1.000 73.5
trnG-GGA-trnR-AGA_p4 trnG-GGA-trnR-AGA AAACCCTTAGCCTTCCAAGC TGGTATTGCGTCCAATAGGA 282–311 1.000 73.5
trnG-GGA-trnR-AGA_p5 trnG-GGA-trnR-AGA AGCCTTCCAAGCTAACGATG TTGGTATTGCGTCCAATAGGA 275–304 1.000 72.0
trnR-AGA-atpA_p1 trnR-AGA-atpA AGCCTTCCAAGCTAACGATG GGGTCGTGAAGCTTATCCAG 1208–1304 1.000 86.0
trnR-AGA-atpA_p2 trnR-AGA-atpA AGCCTTCCAAGCTAACGATG GGTCGTGAAGCTTATCCAGG 1207–1303 1.000 86.0
trnR-AGA-atpA_p3 trnR-AGA-atpA CGAAAGGCGTCCATTGTCTA GGGTCGTGAAGCTTATCCAG 994–1114 1.000 84.7
trnR-AGA-atpA_p4 trnR-AGA-atpA CGAAAGGCGTCCATTGTCTA GGTCGTGAAGCTTATCCAGG 993–1113 1.000 84.7
trnR-AGA-atpA_p5 trnR-AGA-atpA TTCTGTCAAAGCACCCAGAC GGTCGTGAAGCTTATCCAGG 1400–1446 0.500 60.8

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (4)

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

Species Accession Length (bp) Link
Alyssum alyssoides NC_049574.1 151598 View on NCBI ↗
Alyssum dasycarpum NC_049577.1 149999 View on NCBI ↗
Alyssum gmelinii MF169880.1 151742 View on NCBI ↗
Alyssum simplex NC_081108.1 150682 View on NCBI ↗